Starting phenix.real_space_refine
on Fri Dec 27 11:03:17 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pkf_17737/12_2024/8pkf_17737.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pkf_17737/12_2024/8pkf_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pkf_17737/12_2024/8pkf_17737.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pkf_17737/12_2024/8pkf_17737.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pkf_17737/12_2024/8pkf_17737.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pkf_17737/12_2024/8pkf_17737.cif"
  }
  resolution = 2.3673
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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:
    C, B, E, D, F
  Time building chain proxies: 2.97, per 1000 atoms: 0.69
  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: 1.07
  Conformation dependent library (CDL) restraints added in 628.0 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 42.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  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: 1.36

  Time building geometry restraints manager: 1.25 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: 0.00
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:                  0.010
  Normalize map: mean=0, sd=1:             0.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.060
  Find NCS groups from input model:        0.160
  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:13.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.240
-------------------------------------------------------------------------------
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= 0.849
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.77 (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
 TRP   0.002   0.001   TRP B  79 
 HIS   0.002   0.001   HIS D  31 
 PHE   0.012   0.003   PHE B  95 
 TYR   0.014   0.003   TYR B 114 
 ARG   0.001   0.000   ARG A  34 

*********************** 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  : 0.551 
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: 1.5694
  time to fit residues: 230.6207
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  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 13 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   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  98 ASN
C  98 ASN
D  98 ASN
E  98 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.1989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4410  Z= 0.196
  Angle     :  0.585   5.174   6000  Z= 0.329
  Chirality :  0.048   0.145    708
  Planarity :  0.005   0.042    738
  Dihedral  :  5.066  14.881    594
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 4.41
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.20 (0.32), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.67 (0.24), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP F  79 
 HIS   0.008   0.001   HIS D  31 
 PHE   0.017   0.003   PHE C  64 
 TYR   0.012   0.001   TYR B 114 
 ARG   0.002   0.000   ARG B 103 

*********************** 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
  114 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 108
  time to evaluate  : 0.526 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.7700 (ttt90) cc_final: 0.7216 (ttt90)
REVERT: A   66 GLU cc_start: 0.7302 (tt0) cc_final: 0.6945 (tt0)
REVERT: A   70 LYS cc_start: 0.7967 (tttt) cc_final: 0.7528 (tttp)
REVERT: A   80 LYS cc_start: 0.7376 (tttt) cc_final: 0.6848 (ttpt)
REVERT: A  104 ARG cc_start: 0.7277 (mtt180) cc_final: 0.6748 (mtm-85)
REVERT: B   13 MET cc_start: 0.7500 (ttm) cc_final: 0.7277 (ttm)
REVERT: B   15 LYS cc_start: 0.7060 (mtpt) cc_final: 0.6755 (mtpt)
REVERT: B   70 LYS cc_start: 0.7998 (tttt) cc_final: 0.7598 (tttp)
REVERT: B  104 ARG cc_start: 0.6961 (mtt180) cc_final: 0.6353 (mtm-85)
REVERT: C   13 MET cc_start: 0.7200 (ttm) cc_final: 0.6513 (mtp)
REVERT: C   15 LYS cc_start: 0.6995 (mtpt) cc_final: 0.6588 (mtmt)
REVERT: C   62 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6760 (mt-10)
REVERT: C   66 GLU cc_start: 0.7326 (tt0) cc_final: 0.6417 (tm-30)
REVERT: C   92 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7341 (mt-10)
REVERT: C  104 ARG cc_start: 0.7111 (mtt180) cc_final: 0.6212 (mtp180)
REVERT: D   13 MET cc_start: 0.7179 (ttm) cc_final: 0.6303 (mtm)
REVERT: D   15 LYS cc_start: 0.7005 (mtpt) cc_final: 0.6485 (mtpt)
REVERT: D   62 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6935 (mt-10)
REVERT: D   80 LYS cc_start: 0.7362 (tttt) cc_final: 0.6887 (tttm)
REVERT: D  104 ARG cc_start: 0.7244 (mtt180) cc_final: 0.6397 (mtm-85)
REVERT: E   15 LYS cc_start: 0.7161 (mtpt) cc_final: 0.6795 (mtpp)
REVERT: E   34 ARG cc_start: 0.7160 (ttt-90) cc_final: 0.6264 (tmt-80)
REVERT: E   62 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6794 (mt-10)
REVERT: E   80 LYS cc_start: 0.7349 (tttt) cc_final: 0.6849 (tttm)
REVERT: E   92 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7530 (mt-10)
REVERT: E  104 ARG cc_start: 0.7152 (mtt180) cc_final: 0.6431 (mtp180)
REVERT: F   13 MET cc_start: 0.7336 (ttm) cc_final: 0.6542 (mtm)
REVERT: F   26 ILE cc_start: 0.8513 (mt) cc_final: 0.8298 (mt)
REVERT: F   62 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6642 (mt-10)
REVERT: F   70 LYS cc_start: 0.8135 (tttt) cc_final: 0.7808 (tttm)
REVERT: F   80 LYS cc_start: 0.7799 (tttt) cc_final: 0.7463 (tttp)
REVERT: F   89 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7181 (tt0)
REVERT: F  104 ARG cc_start: 0.7713 (mtt180) cc_final: 0.7072 (mtm110)
REVERT: F  118 THR cc_start: 0.7927 (m) cc_final: 0.7490 (p)
  outliers start: 6
  outliers final: 2
  residues processed: 110
  average time/residue: 1.7601
  time to fit residues: 198.3952
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  : 0.527 
-------------------------------------------------------------------------------
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 27 optimal weight:    7.9990
   chunk 15 optimal weight:    7.9990
   chunk 40 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.9388

