Starting phenix.real_space_refine
on Fri Aug 22 14:40:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pkf_17737/08_2025/8pkf_17737.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pkf_17737/08_2025/8pkf_17737.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3673
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pkf_17737/08_2025/8pkf_17737.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pkf_17737/08_2025/8pkf_17737.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pkf_17737/08_2025/8pkf_17737.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pkf_17737/08_2025/8pkf_17737.map"
  }
  resolution = 2.3673
  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=   0.003
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    2790      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 60 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4308
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 718
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 718
          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: 0.77, per 1000 atoms: 0.18
  Number of scatterers: 4308
  At special positions: 0
  Unit cell: (69.116, 86.862, 46.7, 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    2790      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: 0.26
  Conformation dependent library (CDL) restraints added in 126.8 milliseconds
  
  Enol-peptide restraints added in 715.3 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 10 sheets defined
      0.0% alpha, 42.4% 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: 6.478A  pdb=" N   LEU A  12 " --> pdb=" O   MET B  13 " (cutoff:3.500A)
      removed outlier: 7.954A  pdb=" N   LYS B  15 " --> pdb=" O   LEU A  12 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   VAL A  14 " --> pdb=" O   LYS B  15 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   LEU B  12 " --> pdb=" O   MET C  13 " (cutoff:3.500A)
      removed outlier: 7.953A  pdb=" N   LYS C  15 " --> pdb=" O   LEU B  12 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   VAL B  14 " --> pdb=" O   LYS C  15 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   LEU C  12 " --> pdb=" O   MET D  13 " (cutoff:3.500A)
      removed outlier: 7.953A  pdb=" N   LYS D  15 " --> pdb=" O   LEU C  12 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   VAL C  14 " --> pdb=" O   LYS D  15 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   LEU D  12 " --> pdb=" O   MET E  13 " (cutoff:3.500A)
      removed outlier: 7.954A  pdb=" N   LYS E  15 " --> pdb=" O   LEU D  12 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   VAL D  14 " --> pdb=" O   LYS E  15 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   LEU E  12 " --> pdb=" O   MET F  13 " (cutoff:3.500A)
      removed outlier: 7.954A  pdb=" N   LYS F  15 " --> pdb=" O   LEU E  12 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   VAL E  14 " --> pdb=" O   LYS F  15 " (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 21
    Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 34
      removed outlier: 6.480A  pdb=" N   VAL A  30 " --> pdb=" O   HIS B  31 " (cutoff:3.500A)
      removed outlier: 7.922A  pdb=" N   PHE B  33 " --> pdb=" O   VAL A  30 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   VAL A  32 " --> pdb=" O   PHE B  33 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   VAL B  30 " --> pdb=" O   HIS C  31 " (cutoff:3.500A)
      removed outlier: 7.922A  pdb=" N   PHE C  33 " --> pdb=" O   VAL B  30 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   VAL B  32 " --> pdb=" O   PHE C  33 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   VAL C  30 " --> pdb=" O   HIS D  31 " (cutoff:3.500A)
      removed outlier: 7.922A  pdb=" N   PHE D  33 " --> pdb=" O   VAL C  30 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   VAL C  32 " --> pdb=" O   PHE D  33 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   VAL D  30 " --> pdb=" O   HIS E  31 " (cutoff:3.500A)
      removed outlier: 7.923A  pdb=" N   PHE E  33 " --> pdb=" O   VAL D  30 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   VAL D  32 " --> pdb=" O   PHE E  33 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   VAL E  30 " --> pdb=" O   HIS F  31 " (cutoff:3.500A)
      removed outlier: 7.922A  pdb=" N   PHE F  33 " --> pdb=" O   VAL E  30 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   VAL E  32 " --> pdb=" O   PHE F  33 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 62
      removed outlier: 6.391A  pdb=" N   THR A  59 " --> pdb=" O   THR B  60 " (cutoff:3.500A)
      removed outlier: 8.406A  pdb=" N   GLU B  62 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   GLU A  61 " --> pdb=" O   GLU B  62 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   THR B  59 " --> pdb=" O   THR C  60 " (cutoff:3.500A)
      removed outlier: 8.405A  pdb=" N   GLU C  62 " --> pdb=" O   THR B  59 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   GLU B  61 " --> pdb=" O   GLU C  62 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   THR C  59 " --> pdb=" O   THR D  60 " (cutoff:3.500A)
      removed outlier: 8.405A  pdb=" N   GLU D  62 " --> pdb=" O   THR C  59 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   GLU C  61 " --> pdb=" O   GLU D  62 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   THR D  59 " --> pdb=" O   THR E  60 " (cutoff:3.500A)
      removed outlier: 8.404A  pdb=" N   GLU E  62 " --> pdb=" O   THR D  59 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   GLU D  61 " --> pdb=" O   GLU E  62 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   THR E  59 " --> pdb=" O   THR F  60 " (cutoff:3.500A)
      removed outlier: 8.405A  pdb=" N   GLU F  62 " --> pdb=" O   THR E  59 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   GLU E  61 " --> pdb=" O   GLU F  62 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 66
    Processing sheet with id=AA6, first strand: chain 'A' and resid 71 through 80
      removed outlier: 6.280A  pdb=" N   GLU A  72 " --> pdb=" O   ILE B  73 " (cutoff:3.500A)
      removed outlier: 5.731A  pdb=" N   THR B  75 " --> pdb=" O   GLU A  72 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   ASP A  74 " --> pdb=" O   THR B  75 " (cutoff:3.500A)
      removed outlier: 9.999A  pdb=" N   SER B  77 " --> pdb=" O   ASP A  74 " (cutoff:3.500A)
      removed outlier: 9.473A  pdb=" N   LYS A  76 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
      removed outlier: 9.644A  pdb=" N   TRP B  79 " --> pdb=" O   LYS A  76 " (cutoff:3.500A)
      removed outlier: 5.918A  pdb=" N   TYR A  78 " --> pdb=" O   TRP B  79 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   GLU B  72 " --> pdb=" O   ILE C  73 " (cutoff:3.500A)
      removed outlier: 5.730A  pdb=" N   THR C  75 " --> pdb=" O   GLU B  72 " (cutoff:3.500A)
      removed outlier: 7.551A  pdb=" N   ASP B  74 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 9.997A  pdb=" N   SER C  77 " --> pdb=" O   ASP B  74 " (cutoff:3.500A)
      removed outlier: 9.471A  pdb=" N   LYS B  76 " --> pdb=" O   SER C  77 " (cutoff:3.500A)
      removed outlier: 9.644A  pdb=" N   TRP C  79 " --> pdb=" O   LYS B  76 " (cutoff:3.500A)
      removed outlier: 5.917A  pdb=" N   TYR B  78 " --> pdb=" O   TRP C  79 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   GLU C  72 " --> pdb=" O   ILE D  73 " (cutoff:3.500A)
      removed outlier: 5.730A  pdb=" N   THR D  75 " --> pdb=" O   GLU C  72 " (cutoff:3.500A)
      removed outlier: 7.552A  pdb=" N   ASP C  74 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 9.998A  pdb=" N   SER D  77 " --> pdb=" O   ASP C  74 " (cutoff:3.500A)
      removed outlier: 9.471A  pdb=" N   LYS C  76 " --> pdb=" O   SER D  77 " (cutoff:3.500A)
      removed outlier: 9.644A  pdb=" N   TRP D  79 " --> pdb=" O   LYS C  76 " (cutoff:3.500A)
      removed outlier: 5.918A  pdb=" N   TYR C  78 " --> pdb=" O   TRP D  79 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   GLU D  72 " --> pdb=" O   ILE E  73 " (cutoff:3.500A)
      removed outlier: 5.730A  pdb=" N   THR E  75 " --> pdb=" O   GLU D  72 " (cutoff:3.500A)
      removed outlier: 7.552A  pdb=" N   ASP D  74 " --> pdb=" O   THR E  75 " (cutoff:3.500A)
      removed outlier: 9.999A  pdb=" N   SER E  77 " --> pdb=" O   ASP D  74 " (cutoff:3.500A)
      removed outlier: 9.473A  pdb=" N   LYS D  76 " --> pdb=" O   SER E  77 " (cutoff:3.500A)
      removed outlier: 9.644A  pdb=" N   TRP E  79 " --> pdb=" O   LYS D  76 " (cutoff:3.500A)
      removed outlier: 5.918A  pdb=" N   TYR D  78 " --> pdb=" O   TRP E  79 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   GLU E  72 " --> pdb=" O   ILE F  73 " (cutoff:3.500A)
      removed outlier: 5.731A  pdb=" N   THR F  75 " --> pdb=" O   GLU E  72 " (cutoff:3.500A)
      removed outlier: 7.552A  pdb=" N   ASP E  74 " --> pdb=" O   THR F  75 " (cutoff:3.500A)
      removed outlier: 9.998A  pdb=" N   SER F  77 " --> pdb=" O   ASP E  74 " (cutoff:3.500A)
      removed outlier: 9.471A  pdb=" N   LYS E  76 " --> pdb=" O   SER F  77 " (cutoff:3.500A)
      removed outlier: 9.644A  pdb=" N   TRP F  79 " --> pdb=" O   LYS E  76 " (cutoff:3.500A)
      removed outlier: 5.917A  pdb=" N   TYR E  78 " --> pdb=" O   TRP F  79 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 92 through 99
    Processing sheet with id=AA8, first strand: chain 'A' and resid 104 through 107
      removed outlier: 6.345A  pdb=" N   ARG A 104 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   ILE B 107 " --> pdb=" O   ARG A 104 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   THR A 106 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   ARG B 104 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   ILE C 107 " --> pdb=" O   ARG B 104 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   THR B 106 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   ARG C 104 " --> pdb=" O   TYR D 105 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   ILE D 107 " --> pdb=" O   ARG C 104 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   THR C 106 " --> pdb=" O   ILE D 107 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ARG D 104 " --> pdb=" O   TYR E 105 " (cutoff:3.500A)
      removed outlier: 7.891A  pdb=" N   ILE E 107 " --> pdb=" O   ARG D 104 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   THR D 106 " --> pdb=" O   ILE E 107 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ARG E 104 " --> pdb=" O   TYR F 105 " (cutoff:3.500A)
      removed outlier: 7.889A  pdb=" N   ILE F 107 " --> pdb=" O   ARG E 104 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   THR E 106 " --> pdb=" O   ILE F 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 114 through 115
      removed outlier: 7.033A  pdb=" N   TYR A 114 " --> pdb=" O   SER B 115 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   TYR B 114 " --> pdb=" O   SER C 115 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   TYR C 114 " --> pdb=" O   SER D 115 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   TYR D 114 " --> pdb=" O   SER E 115 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   TYR E 114 " --> pdb=" O   SER F 115 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'A' and resid 118 through 122

