Starting phenix.real_space_refine
on Thu Mar  6 01:04:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pkf_17737/03_2025/8pkf_17737.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pkf_17737/03_2025/8pkf_17737.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pkf_17737/03_2025/8pkf_17737.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pkf_17737/03_2025/8pkf_17737.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pkf_17737/03_2025/8pkf_17737.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pkf_17737/03_2025/8pkf_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-5624/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: 2.25, per 1000 atoms: 0.52
  Number of scatterers: 4308
  At special positions: 0
  Unit cell: (69.116, 86.862, 46.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       6     16.00
     O     804      8.00
     N     708      7.00
     C    2790      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.82
  Conformation dependent library (CDL) restraints added in 464.8 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: 0.59
  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: 1.10

  Time building geometry restraints manager: 1.01 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.220
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     13.060
  Find NCS groups from input model:        0.080
  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:12.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.570
-------------------------------------------------------------------------------
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  : 0.492 
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: 1.4716
  time to fit residues: 216.1946
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  : 0.478 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.128601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.107956 restraints weight = 4788.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 2.09
r_work: 0.3607 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3498 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
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  : 0.467 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.8082 (ttt90) cc_final: 0.7717 (ttt90)
REVERT: A   66 GLU cc_start: 0.7742 (tt0) cc_final: 0.7491 (tt0)
REVERT: A   70 LYS cc_start: 0.8640 (tttt) cc_final: 0.8330 (tttp)
REVERT: A   80 LYS cc_start: 0.8325 (tttt) cc_final: 0.7810 (ttpt)
REVERT: B   13 MET cc_start: 0.8295 (ttm) cc_final: 0.8092 (ttm)
REVERT: B   15 LYS cc_start: 0.8038 (mtpt) cc_final: 0.7814 (mtpt)
REVERT: B   70 LYS cc_start: 0.8754 (tttt) cc_final: 0.8516 (tttp)
REVERT: B  104 ARG cc_start: 0.7767 (mtt180) cc_final: 0.7495 (mtm-85)
REVERT: C   13 MET cc_start: 0.7927 (ttm) cc_final: 0.7286 (mtp)
REVERT: C   15 LYS cc_start: 0.8059 (mtpt) cc_final: 0.7743 (mtmt)
REVERT: C   62 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7522 (mt-10)
REVERT: C   66 GLU cc_start: 0.7773 (tt0) cc_final: 0.7207 (tm-30)
REVERT: C  104 ARG cc_start: 0.7883 (mtt180) cc_final: 0.7315 (mtp180)
REVERT: D   13 MET cc_start: 0.7913 (ttm) cc_final: 0.7144 (mtm)
REVERT: D   15 LYS cc_start: 0.7998 (mtpt) cc_final: 0.7577 (mtpt)
REVERT: D   62 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7618 (mt-10)
REVERT: D   80 LYS cc_start: 0.8322 (tttt) cc_final: 0.7865 (tttm)
REVERT: D  104 ARG cc_start: 0.8066 (mtt180) cc_final: 0.7543 (mtm-85)
REVERT: E   15 LYS cc_start: 0.8112 (mtpt) cc_final: 0.7836 (mtpp)
REVERT: E   34 ARG cc_start: 0.8075 (ttt-90) cc_final: 0.7401 (tmt-80)
REVERT: E   62 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7386 (mt-10)
REVERT: E   80 LYS cc_start: 0.8256 (tttt) cc_final: 0.7804 (tttm)
REVERT: E   92 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8053 (mt-10)
REVERT: E  104 ARG cc_start: 0.8019 (mtt180) cc_final: 0.7553 (mtp180)
REVERT: F   13 MET cc_start: 0.8042 (ttm) cc_final: 0.7333 (mtm)
REVERT: F   26 ILE cc_start: 0.8838 (mt) cc_final: 0.8624 (mt)
REVERT: F   62 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7206 (mt-10)
REVERT: F   80 LYS cc_start: 0.8413 (tttt) cc_final: 0.8080 (tttp)
REVERT: F  104 ARG cc_start: 0.8275 (mtt180) cc_final: 0.7860 (mtm110)
REVERT: F  118 THR cc_start: 0.8488 (m) cc_final: 0.8235 (p)
  outliers start: 6
  outliers final: 2
  residues processed: 110
  average time/residue: 2.0103
  time to fit residues: 226.3638
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  : 0.462 
-------------------------------------------------------------------------------
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 49 optimal weight:    4.9990
   chunk 35 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 15 optimal weight:    9.9990
   overall best weight:    1.7584