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.2846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   4410  Z= 0.321
  Angle     :  0.618   5.328   6000  Z= 0.349
  Chirality :  0.051   0.146    708
  Planarity :  0.005   0.036    738
  Dihedral  :  5.174  16.037    594
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 14.10 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.29 (0.32), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.73 (0.25), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  79 
 HIS   0.008   0.002   HIS D  31 
 PHE   0.010   0.002   PHE D  33 
 TYR   0.012   0.002   TYR B 114 
 ARG   0.003   0.000   ARG B  34 

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

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.682 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8072 (mtpt) cc_final: 0.7656 (mtmt)
REVERT: A   21 ARG cc_start: 0.7854 (ttt90) cc_final: 0.7316 (ttt90)
REVERT: A   66 GLU cc_start: 0.7571 (tt0) cc_final: 0.7082 (tt0)
REVERT: A   70 LYS cc_start: 0.7966 (tttt) cc_final: 0.7653 (tttp)
REVERT: A   80 LYS cc_start: 0.7370 (tttt) cc_final: 0.6921 (ttpt)
REVERT: A  104 ARG cc_start: 0.7313 (mtt180) cc_final: 0.6613 (mtm-85)
REVERT: B   15 LYS cc_start: 0.7104 (mtpt) cc_final: 0.6724 (mtpt)
REVERT: B   34 ARG cc_start: 0.7618 (ttt-90) cc_final: 0.7214 (ttt180)
REVERT: B   70 LYS cc_start: 0.7951 (tttt) cc_final: 0.7602 (tttp)
REVERT: B  104 ARG cc_start: 0.7218 (mtt180) cc_final: 0.6323 (mtp180)
REVERT: C   13 MET cc_start: 0.7227 (ttm) cc_final: 0.6677 (mtp)
REVERT: C   15 LYS cc_start: 0.7264 (mtpt) cc_final: 0.6708 (mtmt)
REVERT: C   62 GLU cc_start: 0.7391 (mt-10) cc_final: 0.6983 (mt-10)
REVERT: C   66 GLU cc_start: 0.7604 (tt0) cc_final: 0.6396 (tm-30)
REVERT: C  104 ARG cc_start: 0.7046 (mtt180) cc_final: 0.6205 (mtp180)
REVERT: D   13 MET cc_start: 0.7204 (ttm) cc_final: 0.6734 (mtp)
REVERT: D   15 LYS cc_start: 0.7246 (mtpt) cc_final: 0.6922 (mtpt)
REVERT: D   62 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6587 (tt0)
REVERT: D   66 GLU cc_start: 0.7688 (tt0) cc_final: 0.6392 (tm-30)
REVERT: D   80 LYS cc_start: 0.7372 (tttt) cc_final: 0.6804 (tttm)
REVERT: D   89 GLU cc_start: 0.7317 (mt-10) cc_final: 0.7020 (mt-10)
REVERT: E   15 LYS cc_start: 0.7234 (mtpt) cc_final: 0.6819 (mtmt)
REVERT: E   62 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7027 (mt-10)
REVERT: E   66 GLU cc_start: 0.7456 (tt0) cc_final: 0.6321 (tm-30)
REVERT: E   80 LYS cc_start: 0.7347 (tttt) cc_final: 0.6869 (tttm)
REVERT: E   92 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7163 (mt-10)
REVERT: E  104 ARG cc_start: 0.7113 (mtt180) cc_final: 0.6439 (mtm110)
REVERT: F   13 MET cc_start: 0.7090 (ttm) cc_final: 0.6263 (mtm)
REVERT: F   15 LYS cc_start: 0.7366 (mtpt) cc_final: 0.6811 (mtpt)
REVERT: F   62 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6787 (mt-10)
REVERT: F   66 GLU cc_start: 0.7921 (tt0) cc_final: 0.7160 (tm-30)
REVERT: F   70 LYS cc_start: 0.8245 (tttt) cc_final: 0.7920 (tttm)
REVERT: F   80 LYS cc_start: 0.7742 (tttt) cc_final: 0.7458 (tttp)
REVERT: F   92 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7547 (mt-10)
REVERT: F  104 ARG cc_start: 0.7803 (mtt180) cc_final: 0.7197 (mtm110)
  outliers start: 16
  outliers final: 8
  residues processed: 107
  average time/residue: 1.9295
  time to fit residues: 211.0616
Evaluate side-chains
  108 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
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   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 48 optimal weight:    4.9990
   chunk 36 optimal weight:    8.9990
   chunk 25 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 23 optimal weight:    7.9990
   chunk 32 optimal weight:    0.1980
   chunk 49 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    1.3986