    70 hydrogen bonds defined for protein.
    210 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: 0.67

  Time building geometry restraints manager: 0.36 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: 708
        1.32 -     1.44: 1194
        1.44 -     1.56: 2496
        1.56 -     1.68: 0
        1.68 -     1.81: 12
  Bond restraints: 4410
  Sorted by residual:
  bond pdb=" N   SER A  85 "
       pdb=" CA  SER A  85 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.035 9.10e-03 1.21e+04 1.47e+01
  bond pdb=" N   SER B  85 "
       pdb=" CA  SER B  85 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.035 9.10e-03 1.21e+04 1.46e+01
  bond pdb=" N   SER E  85 "
       pdb=" CA  SER E  85 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 9.10e-03 1.21e+04 1.39e+01
  bond pdb=" N   SER D  85 "
       pdb=" CA  SER D  85 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.034 9.10e-03 1.21e+04 1.38e+01
  bond pdb=" N   SER F  85 "
       pdb=" CA  SER F  85 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.034 9.10e-03 1.21e+04 1.38e+01
  ... (remaining 4405 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 3790
        1.52 -     3.05: 1746
        3.05 -     4.57: 397
        4.57 -     6.10: 49
        6.10 -     7.62: 18
  Bond angle restraints: 6000
  Sorted by residual:
  angle pdb=" C   THR B 106 "
        pdb=" N   ILE B 107 "
        pdb=" CA  ILE B 107 "
      ideal   model   delta    sigma   weight residual
     123.19  115.57    7.62 1.24e+00 6.50e-01 3.78e+01
  angle pdb=" C   THR F 106 "
        pdb=" N   ILE F 107 "
        pdb=" CA  ILE F 107 "
      ideal   model   delta    sigma   weight residual
     123.19  115.57    7.62 1.24e+00 6.50e-01 3.77e+01
  angle pdb=" C   THR D 106 "
        pdb=" N   ILE D 107 "
        pdb=" CA  ILE D 107 "
      ideal   model   delta    sigma   weight residual
     123.19  115.59    7.60 1.24e+00 6.50e-01 3.76e+01
  angle pdb=" C   THR E 106 "
        pdb=" N   ILE E 107 "
        pdb=" CA  ILE E 107 "
      ideal   model   delta    sigma   weight residual
     123.19  115.60    7.59 1.24e+00 6.50e-01 3.74e+01
  angle pdb=" C   THR A 106 "
        pdb=" N   ILE A 107 "
        pdb=" CA  ILE A 107 "
      ideal   model   delta    sigma   weight residual
     123.19  115.64    7.55 1.24e+00 6.50e-01 3.71e+01
  ... (remaining 5995 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.55: 2238
        9.55 -    19.10: 203
       19.10 -    28.65: 97
       28.65 -    38.21: 36
       38.21 -    47.76: 24
  Dihedral angle restraints: 2598
    sinusoidal: 984
      harmonic: 1614
  Sorted by residual:
  dihedral pdb=" N   ALA A  25 "
           pdb=" C   ALA A  25 "
           pdb=" CA  ALA A  25 "
           pdb=" CB  ALA A  25 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.90  115.19    7.71     0      2.50e+00 1.60e-01 9.50e+00
  dihedral pdb=" N   ALA C  25 "
           pdb=" C   ALA C  25 "
           pdb=" CA  ALA C  25 "
           pdb=" CB  ALA C  25 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.90  115.20    7.70     0      2.50e+00 1.60e-01 9.48e+00
  dihedral pdb=" N   ALA E  25 "
           pdb=" C   ALA E  25 "
           pdb=" CA  ALA E  25 "
           pdb=" CB  ALA E  25 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.90  115.22    7.68     0      2.50e+00 1.60e-01 9.44e+00
  ... (remaining 2595 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 268
       0.069 -    0.138: 288
       0.138 -    0.208: 98
       0.208 -    0.277: 48
       0.277 -    0.346: 6
  Chirality restraints: 708
  Sorted by residual:
  chirality pdb=" CA  ASN C  27 "
            pdb=" N   ASN C  27 "
            pdb=" C   ASN C  27 "
            pdb=" CB  ASN C  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.86   -0.35 2.00e-01 2.50e+01 2.99e+00
  chirality pdb=" CA  ASN E  27 "
            pdb=" N   ASN E  27 "
            pdb=" C   ASN E  27 "
            pdb=" CB  ASN E  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.86   -0.35 2.00e-01 2.50e+01 2.98e+00
  chirality pdb=" CA  ASN B  27 "
            pdb=" N   ASN B  27 "
            pdb=" C   ASN B  27 "
            pdb=" CB  ASN B  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.86   -0.35 2.00e-01 2.50e+01 2.98e+00
  ... (remaining 705 not shown)