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.120377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.099655 restraints weight = 4972.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 2.16
r_work: 0.3521 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3408 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.2903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   4410  Z= 0.300
  Angle     :  0.606   5.404   6000  Z= 0.342
  Chirality :  0.052   0.145    708
  Planarity :  0.005   0.035    738
  Dihedral  :  5.120  15.792    594
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 13.89 %
    Favored  : 82.26 %
  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 (0.33), 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   0.005   0.001   TRP B  79 
 HIS   0.008   0.002   HIS D  31 
 PHE   0.010   0.002   PHE E  64 
 TYR   0.013   0.002   TYR D 114 
 ARG   0.003   0.001   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
  117 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.588 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8582 (mtpt) cc_final: 0.8287 (mtmt)
REVERT: A   21 ARG cc_start: 0.8199 (ttt90) cc_final: 0.7772 (ttt90)
REVERT: A   66 GLU cc_start: 0.7921 (tt0) cc_final: 0.7592 (tt0)
REVERT: A   70 LYS cc_start: 0.8678 (tttt) cc_final: 0.8410 (tttp)
REVERT: A   80 LYS cc_start: 0.8249 (tttt) cc_final: 0.7815 (ttpt)
REVERT: B   15 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7904 (mtpt)
REVERT: B   34 ARG cc_start: 0.8353 (ttt-90) cc_final: 0.8038 (ttt180)
REVERT: B   70 LYS cc_start: 0.8760 (tttt) cc_final: 0.8557 (tttp)
REVERT: B  104 ARG cc_start: 0.7979 (mtt180) cc_final: 0.7427 (mtp180)
REVERT: C   13 MET cc_start: 0.7998 (ttm) cc_final: 0.7503 (mtp)
REVERT: C   15 LYS cc_start: 0.8256 (mtpt) cc_final: 0.7896 (mtmt)
REVERT: C   62 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7730 (mt-10)
REVERT: C   66 GLU cc_start: 0.7961 (tt0) cc_final: 0.7229 (tm-30)
REVERT: C  104 ARG cc_start: 0.7960 (mtt180) cc_final: 0.7371 (mtp180)
REVERT: D   13 MET cc_start: 0.7987 (ttm) cc_final: 0.7535 (mtp)
REVERT: D   15 LYS cc_start: 0.8208 (mtpt) cc_final: 0.7966 (mtpt)
REVERT: D   62 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7243 (tt0)
REVERT: D   66 GLU cc_start: 0.8097 (tt0) cc_final: 0.7240 (tm-30)
REVERT: D   80 LYS cc_start: 0.8272 (tttt) cc_final: 0.7715 (tttm)
REVERT: D   89 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7368 (mt-10)
REVERT: E   15 LYS cc_start: 0.8196 (mtpt) cc_final: 0.7843 (mtmt)
REVERT: E   62 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7521 (mt-10)
REVERT: E   66 GLU cc_start: 0.7851 (tt0) cc_final: 0.7110 (tm-30)
REVERT: E   80 LYS cc_start: 0.8218 (tttt) cc_final: 0.7782 (tttm)
REVERT: E   92 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7862 (mt-10)
REVERT: E  104 ARG cc_start: 0.8031 (mtt180) cc_final: 0.7651 (mtm110)
REVERT: F   13 MET cc_start: 0.7917 (ttm) cc_final: 0.7203 (mtm)
REVERT: F   15 LYS cc_start: 0.8326 (mtpt) cc_final: 0.7849 (mtpt)
REVERT: F   62 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7384 (mt-10)
REVERT: F   66 GLU cc_start: 0.8086 (tt0) cc_final: 0.7595 (tm-30)
REVERT: F   80 LYS cc_start: 0.8326 (tttt) cc_final: 0.8035 (ttpp)
REVERT: F   89 GLU cc_start: 0.7767 (tt0) cc_final: 0.7306 (tp30)
REVERT: F   92 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8011 (mt-10)
REVERT: F  104 ARG cc_start: 0.8307 (mtt180) cc_final: 0.7945 (mtm110)
  outliers start: 18
  outliers final: 8
  residues processed: 108
  average time/residue: 2.4530
  time to fit residues: 271.4100
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  : 0.497 
-------------------------------------------------------------------------------
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 44 optimal weight:    3.9990
   chunk 6 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   chunk 40 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0980
   chunk 18 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    2.0186