-------------------------------------------------------------------------------
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
F  88 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.3267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   4410  Z= 0.253
  Angle     :  0.554   6.052   6000  Z= 0.306
  Chirality :  0.050   0.138    708
  Planarity :  0.004   0.036    738
  Dihedral  :  5.017  15.398    594
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 15.81 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.28 (0.33), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.73 (0.25), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  79 
 HIS   0.006   0.001   HIS D  31 
 PHE   0.008   0.002   PHE B  95 
 TYR   0.013   0.002   TYR B 114 
 ARG   0.003   0.000   ARG B  34 

*********************** 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
  119 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.497 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8110 (mtpt) cc_final: 0.7775 (mtpt)
REVERT: A   21 ARG cc_start: 0.7764 (ttt90) cc_final: 0.7380 (ttt90)
REVERT: A   70 LYS cc_start: 0.7953 (tttt) cc_final: 0.7571 (tttp)
REVERT: A   80 LYS cc_start: 0.7464 (tttt) cc_final: 0.7024 (ttpt)
REVERT: A  104 ARG cc_start: 0.7313 (mtt180) cc_final: 0.6534 (mtm-85)
REVERT: B   15 LYS cc_start: 0.7102 (mtpt) cc_final: 0.6844 (mtpt)
REVERT: B   34 ARG cc_start: 0.7641 (ttt-90) cc_final: 0.7250 (ttt180)
REVERT: B   70 LYS cc_start: 0.7941 (tttt) cc_final: 0.7540 (tttp)
REVERT: B  104 ARG cc_start: 0.7330 (mtt180) cc_final: 0.6910 (mtt180)
REVERT: C   15 LYS cc_start: 0.7131 (mtpt) cc_final: 0.6683 (mtmt)
REVERT: C   62 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6969 (mt-10)
REVERT: C   72 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7712 (mt-10)
REVERT: C  104 ARG cc_start: 0.7011 (mtt180) cc_final: 0.6655 (mtm-85)
REVERT: D   13 MET cc_start: 0.7159 (ttm) cc_final: 0.6841 (mtp)
REVERT: D   15 LYS cc_start: 0.7316 (mtpt) cc_final: 0.6854 (mtpt)
REVERT: D   62 GLU cc_start: 0.7460 (mt-10) cc_final: 0.6586 (tt0)
REVERT: D   66 GLU cc_start: 0.7707 (tt0) cc_final: 0.6301 (tm-30)
REVERT: D   80 LYS cc_start: 0.7330 (tttt) cc_final: 0.6737 (tttm)
REVERT: D   89 GLU cc_start: 0.7319 (mt-10) cc_final: 0.7001 (mt-10)
REVERT: D   99 ASP cc_start: 0.7636 (t70) cc_final: 0.7010 (t0)
REVERT: E   15 LYS cc_start: 0.7254 (mtpt) cc_final: 0.6768 (mtmt)
REVERT: E   62 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7076 (mt-10)
REVERT: E   66 GLU cc_start: 0.7444 (tt0) cc_final: 0.6293 (tm-30)
REVERT: E   80 LYS cc_start: 0.7424 (tttt) cc_final: 0.7056 (ttpp)
REVERT: E   92 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7318 (mt-10)
REVERT: E  104 ARG cc_start: 0.7293 (mtt180) cc_final: 0.6897 (mtm-85)
REVERT: F   13 MET cc_start: 0.7089 (ttm) cc_final: 0.6289 (mtm)
REVERT: F   15 LYS cc_start: 0.7499 (mtpt) cc_final: 0.6971 (mtpt)
REVERT: F   62 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7131 (mt-10)
REVERT: F   66 GLU cc_start: 0.8008 (tt0) cc_final: 0.7270 (tm-30)
REVERT: F   70 LYS cc_start: 0.8309 (tttt) cc_final: 0.7977 (tttm)
REVERT: F   80 LYS cc_start: 0.7679 (tttt) cc_final: 0.7337 (tttp)
REVERT: F   92 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7476 (mt-10)
REVERT: F  104 ARG cc_start: 0.7808 (mtt180) cc_final: 0.7254 (mtm110)
  outliers start: 18
  outliers final: 8
  residues processed: 112
  average time/residue: 1.8599
  time to fit residues: 213.1194
Evaluate side-chains
  107 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   98 ASN
Chi-restraints excluded: chain B residue  123 THR
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   75 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 29 optimal weight:   10.0000
   chunk 0 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 13 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   overall best weight:    2.5788

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.3602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   4410  Z= 0.421
  Angle     :  0.643   6.485   6000  Z= 0.362
  Chirality :  0.052   0.145    708
  Planarity :  0.005   0.036    738
  Dihedral  :  5.360  18.766    594
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 16.03 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.38 (0.33), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.81 (0.25), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B  79 
 HIS   0.006   0.001   HIS D  31 
 PHE   0.012   0.003   PHE C  33 
 TYR   0.015   0.003   TYR A 114 
 ARG   0.003   0.000   ARG B  34 