  Planarity restraints: 738
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B  98 "   -0.017 2.00e-02 2.50e+03   3.56e-02 1.26e+01
        pdb=" C   ASN B  98 "    0.061 2.00e-02 2.50e+03
        pdb=" O   ASN B  98 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   ASP B  99 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN F  98 "   -0.017 2.00e-02 2.50e+03   3.56e-02 1.26e+01
        pdb=" C   ASN F  98 "    0.061 2.00e-02 2.50e+03
        pdb=" O   ASN F  98 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   ASP F  99 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN C  98 "   -0.017 2.00e-02 2.50e+03   3.56e-02 1.26e+01
        pdb=" C   ASN C  98 "    0.061 2.00e-02 2.50e+03
        pdb=" O   ASN C  98 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   ASP C  99 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 735 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.86: 1487
        2.86 -     3.37: 3574
        3.37 -     3.88: 7650
        3.88 -     4.39: 8655
        4.39 -     4.90: 16497
  Nonbonded interactions: 37863
  Sorted by model distance:
  nonbonded pdb=" O   ALA D 109 "
            pdb=" OG  SER E 112 "
     model   vdw
     2.355 3.040
  nonbonded pdb=" O   ALA C 109 "
            pdb=" OG  SER D 112 "
     model   vdw
     2.356 3.040
  nonbonded pdb=" O   ALA E 109 "
            pdb=" OG  SER F 112 "
     model   vdw
     2.356 3.040
  nonbonded pdb=" O   ALA A 109 "
            pdb=" OG  SER B 112 "
     model   vdw
     2.356 3.040
  nonbonded pdb=" O   ALA B 109 "
            pdb=" OG  SER C 112 "
     model   vdw
     2.356 3.040
  ... (remaining 37858 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  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:             1.410
  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:          0.070
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     5.560
  Find NCS groups from input model:        0.030
  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:6.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7318
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   0.042   4410  Z= 0.948
  Angle     :  1.726   7.623   6000  Z= 1.275
  Chirality :  0.117   0.346    708
  Planarity :  0.008   0.052    738
  Dihedral  : 11.302  47.757   1554
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 0.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.77 (0.30), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.11 (0.23), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  34 
 TYR   0.014   0.003   TYR B 114 
 PHE   0.012   0.003   PHE B  95 
 TRP   0.002   0.001   TRP B  79 
 HIS   0.002   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.01258 ( 4410)
  covalent geometry    : angle       1.72618 ( 6000)
  hydrogen bonds       : bond        0.13999 (   70)
  hydrogen bonds       : angle       7.51960 (  210)

*********************** 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  : 0.183 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7352 (mt-10)
REVERT: A   66 GLU cc_start: 0.7230 (tt0) cc_final: 0.6943 (tt0)
REVERT: A   80 LYS cc_start: 0.7325 (tttt) cc_final: 0.6926 (ttpt)
REVERT: A  104 ARG cc_start: 0.7339 (mtt180) cc_final: 0.6702 (mtm-85)
REVERT: B   13 MET cc_start: 0.7373 (ttm) cc_final: 0.6492 (mtp)
REVERT: B   15 LYS cc_start: 0.6999 (mtpt) cc_final: 0.6647 (mtpt)
REVERT: B   34 ARG cc_start: 0.7439 (ttt-90) cc_final: 0.7200 (ttt180)
REVERT: B  104 ARG cc_start: 0.6828 (mtt180) cc_final: 0.6226 (mtp180)
REVERT: C   13 MET cc_start: 0.7289 (ttm) cc_final: 0.6985 (ttm)
REVERT: C   15 LYS cc_start: 0.7078 (mtpt) cc_final: 0.6705 (mtpt)
REVERT: C   62 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6918 (mt-10)
REVERT: C   66 GLU cc_start: 0.7328 (tt0) cc_final: 0.6585 (tm-30)
REVERT: C   80 LYS cc_start: 0.7283 (tttt) cc_final: 0.6814 (ttmt)
REVERT: C   89 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6828 (mt-10)
REVERT: C  104 ARG cc_start: 0.7051 (mtt180) cc_final: 0.6245 (mtp180)
REVERT: C  123 THR cc_start: 0.6169 (m) cc_final: 0.5878 (p)
REVERT: D   13 MET cc_start: 0.7190 (ttm) cc_final: 0.6795 (ttm)
REVERT: D   15 LYS cc_start: 0.7082 (mtpt) cc_final: 0.6710 (mtpt)
REVERT: D   59 THR cc_start: 0.7247 (m) cc_final: 0.6981 (p)
REVERT: D   62 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7281 (mt-10)
REVERT: D   66 GLU cc_start: 0.7243 (tt0) cc_final: 0.6857 (tt0)
REVERT: D   80 LYS cc_start: 0.7394 (tttt) cc_final: 0.6781 (tttm)
REVERT: D   89 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7157 (mt-10)
REVERT: D  104 ARG cc_start: 0.7148 (mtt180) cc_final: 0.6296 (mtm-85)
REVERT: E   13 MET cc_start: 0.7352 (ttm) cc_final: 0.6871 (ttm)
REVERT: E   15 LYS cc_start: 0.7254 (mtpt) cc_final: 0.6946 (mtpp)
REVERT: E   21 ARG cc_start: 0.6974 (ttt180) cc_final: 0.6701 (ttm-80)
REVERT: E   34 ARG cc_start: 0.7071 (ttt-90) cc_final: 0.6855 (tpt-90)
REVERT: E   35 LYS cc_start: 0.7262 (tttt) cc_final: 0.6924 (tttm)
REVERT: E   62 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7077 (mt-10)
REVERT: E   80 LYS cc_start: 0.7433 (tttt) cc_final: 0.7088 (ttpp)
REVERT: E   92 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7543 (mt-10)
REVERT: E  104 ARG cc_start: 0.7128 (mtt180) cc_final: 0.6361 (mtp180)
REVERT: F   13 MET cc_start: 0.7362 (ttm) cc_final: 0.6373 (mtm)
REVERT: F   26 ILE cc_start: 0.8510 (mt) cc_final: 0.8273 (mp)
REVERT: F   62 GLU cc_start: 0.7452 (mt-10) cc_final: 0.6803 (mt-10)
REVERT: F   70 LYS cc_start: 0.7822 (tttt) cc_final: 0.7620 (tttm)
REVERT: F   80 LYS cc_start: 0.7870 (tttt) cc_final: 0.7614 (ttpp)
REVERT: F   89 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7319 (tt0)
REVERT: F  104 ARG cc_start: 0.7646 (mtt180) cc_final: 0.7262 (ttp-110)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.7147
  time to fit residues: 104.8708
Evaluate side-chains
  106 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 48 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A  90 HIS
B  98 ASN
C  98 ASN
D  98 ASN
E  98 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.126544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.105908 restraints weight = 4994.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 2.15
r_work: 0.3586 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3475 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.1967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4410  Z= 0.141
  Angle     :  0.592   4.947   6000  Z= 0.334
  Chirality :  0.050   0.142    708
  Planarity :  0.005   0.042    738
  Dihedral  :  5.098  14.927    594
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 14.74 %
    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: -2.23 (0.31), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.69 (0.24), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 103 
 TYR   0.012   0.002   TYR D 114 
 PHE   0.017   0.003   PHE C  64 
 TRP   0.003   0.001   TRP F  79 
 HIS   0.008   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 4410)
  covalent geometry    : angle       0.59211 ( 6000)
  hydrogen bonds       : bond        0.04137 (   70)
  hydrogen bonds       : angle       5.27669 (  210)