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.118890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.098556 restraints weight = 5067.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 2.14
r_work: 0.3496 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3387 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.3532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   4410  Z= 0.342
  Angle     :  0.616   6.027   6000  Z= 0.343
  Chirality :  0.051   0.149    708
  Planarity :  0.005   0.038    738
  Dihedral  :  5.252  16.546    594
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 14.74 %
    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: -2.33 (0.33), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.77 (0.25), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  79 
 HIS   0.006   0.001   HIS D  31 
 PHE   0.009   0.002   PHE E  87 
 TYR   0.015   0.002   TYR A 114 
 ARG   0.006   0.000   ARG D 104 

*********************** 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
  123 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.517 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8684 (mtpt) cc_final: 0.8403 (mtmt)
REVERT: A   21 ARG cc_start: 0.8211 (ttt90) cc_final: 0.7807 (ttt90)
REVERT: A   70 LYS cc_start: 0.8622 (tttt) cc_final: 0.8365 (tttp)
REVERT: A   80 LYS cc_start: 0.8329 (tttt) cc_final: 0.7900 (ttpt)
REVERT: B   15 LYS cc_start: 0.8222 (mtpt) cc_final: 0.7928 (mtpt)
REVERT: B   34 ARG cc_start: 0.8393 (ttt-90) cc_final: 0.8135 (ttt180)
REVERT: B   70 LYS cc_start: 0.8753 (tttt) cc_final: 0.8508 (tttm)
REVERT: B  104 ARG cc_start: 0.8024 (mtt180) cc_final: 0.7437 (mtp180)
REVERT: C   15 LYS cc_start: 0.8350 (mtpt) cc_final: 0.8009 (mtmt)
REVERT: C   62 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7692 (mt-10)
REVERT: C   72 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7788 (mm-30)
REVERT: D   13 MET cc_start: 0.7989 (ttm) cc_final: 0.7717 (mtp)
REVERT: D   15 LYS cc_start: 0.8364 (mtpt) cc_final: 0.8041 (mtpt)
REVERT: D   62 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7327 (tt0)
REVERT: D   66 GLU cc_start: 0.8065 (tt0) cc_final: 0.7125 (tm-30)
REVERT: D   80 LYS cc_start: 0.8251 (tttt) cc_final: 0.7727 (tttm)
REVERT: D   89 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7326 (mt-10)
REVERT: E   15 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7793 (mtmt)
REVERT: E   62 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7588 (mt-10)
REVERT: E   66 GLU cc_start: 0.7788 (tt0) cc_final: 0.7149 (tm-30)
REVERT: E   80 LYS cc_start: 0.8220 (tttt) cc_final: 0.7788 (tttm)
REVERT: E   92 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7919 (mt-10)
REVERT: E  104 ARG cc_start: 0.8156 (mtt180) cc_final: 0.7946 (mtm-85)
REVERT: F   13 MET cc_start: 0.7841 (ttm) cc_final: 0.7145 (mtm)
REVERT: F   15 LYS cc_start: 0.8433 (mtpt) cc_final: 0.8163 (mtpm)
REVERT: F   34 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8141 (ttt180)
REVERT: F   62 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7597 (mt-10)
REVERT: F   66 GLU cc_start: 0.8127 (tt0) cc_final: 0.7680 (tm-30)
REVERT: F   80 LYS cc_start: 0.8356 (tttt) cc_final: 0.8045 (tttp)
REVERT: F   92 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8015 (mt-10)
REVERT: F  104 ARG cc_start: 0.8304 (mtt180) cc_final: 0.7944 (mtm110)
  outliers start: 23
  outliers final: 8
  residues processed: 112
  average time/residue: 1.8195
  time to fit residues: 208.4625
Evaluate side-chains
  108 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain F residue   34 ARG
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain F residue   85 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 18 optimal weight:    8.9990
   chunk 42 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   overall best weight:    2.5988

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.117779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.097525 restraints weight = 5243.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 2.15
r_work: 0.3479 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3371 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.3806