*********************** 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
  119 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.539 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8252 (mtpt) cc_final: 0.6071 (pptt)
REVERT: A   21 ARG cc_start: 0.7856 (ttt90) cc_final: 0.7354 (ttt90)
REVERT: A   70 LYS cc_start: 0.7930 (tttt) cc_final: 0.7549 (tttp)
REVERT: A   80 LYS cc_start: 0.7458 (tttt) cc_final: 0.7000 (ttpt)
REVERT: A  104 ARG cc_start: 0.7365 (mtt180) cc_final: 0.6568 (mtm-85)
REVERT: B   15 LYS cc_start: 0.7177 (mtpt) cc_final: 0.6772 (mtpt)
REVERT: B   34 ARG cc_start: 0.7656 (ttt-90) cc_final: 0.7322 (ttt180)
REVERT: B   70 LYS cc_start: 0.7935 (tttt) cc_final: 0.7531 (tttm)
REVERT: B  104 ARG cc_start: 0.7326 (mtt180) cc_final: 0.7022 (mtt180)
REVERT: C   15 LYS cc_start: 0.7321 (mtpt) cc_final: 0.6854 (mtpt)
REVERT: C   62 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7073 (mt-10)
REVERT: C   72 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7827 (mt-10)
REVERT: C  104 ARG cc_start: 0.7095 (mtt180) cc_final: 0.6691 (mtm-85)
REVERT: D   15 LYS cc_start: 0.7465 (mtpt) cc_final: 0.7025 (mtpt)
REVERT: D   62 GLU cc_start: 0.7533 (mt-10) cc_final: 0.6611 (tt0)
REVERT: D   66 GLU cc_start: 0.7689 (tt0) cc_final: 0.6461 (tm-30)
REVERT: D   80 LYS cc_start: 0.7354 (tttt) cc_final: 0.6796 (tttm)
REVERT: E   15 LYS cc_start: 0.7262 (mtpt) cc_final: 0.6808 (mtmt)
REVERT: E   62 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7108 (mt-10)
REVERT: E   66 GLU cc_start: 0.7386 (tt0) cc_final: 0.6337 (tm-30)
REVERT: E   80 LYS cc_start: 0.7402 (tttt) cc_final: 0.6900 (tttm)
REVERT: E   92 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7194 (mt-10)
REVERT: E  104 ARG cc_start: 0.7254 (mtt180) cc_final: 0.6890 (mtm-85)
REVERT: F   13 MET cc_start: 0.6943 (ttm) cc_final: 0.6235 (mtm)
REVERT: F   15 LYS cc_start: 0.7576 (mtpt) cc_final: 0.7081 (mtpt)
REVERT: F   34 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7499 (ttt180)
REVERT: F   62 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7086 (mt-10)
REVERT: F   70 LYS cc_start: 0.8253 (tttt) cc_final: 0.7886 (tttm)
REVERT: F   80 LYS cc_start: 0.7756 (tttt) cc_final: 0.7421 (tttp)
REVERT: F   92 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7456 (mt-10)
REVERT: F  104 ARG cc_start: 0.7842 (mtt180) cc_final: 0.7228 (mtm110)
  outliers start: 21
  outliers final: 11
  residues processed: 110
  average time/residue: 1.8738
  time to fit residues: 210.8440
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  : 0.503 
-------------------------------------------------------------------------------
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   75 THR
Chi-restraints excluded: chain C residue   82 LEU
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   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 10 optimal weight:    0.0980
   chunk 30 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 24 optimal weight:    7.9990
   chunk 4 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 50 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    2.2188

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.3811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   4410  Z= 0.366
  Angle     :  0.615   6.584   6000  Z= 0.344
  Chirality :  0.051   0.142    708
  Planarity :  0.004   0.035    738
  Dihedral  :  5.430  18.938    594
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 16.24 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.41 (0.33), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.83 (0.25), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  79 
 HIS   0.005   0.001   HIS D  31 
 PHE   0.010   0.002   PHE C  33 
 TYR   0.015   0.002   TYR A 114 
 ARG   0.003   0.000   ARG B  34 