*********************** 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
  113 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 107
  time to evaluate  : 0.196 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.8109 (ttt90) cc_final: 0.7750 (ttt90)
REVERT: A   66 GLU cc_start: 0.7737 (tt0) cc_final: 0.7486 (tt0)
REVERT: A   80 LYS cc_start: 0.8324 (tttt) cc_final: 0.7814 (ttpt)
REVERT: B   13 MET cc_start: 0.8299 (ttm) cc_final: 0.8086 (ttm)
REVERT: B   15 LYS cc_start: 0.8061 (mtpt) cc_final: 0.7743 (mtpt)
REVERT: B   70 LYS cc_start: 0.8745 (tttt) cc_final: 0.8523 (tttp)
REVERT: B  104 ARG cc_start: 0.7792 (mtt180) cc_final: 0.7489 (mtm-85)
REVERT: C   13 MET cc_start: 0.7948 (ttm) cc_final: 0.7300 (mtp)
REVERT: C   15 LYS cc_start: 0.8100 (mtpt) cc_final: 0.7774 (mtmt)
REVERT: C   62 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7535 (mt-10)
REVERT: C   66 GLU cc_start: 0.7777 (tt0) cc_final: 0.7300 (tm-30)
REVERT: C  104 ARG cc_start: 0.7888 (mtt180) cc_final: 0.7310 (mtp180)
REVERT: D   13 MET cc_start: 0.7919 (ttm) cc_final: 0.7146 (mtm)
REVERT: D   15 LYS cc_start: 0.8013 (mtpt) cc_final: 0.7582 (mtpt)
REVERT: D   62 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7642 (mt-10)
REVERT: D   80 LYS cc_start: 0.8340 (tttt) cc_final: 0.7856 (tttm)
REVERT: D  104 ARG cc_start: 0.8078 (mtt180) cc_final: 0.7554 (mtp-110)
REVERT: E   15 LYS cc_start: 0.8135 (mtpt) cc_final: 0.7841 (mtpp)
REVERT: E   34 ARG cc_start: 0.8077 (ttt-90) cc_final: 0.7395 (tmt-80)
REVERT: E   62 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7377 (mt-10)
REVERT: E   80 LYS cc_start: 0.8271 (tttt) cc_final: 0.7816 (tttm)
REVERT: E   92 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8072 (mt-10)
REVERT: E  104 ARG cc_start: 0.8029 (mtt180) cc_final: 0.7609 (mtm110)
REVERT: F   13 MET cc_start: 0.8047 (ttm) cc_final: 0.7350 (mtm)
REVERT: F   15 LYS cc_start: 0.8265 (mtpt) cc_final: 0.8006 (mtpm)
REVERT: F   26 ILE cc_start: 0.8859 (mt) cc_final: 0.8647 (mt)
REVERT: F   62 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7241 (mt-10)
REVERT: F   80 LYS cc_start: 0.8411 (tttt) cc_final: 0.8081 (tttp)
REVERT: F  104 ARG cc_start: 0.8285 (mtt180) cc_final: 0.7927 (mtm110)
REVERT: F  118 THR cc_start: 0.8524 (m) cc_final: 0.8209 (p)
  outliers start: 6
  outliers final: 2
  residues processed: 109
  average time/residue: 0.7440
  time to fit residues: 83.0222
Evaluate side-chains
  105 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 103
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   98 ASN
Chi-restraints excluded: chain B residue  123 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 2 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 21 optimal weight:    6.9990
   chunk 14 optimal weight:    8.9990
   chunk 25 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
A  90 HIS
** B  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  88 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.120665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.100082 restraints weight = 4997.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 2.14
r_work: 0.3507 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3394 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.2995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   4410  Z= 0.210
  Angle     :  0.626   5.444   6000  Z= 0.354
  Chirality :  0.051   0.148    708
  Planarity :  0.005   0.035    738
  Dihedral  :  5.205  16.276    594
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 15.60 %
    Favored  : 80.77 %
  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 (0.32), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.76 (0.25), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  34 
 TYR   0.013   0.002   TYR B 114 
 PHE   0.010   0.003   PHE D  33 
 TRP   0.005   0.001   TRP B  79 
 HIS   0.007   0.002   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 4410)
  covalent geometry    : angle       0.62615 ( 6000)
  hydrogen bonds       : bond        0.03593 (   70)
  hydrogen bonds       : angle       5.48652 (  210)

*********************** 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
  116 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8604 (mtpt) cc_final: 0.8303 (mtmt)
REVERT: A   21 ARG cc_start: 0.8230 (ttt90) cc_final: 0.7786 (ttt90)
REVERT: A   66 GLU cc_start: 0.7912 (tt0) cc_final: 0.7250 (tm-30)
REVERT: A   80 LYS cc_start: 0.8273 (tttt) cc_final: 0.7859 (ttpt)
REVERT: B   15 LYS cc_start: 0.8235 (mtpt) cc_final: 0.8011 (mtpp)
REVERT: B   34 ARG cc_start: 0.8366 (ttt-90) cc_final: 0.8072 (ttt180)
REVERT: B   70 LYS cc_start: 0.8771 (tttt) cc_final: 0.8539 (tttp)
REVERT: B  104 ARG cc_start: 0.7988 (mtt180) cc_final: 0.7762 (mtt90)
REVERT: C   13 MET cc_start: 0.8024 (ttm) cc_final: 0.7565 (mtp)
REVERT: C   15 LYS cc_start: 0.8273 (mtpt) cc_final: 0.7918 (mtmt)
REVERT: C   62 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7656 (mt-10)
REVERT: C   66 GLU cc_start: 0.7968 (tt0) cc_final: 0.7238 (tm-30)
REVERT: D   13 MET cc_start: 0.7991 (ttm) cc_final: 0.7590 (mtp)
REVERT: D   15 LYS cc_start: 0.8261 (mtpt) cc_final: 0.7921 (mtpt)
REVERT: D   62 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7282 (tt0)
REVERT: D   66 GLU cc_start: 0.8118 (tt0) cc_final: 0.7277 (tm-30)
REVERT: D   80 LYS cc_start: 0.8271 (tttt) cc_final: 0.7707 (tttm)
REVERT: D   89 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7392 (mt-10)
REVERT: D   99 ASP cc_start: 0.7885 (t70) cc_final: 0.7587 (t0)
REVERT: E   15 LYS cc_start: 0.8214 (mtpt) cc_final: 0.7835 (mtmt)
REVERT: E   62 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7589 (mt-10)
REVERT: E   66 GLU cc_start: 0.7797 (tt0) cc_final: 0.7092 (tm-30)
REVERT: E   80 LYS cc_start: 0.8291 (tttt) cc_final: 0.7851 (tttm)
REVERT: E   92 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7914 (mt-10)
REVERT: E  104 ARG cc_start: 0.8162 (mtt180) cc_final: 0.7942 (mtm-85)
REVERT: F   13 MET cc_start: 0.7872 (ttm) cc_final: 0.7173 (mtm)
REVERT: F   15 LYS cc_start: 0.8375 (mtpt) cc_final: 0.7979 (mtpt)
REVERT: F   62 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7357 (mt-10)
REVERT: F   66 GLU cc_start: 0.8085 (tt0) cc_final: 0.7616 (tm-30)
REVERT: F   80 LYS cc_start: 0.8346 (tttt) cc_final: 0.8058 (ttpp)
REVERT: F   89 GLU cc_start: 0.7763 (tt0) cc_final: 0.7336 (tt0)
REVERT: F   92 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8034 (mt-10)
REVERT: F  104 ARG cc_start: 0.8313 (mtt180) cc_final: 0.7988 (mtm110)
  outliers start: 17
  outliers final: 9
  residues processed: 107
  average time/residue: 0.8707
  time to fit residues: 95.0667
Evaluate side-chains
  109 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   85 SER
Chi-restraints excluded: chain F residue   75 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 42 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 12 optimal weight:    0.5980
   chunk 32 optimal weight:    0.0070
   overall best weight:    1.7204