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= 0.427
  Angle     :  0.655   6.648   6000  Z= 0.368
  Chirality :  0.052   0.147    708
  Planarity :  0.005   0.036    738
  Dihedral  :  5.498  20.089    594
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 15.60 %
    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: -2.45 (0.33), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.86 (0.25), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP B  79 
 HIS   0.006   0.001   HIS D  31 
 PHE   0.011   0.003   PHE C  33 
 TYR   0.014   0.003   TYR A 114 
 ARG   0.003   0.001   ARG D  21 

*********************** 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
  121 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.533 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8707 (mtpt) cc_final: 0.6845 (pptt)
REVERT: A   21 ARG cc_start: 0.8280 (ttt90) cc_final: 0.7874 (ttt90)
REVERT: A   70 LYS cc_start: 0.8643 (tttt) cc_final: 0.8439 (tttp)
REVERT: A   80 LYS cc_start: 0.8308 (tttt) cc_final: 0.7836 (ttpt)
REVERT: B   34 ARG cc_start: 0.8405 (ttt-90) cc_final: 0.8172 (ttt180)
REVERT: B   70 LYS cc_start: 0.8796 (tttt) cc_final: 0.8585 (tttm)
REVERT: C   15 LYS cc_start: 0.8403 (mtpt) cc_final: 0.8075 (mtpt)
REVERT: C   62 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7608 (mt-10)
REVERT: C   63 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7275 (tt0)
REVERT: C   72 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7899 (mm-30)
REVERT: D   15 LYS cc_start: 0.8377 (mtpt) cc_final: 0.8037 (mtpt)
REVERT: D   21 ARG cc_start: 0.7902 (ttt90) cc_final: 0.7553 (ttt180)
REVERT: D   62 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7264 (tt0)
REVERT: D   66 GLU cc_start: 0.8030 (tt0) cc_final: 0.7226 (tm-30)
REVERT: D   80 LYS cc_start: 0.8206 (tttt) cc_final: 0.7804 (ttpp)
REVERT: E   15 LYS cc_start: 0.8303 (mtpt) cc_final: 0.7994 (mtmt)
REVERT: E   62 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7611 (mt-10)
REVERT: E   66 GLU cc_start: 0.7790 (tt0) cc_final: 0.7121 (tm-30)
REVERT: E   80 LYS cc_start: 0.8311 (tttt) cc_final: 0.7875 (tttm)
REVERT: E  104 ARG cc_start: 0.8199 (mtt180) cc_final: 0.7698 (mtm110)
REVERT: F   13 MET cc_start: 0.7763 (ttm) cc_final: 0.7151 (mtm)
REVERT: F   15 LYS cc_start: 0.8494 (mtpt) cc_final: 0.8129 (mtpt)
REVERT: F   34 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8168 (ttt180)
REVERT: F   62 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7600 (mt-10)
REVERT: F   80 LYS cc_start: 0.8391 (tttt) cc_final: 0.8103 (tttp)
REVERT: F   92 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8130 (mt-10)
REVERT: F  104 ARG cc_start: 0.8219 (mtt180) cc_final: 0.7870 (mtm110)
  outliers start: 24
  outliers final: 10
  residues processed: 110
  average time/residue: 1.8833
  time to fit residues: 211.9324
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  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain F residue   34 ARG
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain F residue   85 SER
Chi-restraints excluded: chain F residue  123 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0000
   chunk 19 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.7384

-------------------------------------------------------------------------------
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 = 0.3967 r_free = 0.3967 target = 0.122676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.102783 restraints weight = 5073.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3696 rms_B_bonded: 2.11
r_work: 0.3573 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3465 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.3829