*********************** 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
  119 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.471 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8265 (mtpt) cc_final: 0.5949 (pptt)
REVERT: A   21 ARG cc_start: 0.7832 (ttt90) cc_final: 0.7344 (ttt90)
REVERT: A   70 LYS cc_start: 0.7918 (tttt) cc_final: 0.7590 (tttp)
REVERT: A   80 LYS cc_start: 0.7456 (tttt) cc_final: 0.6929 (ttpt)
REVERT: A  104 ARG cc_start: 0.7409 (mtt180) cc_final: 0.6608 (mtm-85)
REVERT: B   15 LYS cc_start: 0.7248 (mtpt) cc_final: 0.6950 (mtpt)
REVERT: B   34 ARG cc_start: 0.7670 (ttt-90) cc_final: 0.7326 (ttt180)
REVERT: B   70 LYS cc_start: 0.7925 (tttt) cc_final: 0.7537 (tttm)
REVERT: B  104 ARG cc_start: 0.7380 (mtt180) cc_final: 0.7141 (mtt180)
REVERT: C   15 LYS cc_start: 0.7253 (mtpt) cc_final: 0.6794 (mtmt)
REVERT: C   62 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7018 (mt-10)
REVERT: C   72 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7817 (mt-10)
REVERT: C  104 ARG cc_start: 0.7087 (mtt180) cc_final: 0.6756 (mtm-85)
REVERT: D   15 LYS cc_start: 0.7315 (mtpt) cc_final: 0.6904 (mtpt)
REVERT: D   62 GLU cc_start: 0.7505 (mt-10) cc_final: 0.6560 (tt0)
REVERT: D   66 GLU cc_start: 0.7667 (tt0) cc_final: 0.6337 (tm-30)
REVERT: D   80 LYS cc_start: 0.7350 (tttt) cc_final: 0.7001 (ttpp)
REVERT: D   99 ASP cc_start: 0.7910 (t0) cc_final: 0.7125 (t0)
REVERT: E   15 LYS cc_start: 0.7323 (mtpt) cc_final: 0.6871 (mtmt)
REVERT: E   62 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7134 (mt-10)
REVERT: E   66 GLU cc_start: 0.7388 (tt0) cc_final: 0.6335 (tm-30)
REVERT: E   80 LYS cc_start: 0.7363 (tttt) cc_final: 0.7010 (ttpp)
REVERT: E  104 ARG cc_start: 0.7286 (mtt180) cc_final: 0.6957 (mtm-85)
REVERT: F   13 MET cc_start: 0.6967 (ttm) cc_final: 0.6280 (mtm)
REVERT: F   15 LYS cc_start: 0.7569 (mtpt) cc_final: 0.7222 (mtpm)
REVERT: F   34 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7497 (ttt180)
REVERT: F   62 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7050 (mt-10)
REVERT: F   70 LYS cc_start: 0.8258 (tttt) cc_final: 0.7883 (tttm)
REVERT: F   80 LYS cc_start: 0.7759 (tttt) cc_final: 0.7441 (tttp)
REVERT: F   92 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7602 (mt-10)
REVERT: F  104 ARG cc_start: 0.7738 (mtt180) cc_final: 0.7191 (mtm110)
  outliers start: 19
  outliers final: 12
  residues processed: 112
  average time/residue: 1.8564
  time to fit residues: 213.0462
Evaluate side-chains
  113 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
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   75 THR
Chi-restraints excluded: chain D residue   82 LEU
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   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 29 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 24 optimal weight:    8.9990
   chunk 20 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   overall best weight:    1.1182

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.3831

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= 0.225
  Angle     :  0.534   7.257   6000  Z= 0.295
  Chirality :  0.049   0.133    708
  Planarity :  0.004   0.032    738
  Dihedral  :  5.158  16.367    594
  Min Nonbonded Distance : 2.649

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.32 (0.34), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.76 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  79 
 HIS   0.004   0.001   HIS D  31 
 PHE   0.011   0.002   PHE B  64 
 TYR   0.014   0.002   TYR C 114 
 ARG   0.003   0.000   ARG E 103 

*********************** 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
  117 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 LYS cc_start: 0.8299 (mtpt) cc_final: 0.7943 (mtpt)
REVERT: A   21 ARG cc_start: 0.7774 (ttt90) cc_final: 0.7289 (ttt90)
REVERT: A   70 LYS cc_start: 0.7897 (tttt) cc_final: 0.7460 (tttp)
REVERT: A   80 LYS cc_start: 0.7481 (tttt) cc_final: 0.6934 (ttpt)
REVERT: A  104 ARG cc_start: 0.7451 (mtt180) cc_final: 0.6647 (mtm-85)
REVERT: B   15 LYS cc_start: 0.7280 (mtpt) cc_final: 0.6952 (mtpt)
REVERT: B   34 ARG cc_start: 0.7632 (ttt-90) cc_final: 0.7263 (ttt180)
REVERT: B   70 LYS cc_start: 0.7952 (tttt) cc_final: 0.7538 (tttp)
REVERT: B  104 ARG cc_start: 0.7380 (mtt180) cc_final: 0.7168 (mtt180)
REVERT: C   15 LYS cc_start: 0.7256 (mtpt) cc_final: 0.6865 (mtmt)
REVERT: C   62 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6890 (mt-10)
REVERT: C   72 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7778 (mt-10)
REVERT: D   15 LYS cc_start: 0.7259 (mtpt) cc_final: 0.7023 (mtpt)
REVERT: D   34 ARG cc_start: 0.7517 (ttt-90) cc_final: 0.7305 (tmt90)
REVERT: D   62 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7168 (mt-10)
REVERT: D   66 GLU cc_start: 0.7464 (tt0) cc_final: 0.6183 (tm-30)
REVERT: D   80 LYS cc_start: 0.7315 (tttt) cc_final: 0.6977 (ttpp)
REVERT: D   99 ASP cc_start: 0.7873 (t0) cc_final: 0.7081 (t0)
REVERT: E   15 LYS cc_start: 0.7379 (mtpt) cc_final: 0.6967 (mtmt)
REVERT: E   62 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7032 (mt-10)
REVERT: E   66 GLU cc_start: 0.7396 (tt0) cc_final: 0.6369 (tm-30)
REVERT: E   80 LYS cc_start: 0.7349 (tttt) cc_final: 0.6982 (ttpp)
REVERT: E  104 ARG cc_start: 0.7261 (mtt180) cc_final: 0.6939 (mtm-85)
REVERT: F   13 MET cc_start: 0.7033 (ttm) cc_final: 0.6263 (mtm)
REVERT: F   15 LYS cc_start: 0.7549 (mtpt) cc_final: 0.7050 (mtpt)
REVERT: F   34 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7528 (ttt180)
REVERT: F   62 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7084 (mt-10)
REVERT: F   70 LYS cc_start: 0.8280 (tttt) cc_final: 0.7891 (tttm)
REVERT: F   80 LYS cc_start: 0.7691 (tttt) cc_final: 0.7363 (tttp)
REVERT: F   92 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7624 (mt-10)
REVERT: F  104 ARG cc_start: 0.7688 (mtt180) cc_final: 0.7179 (mtm110)
  outliers start: 14
  outliers final: 9
  residues processed: 109
  average time/residue: 1.9482
  time to fit residues: 217.0375
Evaluate side-chains
  112 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
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   82 LEU
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   85 SER
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  123 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 47 optimal weight:    0.1980
   chunk 49 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0570
   chunk 48 optimal weight:    0.6980
   chunk 29 optimal weight:    8.9990
   chunk 21 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.7500