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

Flipped N/Q/H residues before XYZ refinement:
A  31 HIS
A  90 HIS
** B  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  98 ASN
C  98 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.120493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.100179 restraints weight = 5001.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 2.12
r_work: 0.3515 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3407 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.3454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   4410  Z= 0.191
  Angle     :  0.587   6.207   6000  Z= 0.327
  Chirality :  0.050   0.140    708
  Planarity :  0.004   0.037    738
  Dihedral  :  5.140  16.069    594
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 15.81 %
    Favored  : 79.49 %
  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: -2.33 (0.33), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.77 (0.25), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 104 
 TYR   0.013   0.002   TYR B 114 
 PHE   0.008   0.002   PHE C  33 
 TRP   0.005   0.001   TRP B  79 
 HIS   0.006   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 4410)
  covalent geometry    : angle       0.58698 ( 6000)
  hydrogen bonds       : bond        0.03075 (   70)
  hydrogen bonds       : angle       5.23324 (  210)

*********************** 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
  124 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8649 (mtpt) cc_final: 0.8399 (mtmt)
REVERT: A   21 ARG cc_start: 0.8185 (ttt90) cc_final: 0.7865 (ttt90)
REVERT: A   80 LYS cc_start: 0.8326 (tttt) cc_final: 0.7878 (ttpt)
REVERT: B   15 LYS cc_start: 0.8212 (mtpt) cc_final: 0.7976 (mtpt)
REVERT: B   34 ARG cc_start: 0.8393 (ttt-90) cc_final: 0.8131 (ttt180)
REVERT: B   70 LYS cc_start: 0.8768 (tttt) cc_final: 0.8528 (tttp)
REVERT: B  104 ARG cc_start: 0.8102 (mtt180) cc_final: 0.7839 (mtt180)
REVERT: C   15 LYS cc_start: 0.8340 (mtpt) cc_final: 0.7994 (mtmt)
REVERT: C   62 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7635 (mt-10)
REVERT: C   72 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7747 (mm-30)
REVERT: D   13 MET cc_start: 0.8000 (ttm) cc_final: 0.7704 (mtp)
REVERT: D   15 LYS cc_start: 0.8398 (mtpt) cc_final: 0.8082 (mtpt)
REVERT: D   21 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7656 (ttt180)
REVERT: D   62 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7284 (tt0)
REVERT: D   66 GLU cc_start: 0.8083 (tt0) cc_final: 0.7327 (tm-30)
REVERT: D   80 LYS cc_start: 0.8250 (tttt) cc_final: 0.7672 (tttm)
REVERT: D   89 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7338 (mt-10)
REVERT: E   15 LYS cc_start: 0.8229 (mtpt) cc_final: 0.7835 (mtmt)
REVERT: E   62 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7597 (mt-10)
REVERT: E   66 GLU cc_start: 0.7794 (tt0) cc_final: 0.7080 (tm-30)
REVERT: E   80 LYS cc_start: 0.8212 (tttt) cc_final: 0.7785 (tttm)
REVERT: E   92 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7940 (mt-10)
REVERT: E  104 ARG cc_start: 0.8193 (mtt180) cc_final: 0.7958 (mtm-85)
REVERT: F   13 MET cc_start: 0.7858 (ttm) cc_final: 0.7149 (mtm)
REVERT: F   15 LYS cc_start: 0.8412 (mtpt) cc_final: 0.7994 (mtpt)
REVERT: F   34 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8155 (ttt180)
REVERT: F   62 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7606 (mt-10)
REVERT: F   66 GLU cc_start: 0.8131 (tt0) cc_final: 0.7645 (tm-30)
REVERT: F   80 LYS cc_start: 0.8317 (tttt) cc_final: 0.8010 (tttp)
REVERT: F   92 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8040 (mt-10)
REVERT: F  104 ARG cc_start: 0.8327 (mtt180) cc_final: 0.7977 (mtm110)
  outliers start: 22
  outliers final: 7
  residues processed: 113
  average time/residue: 0.8162
  time to fit residues: 94.3957
Evaluate side-chains
  111 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain D residue   21 ARG
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain F residue   34 ARG
Chi-restraints excluded: chain F residue   75 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 37 optimal weight:    0.2980
   chunk 16 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 47 optimal weight:    5.9990
   chunk 22 optimal weight:    0.7980
   chunk 20 optimal weight:    7.9990
   chunk 18 optimal weight:    7.9990
   chunk 5 optimal weight:    0.0070
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.9800

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

Flipped N/Q/H residues before XYZ refinement:
A  90 HIS
** B  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  98 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.122984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.102807 restraints weight = 5024.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3690 rms_B_bonded: 2.14
r_work: 0.3563 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3453 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.3575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4410  Z= 0.130
  Angle     :  0.522   6.466   6000  Z= 0.288
  Chirality :  0.049   0.129    708
  Planarity :  0.004   0.033    738
  Dihedral  :  4.924  15.158    594
  Min Nonbonded Distance : 2.653

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 17.74 %
    Favored  : 79.27 %
  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: -2.29 (0.34), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.74 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 104 
 TYR   0.013   0.002   TYR C 114 
 PHE   0.009   0.002   PHE B  64 
 TRP   0.003   0.001   TRP A  79 
 HIS   0.005   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 4410)
  covalent geometry    : angle       0.52223 ( 6000)
  hydrogen bonds       : bond        0.02588 (   70)
  hydrogen bonds       : angle       4.93014 (  210)