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= 0.189
  Angle     :  0.520   7.099   6000  Z= 0.285
  Chirality :  0.049   0.134    708
  Planarity :  0.004   0.032    738
  Dihedral  :  5.044  16.089    594
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 18.38 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.30 (0.34), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.75 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP D  79 
 HIS   0.004   0.001   HIS D  31 
 PHE   0.012   0.002   PHE B  64 
 TYR   0.014   0.001   TYR C 114 
 ARG   0.004   0.001   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
  112 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.533 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8688 (mtpt) cc_final: 0.8478 (mtpt)
REVERT: A   21 ARG cc_start: 0.8134 (ttt90) cc_final: 0.7795 (ttt90)
REVERT: A   70 LYS cc_start: 0.8623 (tttt) cc_final: 0.8367 (tttp)
REVERT: A   80 LYS cc_start: 0.8267 (tttt) cc_final: 0.7820 (ttpt)
REVERT: A  104 ARG cc_start: 0.8267 (mtm-85) cc_final: 0.8028 (mtm-85)
REVERT: B   34 ARG cc_start: 0.8419 (ttt-90) cc_final: 0.8138 (ttt180)
REVERT: B   70 LYS cc_start: 0.8786 (tttt) cc_final: 0.8545 (tttp)
REVERT: C   15 LYS cc_start: 0.8343 (mtpt) cc_final: 0.8053 (mtmt)
REVERT: C   62 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7563 (mt-10)
REVERT: C  104 ARG cc_start: 0.8180 (mtm-85) cc_final: 0.7852 (mtt-85)
REVERT: D   15 LYS cc_start: 0.8352 (mtpt) cc_final: 0.8110 (mtpt)
REVERT: D   62 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7260 (tt0)
REVERT: D   66 GLU cc_start: 0.7970 (tt0) cc_final: 0.7176 (tm-30)
REVERT: D   80 LYS cc_start: 0.8138 (tttt) cc_final: 0.7655 (ttpp)
REVERT: D   99 ASP cc_start: 0.7793 (t0) cc_final: 0.7376 (t0)
REVERT: E   15 LYS cc_start: 0.8325 (mtpt) cc_final: 0.7924 (mtmt)
REVERT: E   62 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7558 (mt-10)
REVERT: E   66 GLU cc_start: 0.7768 (tt0) cc_final: 0.7145 (tm-30)
REVERT: E   80 LYS cc_start: 0.8148 (tttt) cc_final: 0.7800 (ttpp)
REVERT: E  104 ARG cc_start: 0.8136 (mtt180) cc_final: 0.7677 (mtm110)
REVERT: F   13 MET cc_start: 0.7860 (ttm) cc_final: 0.7206 (mtm)
REVERT: F   15 LYS cc_start: 0.8401 (mtpt) cc_final: 0.8038 (mtpt)
REVERT: F   62 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7550 (mt-10)
REVERT: F   80 LYS cc_start: 0.8242 (tttt) cc_final: 0.7916 (tttp)
REVERT: F   92 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8119 (mt-10)
REVERT: F  104 ARG cc_start: 0.8164 (mtt180) cc_final: 0.7841 (mtm110)
  outliers start: 10
  outliers final: 3
  residues processed: 108
  average time/residue: 1.9312
  time to fit residues: 213.1945
Evaluate side-chains
  102 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 99
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain F residue   75 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    0.3980
   chunk 7 optimal weight:    0.0570
   chunk 51 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 31 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 38 optimal weight:    7.9990
   chunk 5 optimal weight:    0.8980
   chunk 46 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.5698

-------------------------------------------------------------------------------
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 = 0.4006 r_free = 0.4006 target = 0.125654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.105879 restraints weight = 5079.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3725 rms_B_bonded: 2.08
r_work: 0.3603 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3497 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.3880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4410  Z= 0.170
  Angle     :  0.494   7.109   6000  Z= 0.269
  Chirality :  0.048   0.126    708
  Planarity :  0.003   0.028    738
  Dihedral  :  4.789  14.772    594
  Min Nonbonded Distance : 2.656

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 18.38 %
    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: -2.23 (0.35), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.69 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 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   0.012   0.001   TYR C 114 
 ARG   0.004   0.000   ARG C 104 