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.3862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4410  Z= 0.182
  Angle     :  0.504   7.510   6000  Z= 0.276
  Chirality :  0.048   0.127    708
  Planarity :  0.004   0.030    738
  Dihedral  :  4.934  15.639    594
  Min Nonbonded Distance : 2.650

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 18.16 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.28 (0.35), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.73 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP D  79 
 HIS   0.004   0.001   HIS D  31 
 PHE   0.010   0.002   PHE B  64 
 TYR   0.013   0.001   TYR C 114 
 ARG   0.003   0.000   ARG B  34 

*********************** 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: 13
    poor density    : 100
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 LYS cc_start: 0.8274 (mtpt) cc_final: 0.7908 (mtmt)
REVERT: A   21 ARG cc_start: 0.7753 (ttt90) cc_final: 0.7254 (ttt90)
REVERT: A   34 ARG cc_start: 0.7359 (ttt-90) cc_final: 0.6981 (ttt-90)
REVERT: A   70 LYS cc_start: 0.7830 (tttt) cc_final: 0.7451 (tttp)
REVERT: A   80 LYS cc_start: 0.7506 (tttt) cc_final: 0.6987 (ttpt)
REVERT: A  104 ARG cc_start: 0.7397 (mtt180) cc_final: 0.6562 (mtm-85)
REVERT: B   15 LYS cc_start: 0.7256 (mtpt) cc_final: 0.6838 (mtpt)
REVERT: B   34 ARG cc_start: 0.7624 (ttt-90) cc_final: 0.7333 (ttt180)
REVERT: B   70 LYS cc_start: 0.7958 (tttt) cc_final: 0.7556 (tttp)
REVERT: B  104 ARG cc_start: 0.7306 (mtt180) cc_final: 0.7093 (mtt180)
REVERT: C   15 LYS cc_start: 0.7235 (mtpt) cc_final: 0.6843 (mtmt)
REVERT: C   62 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6852 (mt-10)
REVERT: C   72 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7703 (mt-10)
REVERT: D   15 LYS cc_start: 0.7434 (mtpt) cc_final: 0.7097 (mtpt)
REVERT: D   62 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7178 (mt-10)
REVERT: D   66 GLU cc_start: 0.7490 (tt0) cc_final: 0.6182 (tm-30)
REVERT: D   80 LYS cc_start: 0.7293 (tttt) cc_final: 0.6757 (tttm)
REVERT: D   99 ASP cc_start: 0.7908 (t0) cc_final: 0.7106 (t0)
REVERT: E   15 LYS cc_start: 0.7424 (mtpt) cc_final: 0.7066 (mtmt)
REVERT: E   62 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7012 (mt-10)
REVERT: E   66 GLU cc_start: 0.7424 (tt0) cc_final: 0.6398 (tm-30)
REVERT: E   80 LYS cc_start: 0.7280 (tttt) cc_final: 0.6754 (tttm)
REVERT: E  104 ARG cc_start: 0.7269 (mtt180) cc_final: 0.6944 (mtm-85)
REVERT: F   13 MET cc_start: 0.7024 (ttm) cc_final: 0.6266 (mtm)
REVERT: F   15 LYS cc_start: 0.7552 (mtpt) cc_final: 0.7055 (mtpt)
REVERT: F   34 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7530 (ttt180)
REVERT: F   62 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7160 (mt-10)
REVERT: F   70 LYS cc_start: 0.8309 (tttt) cc_final: 0.7931 (tttm)
REVERT: F   80 LYS cc_start: 0.7609 (tttt) cc_final: 0.7270 (tttp)
REVERT: F   92 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7614 (mt-10)
REVERT: F  104 ARG cc_start: 0.7673 (mtt180) cc_final: 0.7172 (mtm110)
  outliers start: 13
  outliers final: 7
  residues processed: 107
  average time/residue: 1.9607
  time to fit residues: 214.3656
Evaluate side-chains
  107 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
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   82 LEU
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   85 SER
Chi-restraints excluded: chain F residue   34 ARG
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain F residue  123 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 43 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   chunk 48 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 24 optimal weight:    7.9990
   chunk 35 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   overall best weight:    2.3788