*********************** 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
  115 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.184 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8676 (mtpt) cc_final: 0.8425 (mtmt)
REVERT: A   18 ASP cc_start: 0.8104 (t0) cc_final: 0.7883 (t0)
REVERT: A   21 ARG cc_start: 0.8151 (ttt90) cc_final: 0.7800 (ttt90)
REVERT: A   80 LYS cc_start: 0.8286 (tttt) cc_final: 0.7861 (ttpt)
REVERT: B   15 LYS cc_start: 0.8251 (mtpt) cc_final: 0.7962 (mtpt)
REVERT: B   34 ARG cc_start: 0.8376 (ttt-90) cc_final: 0.8077 (ttt180)
REVERT: B   70 LYS cc_start: 0.8747 (tttt) cc_final: 0.8505 (tttp)
REVERT: C   15 LYS cc_start: 0.8334 (mtpt) cc_final: 0.8006 (mtpt)
REVERT: C   62 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7585 (mt-10)
REVERT: D   13 MET cc_start: 0.8002 (ttm) cc_final: 0.7700 (mtp)
REVERT: D   15 LYS cc_start: 0.8293 (mtpt) cc_final: 0.7974 (mtpt)
REVERT: D   34 ARG cc_start: 0.8448 (ttt-90) cc_final: 0.8200 (tmt90)
REVERT: D   62 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7283 (tt0)
REVERT: D   66 GLU cc_start: 0.8068 (tt0) cc_final: 0.7303 (tm-30)
REVERT: D   80 LYS cc_start: 0.8172 (tttt) cc_final: 0.7602 (tttm)
REVERT: D   99 ASP cc_start: 0.7918 (t0) cc_final: 0.7461 (t0)
REVERT: E   15 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7899 (mtmt)
REVERT: E   62 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7528 (mt-10)
REVERT: E   66 GLU cc_start: 0.7729 (tt0) cc_final: 0.7133 (tm-30)
REVERT: E   80 LYS cc_start: 0.8224 (tttt) cc_final: 0.7870 (ttpp)
REVERT: E   92 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7927 (mt-10)
REVERT: E  104 ARG cc_start: 0.8203 (mtt180) cc_final: 0.7741 (mtm110)
REVERT: F   13 MET cc_start: 0.7791 (ttm) cc_final: 0.7149 (mtm)
REVERT: F   15 LYS cc_start: 0.8400 (mtpt) cc_final: 0.8046 (mtpt)
REVERT: F   34 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8183 (ttt180)
REVERT: F   62 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7559 (mt-10)
REVERT: F   66 GLU cc_start: 0.8116 (tt0) cc_final: 0.7641 (tm-30)
REVERT: F   80 LYS cc_start: 0.8250 (tttt) cc_final: 0.7947 (tttp)
REVERT: F   92 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8021 (mt-10)
REVERT: F  104 ARG cc_start: 0.8266 (mtt180) cc_final: 0.7906 (mtm110)
  outliers start: 14
  outliers final: 5
  residues processed: 108
  average time/residue: 0.9300
  time to fit residues: 102.6175
Evaluate side-chains
  103 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain F residue   34 ARG
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain F residue   85 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 15 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 50 optimal weight:    0.5980
   overall best weight:    2.3188

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

Flipped N/Q/H residues before XYZ refinement:
A  90 HIS
** B  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  98 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.118845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.098475 restraints weight = 5228.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 2.17
r_work: 0.3493 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3382 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.3859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   4410  Z= 0.252
  Angle     :  0.633   6.567   6000  Z= 0.355
  Chirality :  0.051   0.142    708
  Planarity :  0.005   0.034    738
  Dihedral  :  5.366  18.270    594
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 16.24 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.33), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.79 (0.25), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 104 
 TYR   0.013   0.002   TYR A 114 
 PHE   0.011   0.003   PHE E  87 
 TRP   0.006   0.002   TRP B  79 
 HIS   0.005   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00589 ( 4410)
  covalent geometry    : angle       0.63345 ( 6000)
  hydrogen bonds       : bond        0.03091 (   70)
  hydrogen bonds       : angle       5.26847 (  210)

*********************** 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
  121 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8729 (mtpt) cc_final: 0.6783 (pptt)
REVERT: A   21 ARG cc_start: 0.8231 (ttt90) cc_final: 0.7798 (ttt90)
REVERT: A   80 LYS cc_start: 0.8312 (tttt) cc_final: 0.7817 (ttpt)
REVERT: A  104 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.8077 (mtm-85)
REVERT: B   15 LYS cc_start: 0.8353 (mtpt) cc_final: 0.8068 (mtpt)
REVERT: B   34 ARG cc_start: 0.8376 (ttt-90) cc_final: 0.8126 (ttt180)
REVERT: B   70 LYS cc_start: 0.8768 (tttt) cc_final: 0.8552 (tttp)
REVERT: C   15 LYS cc_start: 0.8391 (mtpt) cc_final: 0.8074 (mtpt)
REVERT: C   62 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7581 (mt-10)
REVERT: C   63 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7320 (tt0)
REVERT: C   72 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7870 (mm-30)
REVERT: D   13 MET cc_start: 0.7971 (ttm) cc_final: 0.7757 (mtp)
REVERT: D   15 LYS cc_start: 0.8346 (mtpt) cc_final: 0.8030 (mtpt)
REVERT: D   34 ARG cc_start: 0.8433 (ttt-90) cc_final: 0.8222 (tmt90)
REVERT: D   62 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7748 (mt-10)
REVERT: D   66 GLU cc_start: 0.8035 (tt0) cc_final: 0.7222 (tm-30)
REVERT: D   80 LYS cc_start: 0.8177 (tttt) cc_final: 0.7658 (tttm)
REVERT: D   99 ASP cc_start: 0.7943 (t0) cc_final: 0.7412 (t0)
REVERT: E   15 LYS cc_start: 0.8304 (mtpt) cc_final: 0.7980 (mtmt)
REVERT: E   62 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7606 (mt-10)
REVERT: E   66 GLU cc_start: 0.7789 (tt0) cc_final: 0.7138 (tm-30)
REVERT: E   80 LYS cc_start: 0.8279 (tttt) cc_final: 0.7925 (ttpp)
REVERT: F   13 MET cc_start: 0.7737 (ttm) cc_final: 0.7146 (mtm)
REVERT: F   15 LYS cc_start: 0.8499 (mtpt) cc_final: 0.8250 (mtpm)
REVERT: F   34 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8130 (ttt180)
REVERT: F   62 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7649 (mt-10)
REVERT: F   80 LYS cc_start: 0.8373 (tttt) cc_final: 0.8093 (tttp)
REVERT: F   92 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8141 (mt-10)
REVERT: F  104 ARG cc_start: 0.8240 (mtt180) cc_final: 0.7911 (mtm110)
  outliers start: 22
  outliers final: 10
  residues processed: 110
  average time/residue: 0.8462
  time to fit residues: 95.0710
Evaluate side-chains
  110 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain F residue   34 ARG
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain F residue   85 SER
Chi-restraints excluded: chain F residue  123 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9980
   chunk 9 optimal weight:    6.9990
   chunk 11 optimal weight:    6.9990
   chunk 51 optimal weight:    0.0570
   chunk 15 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   overall best weight:    0.9900

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

Flipped N/Q/H residues before XYZ refinement:
A  90 HIS
** B  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  98 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.121832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.101836 restraints weight = 5126.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3685 rms_B_bonded: 2.13
r_work: 0.3553 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3444 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.3869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4410  Z= 0.133
  Angle     :  0.528   7.241   6000  Z= 0.291
  Chirality :  0.049   0.132    708
  Planarity :  0.004   0.030    738
  Dihedral  :  5.073  16.012    594
  Min Nonbonded Distance : 2.650