*********************** 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
  110 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.461 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.8164 (ttt90) cc_final: 0.7822 (ttt90)
REVERT: A   34 ARG cc_start: 0.8303 (ttt-90) cc_final: 0.8013 (ttt-90)
REVERT: A   70 LYS cc_start: 0.8557 (tttt) cc_final: 0.8241 (tttp)
REVERT: A   80 LYS cc_start: 0.8259 (tttt) cc_final: 0.7833 (ttpt)
REVERT: A  104 ARG cc_start: 0.8233 (mtm-85) cc_final: 0.7988 (mtm-85)
REVERT: B   70 LYS cc_start: 0.8778 (tttt) cc_final: 0.8537 (tttp)
REVERT: C   15 LYS cc_start: 0.8346 (mtpt) cc_final: 0.8090 (mtmt)
REVERT: C   62 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7607 (mt-10)
REVERT: C   89 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7658 (mt-10)
REVERT: D   15 LYS cc_start: 0.8438 (mtpt) cc_final: 0.8157 (mtpt)
REVERT: D   62 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7267 (tt0)
REVERT: D   66 GLU cc_start: 0.7840 (tt0) cc_final: 0.7116 (tm-30)
REVERT: D   80 LYS cc_start: 0.8151 (tttt) cc_final: 0.7755 (ttpp)
REVERT: D   99 ASP cc_start: 0.7790 (t0) cc_final: 0.7375 (t0)
REVERT: E   62 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7559 (mt-10)
REVERT: E   66 GLU cc_start: 0.7800 (tt0) cc_final: 0.7115 (tm-30)
REVERT: E   80 LYS cc_start: 0.8184 (tttt) cc_final: 0.7731 (tttm)
REVERT: E  104 ARG cc_start: 0.8150 (mtt180) cc_final: 0.7721 (mtm110)
REVERT: F   13 MET cc_start: 0.7897 (ttm) cc_final: 0.7276 (mtm)
REVERT: F   15 LYS cc_start: 0.8419 (mtpt) cc_final: 0.8079 (mtpt)
REVERT: F   34 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8138 (ttt180)
REVERT: F   62 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7601 (mt-10)
REVERT: F   92 GLU cc_start: 0.8262 (mt-10) cc_final: 0.8058 (mt-10)
REVERT: F  104 ARG cc_start: 0.8186 (mtt180) cc_final: 0.7891 (mtm110)
  outliers start: 12
  outliers final: 5
  residues processed: 105
  average time/residue: 1.8667
  time to fit residues: 200.3556
Evaluate side-chains
  101 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
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 F residue   34 ARG
Chi-restraints excluded: chain F residue   75 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 32 optimal weight:    7.9990
   chunk 50 optimal weight:    7.9990
   chunk 24 optimal weight:    5.9990
   chunk 40 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0970
   chunk 35 optimal weight:    0.5980
   overall best weight:    1.7384

-------------------------------------------------------------------------------
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 = 0.3943 r_free = 0.3943 target = 0.121340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.100767 restraints weight = 4981.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3655 rms_B_bonded: 2.13
r_work: 0.3529 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3423 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.3994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   4410  Z= 0.308
  Angle     :  0.580   7.280   6000  Z= 0.320
  Chirality :  0.050   0.135    708
  Planarity :  0.004   0.031    738
  Dihedral  :  5.125  15.874    594
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 17.95 %
    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: -2.27 (0.34), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.72 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  79 
 HIS   0.004   0.001   HIS D  31 
 PHE   0.009   0.002   PHE E  87 
 TYR   0.013   0.002   TYR A 114 
 ARG   0.003   0.001   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
  114 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.449 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8711 (mtpt) cc_final: 0.6748 (pptt)
REVERT: A   21 ARG cc_start: 0.8176 (ttt90) cc_final: 0.7757 (ttt90)
REVERT: A   34 ARG cc_start: 0.8124 (ttt-90) cc_final: 0.7877 (ttt-90)
REVERT: A   70 LYS cc_start: 0.8581 (tttt) cc_final: 0.8296 (tttp)
REVERT: A   80 LYS cc_start: 0.8282 (tttt) cc_final: 0.7771 (ttpt)
REVERT: A  104 ARG cc_start: 0.8273 (mtm-85) cc_final: 0.8017 (mtm-85)
REVERT: B   70 LYS cc_start: 0.8752 (tttt) cc_final: 0.8537 (tttm)
REVERT: C   15 LYS cc_start: 0.8327 (mtpt) cc_final: 0.8048 (mtmt)
REVERT: C   62 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7576 (mt-10)
REVERT: C   92 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7576 (mt-10)
REVERT: D   15 LYS cc_start: 0.8416 (mtpt) cc_final: 0.8145 (mtpt)
REVERT: D   62 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7703 (mt-10)
REVERT: D   66 GLU cc_start: 0.7830 (tt0) cc_final: 0.7018 (tm-30)
REVERT: D   80 LYS cc_start: 0.8106 (tttt) cc_final: 0.7806 (ttpp)
REVERT: D   99 ASP cc_start: 0.7940 (t0) cc_final: 0.7423 (t0)
REVERT: E   62 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7601 (mt-10)
REVERT: E   66 GLU cc_start: 0.7797 (tt0) cc_final: 0.7180 (tm-30)
REVERT: E   80 LYS cc_start: 0.8190 (tttt) cc_final: 0.7729 (tttm)
REVERT: F   13 MET cc_start: 0.7766 (ttm) cc_final: 0.7124 (mtm)
REVERT: F   15 LYS cc_start: 0.8445 (mtpt) cc_final: 0.8078 (mtpt)
REVERT: F   34 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8159 (ttt180)
REVERT: F   62 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7631 (mt-10)
REVERT: F   80 LYS cc_start: 0.8263 (tttt) cc_final: 0.7969 (tttp)
REVERT: F   92 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8092 (mt-10)
REVERT: F  104 ARG cc_start: 0.8217 (mtt180) cc_final: 0.7863 (mtm110)
  outliers start: 13
  outliers final: 7
  residues processed: 106
  average time/residue: 1.9119
  time to fit residues: 207.0707
Evaluate side-chains
  108 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
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 C residue   92 GLU
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain E residue   92 GLU
Chi-restraints excluded: chain F residue   34 ARG
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain F residue   85 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 33 optimal weight:    8.9990
   chunk 25 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0870
   chunk 37 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 27 optimal weight:    6.9990
   chunk 4 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0270
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.8222