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.4007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   4410  Z= 0.394
  Angle     :  0.621   7.413   6000  Z= 0.346
  Chirality :  0.051   0.144    708
  Planarity :  0.004   0.032    738
  Dihedral  :  5.408  18.327    594
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 17.52 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.37 (0.34), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  79 
 HIS   0.004   0.001   HIS D  31 
 PHE   0.011   0.002   PHE E  87 
 TYR   0.014   0.002   TYR A 114 
 ARG   0.003   0.001   ARG D 104 

*********************** 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
  118 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.512 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8318 (mtpt) cc_final: 0.5989 (pptt)
REVERT: A   21 ARG cc_start: 0.7862 (ttt90) cc_final: 0.7346 (ttt90)
REVERT: A   34 ARG cc_start: 0.7269 (ttt-90) cc_final: 0.6887 (ttt-90)
REVERT: A   70 LYS cc_start: 0.7865 (tttt) cc_final: 0.7531 (tttp)
REVERT: A   80 LYS cc_start: 0.7484 (tttt) cc_final: 0.6939 (ttpt)
REVERT: A  104 ARG cc_start: 0.7351 (mtt180) cc_final: 0.6579 (mtm-85)
REVERT: B   15 LYS cc_start: 0.7281 (mtpt) cc_final: 0.7012 (mtpp)
REVERT: B   34 ARG cc_start: 0.7568 (ttt-90) cc_final: 0.7307 (ttt180)
REVERT: B   70 LYS cc_start: 0.7819 (tttt) cc_final: 0.7446 (tttp)
REVERT: C   15 LYS cc_start: 0.7182 (mtpt) cc_final: 0.6809 (mtmt)
REVERT: C   62 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6923 (mt-10)
REVERT: C   63 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6500 (tt0)
REVERT: C   72 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7838 (mt-10)
REVERT: C  104 ARG cc_start: 0.7132 (mtt180) cc_final: 0.6809 (mtm-85)
REVERT: D   15 LYS cc_start: 0.7349 (mtpt) cc_final: 0.6979 (mtpt)
REVERT: D   62 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7145 (mt-10)
REVERT: D   66 GLU cc_start: 0.7474 (tt0) cc_final: 0.6047 (tm-30)
REVERT: D   80 LYS cc_start: 0.7278 (tttt) cc_final: 0.6960 (ttpp)
REVERT: D   99 ASP cc_start: 0.7918 (t0) cc_final: 0.7048 (t0)
REVERT: E   15 LYS cc_start: 0.7418 (mtpt) cc_final: 0.6968 (mtmt)
REVERT: E   62 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7036 (mt-10)
REVERT: E   66 GLU cc_start: 0.7415 (tt0) cc_final: 0.6402 (tm-30)
REVERT: E   80 LYS cc_start: 0.7353 (tttt) cc_final: 0.6979 (ttpp)
REVERT: E  104 ARG cc_start: 0.7407 (mtt180) cc_final: 0.7058 (mtm-85)
REVERT: F   13 MET cc_start: 0.6919 (ttm) cc_final: 0.6251 (mtm)
REVERT: F   15 LYS cc_start: 0.7537 (mtpt) cc_final: 0.7136 (mtpm)
REVERT: F   34 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7496 (ttt180)
REVERT: F   62 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7103 (mt-10)
REVERT: F   70 LYS cc_start: 0.8286 (tttt) cc_final: 0.7928 (tttm)
REVERT: F   80 LYS cc_start: 0.7746 (tttt) cc_final: 0.7442 (tttp)
REVERT: F   92 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7608 (mt-10)
REVERT: F  104 ARG cc_start: 0.7779 (mtt180) cc_final: 0.7166 (mtm110)
  outliers start: 15
  outliers final: 11
  residues processed: 111
  average time/residue: 2.0052
  time to fit residues: 227.6218
Evaluate side-chains
  114 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   85 SER
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
Chi-restraints excluded: chain F residue  123 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 33 optimal weight:    8.9990
   chunk 26 optimal weight:    2.9990
   chunk 34 optimal weight:    0.3980
   chunk 45 optimal weight:    0.0270
   chunk 13 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 11 optimal weight:    8.9990
   chunk 42 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.6438