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 18.59 %
    Favored  : 79.27 %
  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: -2.27 (0.34), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.72 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 104 
 TYR   0.014   0.001   TYR C 114 
 PHE   0.010   0.002   PHE B  64 
 TRP   0.003   0.001   TRP A  79 
 HIS   0.004   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 4410)
  covalent geometry    : angle       0.52782 ( 6000)
  hydrogen bonds       : bond        0.02506 (   70)
  hydrogen bonds       : angle       5.01244 (  210)

*********************** 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
  109 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.151 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8722 (mtpt) cc_final: 0.8512 (mtpt)
REVERT: A   21 ARG cc_start: 0.8147 (ttt90) cc_final: 0.7808 (ttt90)
REVERT: A   80 LYS cc_start: 0.8280 (tttt) cc_final: 0.7819 (ttpt)
REVERT: A  104 ARG cc_start: 0.8304 (mtm-85) cc_final: 0.8078 (mtm-85)
REVERT: B   15 LYS cc_start: 0.8299 (mtpt) cc_final: 0.7996 (mtpt)
REVERT: B   34 ARG cc_start: 0.8388 (ttt-90) cc_final: 0.8130 (ttt180)
REVERT: B   70 LYS cc_start: 0.8707 (tttt) cc_final: 0.8471 (tttp)
REVERT: C   15 LYS cc_start: 0.8318 (mtpt) cc_final: 0.8035 (mtmt)
REVERT: C   62 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7580 (mt-10)
REVERT: D   13 MET cc_start: 0.7944 (ttm) cc_final: 0.7732 (mtp)
REVERT: D   15 LYS cc_start: 0.8346 (mtpt) cc_final: 0.8105 (mtpt)
REVERT: D   21 ARG cc_start: 0.7771 (ttt90) cc_final: 0.7375 (ttt180)
REVERT: D   34 ARG cc_start: 0.8487 (ttt-90) cc_final: 0.8265 (tmt90)
REVERT: D   62 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7711 (mt-10)
REVERT: D   66 GLU cc_start: 0.7908 (tt0) cc_final: 0.7112 (tm-30)
REVERT: D   80 LYS cc_start: 0.8150 (tttt) cc_final: 0.7669 (ttpp)
REVERT: D   99 ASP cc_start: 0.7882 (t0) cc_final: 0.7407 (t0)
REVERT: E   62 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7555 (mt-10)
REVERT: E   66 GLU cc_start: 0.7764 (tt0) cc_final: 0.7138 (tm-30)
REVERT: E   80 LYS cc_start: 0.8200 (tttt) cc_final: 0.7817 (tttm)
REVERT: F   13 MET cc_start: 0.7826 (ttm) cc_final: 0.7186 (mtm)
REVERT: F   15 LYS cc_start: 0.8412 (mtpt) cc_final: 0.8030 (mtpt)
REVERT: F   34 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8182 (ttt180)
REVERT: F   62 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7546 (mt-10)
REVERT: F   80 LYS cc_start: 0.8276 (tttt) cc_final: 0.7965 (tttp)
REVERT: F   92 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8126 (mt-10)
REVERT: F  104 ARG cc_start: 0.8180 (mtt180) cc_final: 0.7876 (mtm110)
  outliers start: 10
  outliers final: 6
  residues processed: 103
  average time/residue: 0.9123
  time to fit residues: 95.8745
Evaluate side-chains
  104 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain D residue   72 GLU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain F residue   34 ARG
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain F residue   85 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 52 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   chunk 11 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  90 HIS
** B  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  98 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.124433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.104379 restraints weight = 5165.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.3710 rms_B_bonded: 2.11
r_work: 0.3583 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3472 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.3930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4410  Z= 0.113
  Angle     :  0.504   7.391   6000  Z= 0.276
  Chirality :  0.048   0.128    708
  Planarity :  0.003   0.029    738
  Dihedral  :  4.858  15.256    594
  Min Nonbonded Distance : 2.650

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 17.31 %
    Favored  : 79.70 %
  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: -2.23 (0.35), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.69 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 104 
 TYR   0.013   0.001   TYR C 114 
 PHE   0.009   0.002   PHE B  64 
 TRP   0.002   0.001   TRP D  79 
 HIS   0.004   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 4410)
  covalent geometry    : angle       0.50415 ( 6000)
  hydrogen bonds       : bond        0.02266 (   70)
  hydrogen bonds       : angle       4.81000 (  210)

*********************** 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
  113 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8685 (mtpt) cc_final: 0.8479 (mtmt)
REVERT: A   21 ARG cc_start: 0.8185 (ttt90) cc_final: 0.7842 (ttt90)
REVERT: A   80 LYS cc_start: 0.8277 (tttt) cc_final: 0.7851 (ttpt)
REVERT: A  104 ARG cc_start: 0.8231 (mtm-85) cc_final: 0.7989 (mtm-85)
REVERT: B   15 LYS cc_start: 0.8311 (mtpt) cc_final: 0.8046 (mtpt)
REVERT: B   34 ARG cc_start: 0.8370 (ttt-90) cc_final: 0.8153 (ttt180)
REVERT: B   70 LYS cc_start: 0.8714 (tttt) cc_final: 0.8490 (tttp)
REVERT: C   15 LYS cc_start: 0.8348 (mtpt) cc_final: 0.8101 (mtmt)
REVERT: C   62 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7588 (mt-10)
REVERT: D   13 MET cc_start: 0.7993 (ttm) cc_final: 0.7738 (mtp)
REVERT: D   15 LYS cc_start: 0.8418 (mtpt) cc_final: 0.8165 (mtpt)
REVERT: D   62 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7711 (mt-10)
REVERT: D   66 GLU cc_start: 0.7859 (tt0) cc_final: 0.7117 (tm-30)
REVERT: D   80 LYS cc_start: 0.8142 (tttt) cc_final: 0.7708 (ttpp)
REVERT: D   99 ASP cc_start: 0.7826 (t0) cc_final: 0.7379 (t0)
REVERT: E   15 LYS cc_start: 0.8439 (mtmt) cc_final: 0.8216 (mtmt)
REVERT: E   62 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7563 (mt-10)
REVERT: E   66 GLU cc_start: 0.7798 (tt0) cc_final: 0.7175 (tm-30)
REVERT: E   80 LYS cc_start: 0.8194 (tttt) cc_final: 0.7777 (tttm)
REVERT: F   13 MET cc_start: 0.7884 (ttm) cc_final: 0.7252 (mtm)
REVERT: F   15 LYS cc_start: 0.8418 (mtpt) cc_final: 0.8060 (mtpt)
REVERT: F   34 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8161 (ttt180)
REVERT: F   62 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7543 (mt-10)
REVERT: F  104 ARG cc_start: 0.8220 (mtt180) cc_final: 0.7943 (mtm110)
  outliers start: 14
  outliers final: 8
  residues processed: 105
  average time/residue: 0.9127
  time to fit residues: 97.8119
Evaluate side-chains
  106 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain D residue   72 GLU
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   92 GLU
Chi-restraints excluded: chain F residue   34 ARG
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain F residue   85 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   chunk 21 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0020
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.7588