-------------------------------------------------------------------------------
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 = 0.3978 r_free = 0.3978 target = 0.123376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.103246 restraints weight = 5131.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3690 rms_B_bonded: 2.10
r_work: 0.3565 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3457 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.3998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4410  Z= 0.193
  Angle     :  0.511   7.530   6000  Z= 0.280
  Chirality :  0.049   0.131    708
  Planarity :  0.004   0.029    738
  Dihedral  :  4.915  15.372    594
  Min Nonbonded Distance : 2.652

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 18.38 %
    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: -2.22 (0.35), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.68 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A  79 
 HIS   0.004   0.001   HIS D  31 
 PHE   0.009   0.002   PHE B  64 
 TYR   0.013   0.001   TYR C 114 
 ARG   0.003   0.000   ARG E 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
  109 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.468 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8687 (mtpt) cc_final: 0.8482 (mtmt)
REVERT: A   21 ARG cc_start: 0.8223 (ttt90) cc_final: 0.7914 (ttt90)
REVERT: A   34 ARG cc_start: 0.8210 (ttt-90) cc_final: 0.7963 (ttt-90)
REVERT: A   70 LYS cc_start: 0.8572 (tttt) cc_final: 0.8341 (tttp)
REVERT: A   80 LYS cc_start: 0.8249 (tttt) cc_final: 0.7837 (ttpt)
REVERT: A  104 ARG cc_start: 0.8262 (mtm-85) cc_final: 0.8009 (mtm-85)
REVERT: B   70 LYS cc_start: 0.8777 (tttt) cc_final: 0.8552 (tttp)
REVERT: C   15 LYS cc_start: 0.8388 (mtpt) cc_final: 0.8101 (mtmt)
REVERT: C   62 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7603 (mt-10)
REVERT: C   92 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7579 (mt-10)
REVERT: D   15 LYS cc_start: 0.8414 (mtpt) cc_final: 0.8179 (mtpt)
REVERT: D   62 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7686 (mt-10)
REVERT: D   66 GLU cc_start: 0.7847 (tt0) cc_final: 0.7117 (tm-30)
REVERT: D   80 LYS cc_start: 0.8167 (tttt) cc_final: 0.7872 (ttpp)
REVERT: D   99 ASP cc_start: 0.7772 (t0) cc_final: 0.7340 (t0)
REVERT: E   62 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7540 (mt-10)
REVERT: E   66 GLU cc_start: 0.7814 (tt0) cc_final: 0.7221 (tm-30)
REVERT: E   80 LYS cc_start: 0.8227 (tttt) cc_final: 0.7788 (tttm)
REVERT: F   13 MET cc_start: 0.7906 (ttm) cc_final: 0.7266 (mtm)
REVERT: F   15 LYS cc_start: 0.8449 (mtpt) cc_final: 0.8088 (mtpt)
REVERT: F   34 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8166 (ttt180)
REVERT: F   62 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7628 (mt-10)
REVERT: F   80 LYS cc_start: 0.8276 (tttt) cc_final: 0.7992 (tttp)
REVERT: F  104 ARG cc_start: 0.8184 (mtt180) cc_final: 0.7943 (mtm110)
  outliers start: 11
  outliers final: 7
  residues processed: 103
  average time/residue: 2.0917
  time to fit residues: 219.8843
Evaluate side-chains
  106 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
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 C residue   92 GLU
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain F residue   34 ARG
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain F residue   85 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   chunk 12 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 14 optimal weight:    9.9990
   chunk 45 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  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 = 0.3926 r_free = 0.3926 target = 0.119855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.099220 restraints weight = 5021.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 2.13
r_work: 0.3512 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3404 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.4117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   4410  Z= 0.388
  Angle     :  0.620   7.413   6000  Z= 0.344
  Chirality :  0.051   0.143    708
  Planarity :  0.004   0.031    738
  Dihedral  :  5.331  18.035    594
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 19.02 %
    Favored  : 78.42 %
  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   0.006   0.002   TRP D  79 
 HIS   0.004   0.001   HIS D  31 
 PHE   0.010   0.002   PHE E  87 
 TYR   0.014   0.002   TYR A 114 
 ARG   0.004   0.001   ARG B 104 