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.3959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4410  Z= 0.177
  Angle     :  0.514   8.013   6000  Z= 0.281
  Chirality :  0.049   0.129    708
  Planarity :  0.004   0.030    738
  Dihedral  :  5.036  16.137    594
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 18.16 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.28 (0.34), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.73 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP D  79 
 HIS   0.004   0.001   HIS D  31 
 PHE   0.011   0.002   PHE B  64 
 TYR   0.014   0.001   TYR C 114 
 ARG   0.002   0.000   ARG E 103 

********************** 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
  109 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.571 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8283 (mtpt) cc_final: 0.7896 (mtmt)
REVERT: A   21 ARG cc_start: 0.7829 (ttt90) cc_final: 0.7290 (ttt90)
REVERT: A   34 ARG cc_start: 0.7346 (ttt-90) cc_final: 0.6934 (ttt-90)
REVERT: A   70 LYS cc_start: 0.7878 (tttt) cc_final: 0.7476 (tttp)
REVERT: A   80 LYS cc_start: 0.7514 (tttt) cc_final: 0.7011 (ttpt)
REVERT: A  104 ARG cc_start: 0.7436 (mtt180) cc_final: 0.6680 (mtm-85)
REVERT: B   15 LYS cc_start: 0.7238 (mtpt) cc_final: 0.6795 (mtpt)
REVERT: B   34 ARG cc_start: 0.7550 (ttt-90) cc_final: 0.7277 (ttt180)
REVERT: B   70 LYS cc_start: 0.7934 (tttt) cc_final: 0.7528 (tttp)
REVERT: C   15 LYS cc_start: 0.7177 (mtpt) cc_final: 0.6801 (mtmt)
REVERT: C   62 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6958 (mt-10)
REVERT: C   72 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7698 (mt-10)
REVERT: C   89 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7120 (mt-10)
REVERT: C  104 ARG cc_start: 0.7076 (mtt180) cc_final: 0.6767 (mtm-85)
REVERT: D   15 LYS cc_start: 0.7404 (mtpt) cc_final: 0.7061 (mtpt)
REVERT: D   62 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7166 (mt-10)
REVERT: D   66 GLU cc_start: 0.7511 (tt0) cc_final: 0.6195 (tm-30)
REVERT: D   80 LYS cc_start: 0.7322 (tttt) cc_final: 0.6987 (ttpp)
REVERT: D   99 ASP cc_start: 0.7850 (t0) cc_final: 0.7075 (t0)
REVERT: E   15 LYS cc_start: 0.7404 (mtpt) cc_final: 0.7043 (mtmt)
REVERT: E   62 GLU cc_start: 0.7408 (mt-10) cc_final: 0.6932 (mt-10)
REVERT: E   66 GLU cc_start: 0.7468 (tt0) cc_final: 0.6459 (tm-30)
REVERT: E   80 LYS cc_start: 0.7319 (tttt) cc_final: 0.6842 (tttm)
REVERT: E  104 ARG cc_start: 0.7338 (mtt180) cc_final: 0.7001 (mtm-85)
REVERT: F   13 MET cc_start: 0.6983 (ttm) cc_final: 0.6248 (mtm)
REVERT: F   15 LYS cc_start: 0.7552 (mtpt) cc_final: 0.7082 (mtpt)
REVERT: F   34 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7540 (ttt180)
REVERT: F   62 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7144 (mt-10)
REVERT: F   70 LYS cc_start: 0.8273 (tttt) cc_final: 0.7940 (tttp)
REVERT: F   80 LYS cc_start: 0.7640 (tttt) cc_final: 0.7351 (tttp)
REVERT: F   92 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7600 (mt-10)
REVERT: F  104 ARG cc_start: 0.7688 (mtt180) cc_final: 0.7176 (mtm110)
  outliers start: 12
  outliers final: 7
  residues processed: 104
  average time/residue: 2.0443
  time to fit residues: 217.3980
Evaluate side-chains
  105 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   85 SER
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 44 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0170
   chunk 7 optimal weight:    6.9990
   chunk 37 optimal weight:    0.8980
   chunk 2 optimal weight:    7.9990
   chunk 30 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9990
   chunk 36 optimal weight:    6.9990
   chunk 1 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    1.1824

-------------------------------------------------------------------------------
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 = 0.3952 r_free = 0.3952 target = 0.122083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.102450 restraints weight = 5035.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 2.05
r_work: 0.3545 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3440 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.3985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   4410  Z= 0.235
  Angle     :  0.534   7.950   6000  Z= 0.293
  Chirality :  0.049   0.132    708
  Planarity :  0.004   0.030    738
  Dihedral  :  5.072  15.818    594
  Min Nonbonded Distance : 2.646

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 18.16 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.25 (0.35), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.71 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  79 
 HIS   0.004   0.001   HIS D  31 
 PHE   0.009   0.002   PHE B  64 
 TYR   0.012   0.002   TYR C 114 
 ARG   0.002   0.000   ARG E 103 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3450.92 seconds
wall clock time: 62 minutes 16.71 seconds (3736.71 seconds total)