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

Flipped N/Q/H residues before XYZ refinement:
A  90 HIS
** B  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  98 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.124953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.105008 restraints weight = 5175.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.3720 rms_B_bonded: 2.11
r_work: 0.3593 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3485 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.3976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4410  Z= 0.114
  Angle     :  0.500   7.652   6000  Z= 0.273
  Chirality :  0.048   0.128    708
  Planarity :  0.003   0.029    738
  Dihedral  :  4.789  15.027    594
  Min Nonbonded Distance : 2.651

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 17.74 %
    Favored  : 79.49 %
  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: -2.20 (0.35), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.67 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 104 
 TYR   0.012   0.001   TYR C 114 
 PHE   0.008   0.002   PHE B  64 
 TRP   0.002   0.001   TRP D  79 
 HIS   0.004   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 4410)
  covalent geometry    : angle       0.50045 ( 6000)
  hydrogen bonds       : bond        0.02204 (   70)
  hydrogen bonds       : angle       4.75717 (  210)

*********************** 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
  111 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.192 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.8183 (ttt90) cc_final: 0.7886 (ttt90)
REVERT: A   34 ARG cc_start: 0.8228 (ttt-90) cc_final: 0.7932 (ttt-90)
REVERT: A   80 LYS cc_start: 0.8271 (tttt) cc_final: 0.7840 (ttpt)
REVERT: B   15 LYS cc_start: 0.8296 (mtpt) cc_final: 0.8039 (mtpt)
REVERT: C   15 LYS cc_start: 0.8340 (mtpt) cc_final: 0.8080 (mtmt)
REVERT: C   62 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7555 (mt-10)
REVERT: C   92 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7588 (mt-10)
REVERT: D   13 MET cc_start: 0.8012 (ttm) cc_final: 0.7769 (mtp)
REVERT: D   15 LYS cc_start: 0.8418 (mtpt) cc_final: 0.8169 (mtpt)
REVERT: D   62 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7713 (mt-10)
REVERT: D   66 GLU cc_start: 0.7864 (tt0) cc_final: 0.7175 (tm-30)
REVERT: D   80 LYS cc_start: 0.8164 (tttt) cc_final: 0.7844 (ttpp)
REVERT: D   99 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7371 (t0)
REVERT: E   62 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7586 (mt-10)
REVERT: E   66 GLU cc_start: 0.7808 (tt0) cc_final: 0.7254 (tm-30)
REVERT: E   80 LYS cc_start: 0.8206 (tttt) cc_final: 0.7759 (tttm)
REVERT: F   13 MET cc_start: 0.7856 (ttm) cc_final: 0.7247 (mtm)
REVERT: F   15 LYS cc_start: 0.8437 (mtpt) cc_final: 0.8082 (mtpt)
REVERT: F   34 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8123 (ttt180)
REVERT: F   62 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7612 (mt-10)
REVERT: F  104 ARG cc_start: 0.8211 (mtt180) cc_final: 0.7964 (mtm110)
  outliers start: 13
  outliers final: 8
  residues processed: 102
  average time/residue: 0.9887
  time to fit residues: 102.8926
Evaluate side-chains
  107 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain D residue   99 ASP
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   92 GLU
Chi-restraints excluded: chain F residue   34 ARG
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain F residue   85 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 3 optimal weight:    0.0010
   chunk 24 optimal weight:    8.9990
   chunk 42 optimal weight:    6.9990
   chunk 26 optimal weight:    4.9990
   chunk 47 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
A  90 HIS
** B  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  98 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.125448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.105598 restraints weight = 5083.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.3727 rms_B_bonded: 2.10
r_work: 0.3601 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3494 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.4028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4410  Z= 0.108
  Angle     :  0.498   7.992   6000  Z= 0.269
  Chirality :  0.048   0.127    708
  Planarity :  0.003   0.028    738
  Dihedral  :  4.737  14.375    594
  Min Nonbonded Distance : 2.650

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 18.38 %
    Favored  : 79.49 %
  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: -2.21 (0.35), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.67 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  34 
 TYR   0.012   0.001   TYR C 114 
 PHE   0.008   0.002   PHE B  64 
 TRP   0.002   0.001   TRP D  79 
 HIS   0.004   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 4410)
  covalent geometry    : angle       0.49757 ( 6000)
  hydrogen bonds       : bond        0.02146 (   70)
  hydrogen bonds       : angle       4.69596 (  210)

********************** 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
  108 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.8181 (ttt90) cc_final: 0.7888 (ttt90)
REVERT: A   34 ARG cc_start: 0.8215 (ttt-90) cc_final: 0.7994 (ttt-90)
REVERT: A   80 LYS cc_start: 0.8217 (tttt) cc_final: 0.7776 (ttpt)
REVERT: B   15 LYS cc_start: 0.8293 (mtpt) cc_final: 0.8040 (mtpt)
REVERT: B  104 ARG cc_start: 0.8112 (mtt90) cc_final: 0.7781 (mtt180)
REVERT: C   15 LYS cc_start: 0.8362 (mtpt) cc_final: 0.8075 (mtmt)
REVERT: C   62 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7594 (mt-10)
REVERT: C   92 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7585 (mt-10)
REVERT: D   13 MET cc_start: 0.8014 (ttm) cc_final: 0.7770 (mtp)
REVERT: D   15 LYS cc_start: 0.8414 (mtpt) cc_final: 0.8172 (mtpt)
REVERT: D   62 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7742 (mt-10)
REVERT: D   66 GLU cc_start: 0.7881 (tt0) cc_final: 0.7184 (tm-30)
REVERT: D   80 LYS cc_start: 0.8163 (tttt) cc_final: 0.7847 (ttpp)
REVERT: D   99 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7338 (t0)
REVERT: E   62 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7567 (mt-10)
REVERT: E   66 GLU cc_start: 0.7795 (tt0) cc_final: 0.7252 (tm-30)
REVERT: E   80 LYS cc_start: 0.8189 (tttt) cc_final: 0.7744 (tttm)
REVERT: F   13 MET cc_start: 0.7857 (ttm) cc_final: 0.7256 (mtm)
REVERT: F   15 LYS cc_start: 0.8438 (mtpt) cc_final: 0.8077 (mtpt)
REVERT: F   62 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7627 (mt-10)
REVERT: F  104 ARG cc_start: 0.8205 (mtt180) cc_final: 0.7963 (mtm110)
  outliers start: 10
  outliers final: 7
  residues processed: 101
  average time/residue: 0.9840
  time to fit residues: 101.3621
Evaluate side-chains
  107 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain D residue   99 ASP
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   92 GLU
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain F residue   85 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   chunk 28 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 2 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 29 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
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  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.118428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.098046 restraints weight = 5186.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 2.16
r_work: 0.3500 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3391 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.4139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.040   4410  Z= 0.289
  Angle     :  0.657   7.829   6000  Z= 0.366
  Chirality :  0.052   0.146    708
  Planarity :  0.004   0.031    738
  Dihedral  :  5.415  18.350    594
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 17.95 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.34), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.79 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D 104 
 TYR   0.015   0.003   TYR A 116 
 PHE   0.012   0.003   PHE E  87 
 TRP   0.008   0.002   TRP D  79 
 HIS   0.004   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00678 ( 4410)
  covalent geometry    : angle       0.65740 ( 6000)
  hydrogen bonds       : bond        0.03126 (   70)
  hydrogen bonds       : angle       5.29266 (  210)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2339.44 seconds
wall clock time: 40 minutes 27.82 seconds (2427.82 seconds total)