********************** 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
  110 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.565 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8741 (mtpt) cc_final: 0.6934 (pptt)
REVERT: A   21 ARG cc_start: 0.8223 (ttt90) cc_final: 0.7803 (ttt90)
REVERT: A   70 LYS cc_start: 0.8607 (tttt) cc_final: 0.8312 (tttp)
REVERT: A   80 LYS cc_start: 0.8291 (tttt) cc_final: 0.7789 (ttpt)
REVERT: B   70 LYS cc_start: 0.8719 (tttt) cc_final: 0.8509 (tttp)
REVERT: C   15 LYS cc_start: 0.8323 (mtpt) cc_final: 0.8030 (mtmt)
REVERT: C   62 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7553 (mt-10)
REVERT: C   63 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7324 (tt0)
REVERT: C   92 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7628 (mt-10)
REVERT: D   15 LYS cc_start: 0.8339 (mtpt) cc_final: 0.8043 (mtpt)
REVERT: D   62 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7729 (mt-10)
REVERT: D   66 GLU cc_start: 0.7807 (tt0) cc_final: 0.6898 (tm-30)
REVERT: D   80 LYS cc_start: 0.8138 (tttt) cc_final: 0.7855 (ttpp)
REVERT: D   99 ASP cc_start: 0.7873 (t0) cc_final: 0.7356 (t0)
REVERT: E   62 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7541 (mt-10)
REVERT: E   66 GLU cc_start: 0.7828 (tt0) cc_final: 0.7213 (tm-30)
REVERT: E   80 LYS cc_start: 0.8217 (tttt) cc_final: 0.7766 (tttm)
REVERT: F   13 MET cc_start: 0.7725 (ttm) cc_final: 0.7122 (mtm)
REVERT: F   15 LYS cc_start: 0.8450 (mtpt) cc_final: 0.8185 (mtpm)
REVERT: F   34 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8173 (ttt180)
REVERT: F   62 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7598 (mt-10)
REVERT: F   80 LYS cc_start: 0.8360 (tttt) cc_final: 0.8083 (tttp)
REVERT: F  104 ARG cc_start: 0.8219 (mtt180) cc_final: 0.7853 (mtm110)
  outliers start: 12
  outliers final: 7
  residues processed: 103
  average time/residue: 3.1171
  time to fit residues: 329.1585
Evaluate side-chains
  107 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
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 C residue   92 GLU
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain F residue   34 ARG
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain F residue   85 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0770
   chunk 0 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 1 optimal weight:    4.9990
   chunk 17 optimal weight:    0.7980
   chunk 39 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.6938

-------------------------------------------------------------------------------
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 = 0.3978 r_free = 0.3978 target = 0.123030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.102911 restraints weight = 5114.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3687 rms_B_bonded: 2.09
r_work: 0.3562 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3454 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.4074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4410  Z= 0.184
  Angle     :  0.520   8.068   6000  Z= 0.284
  Chirality :  0.049   0.129    708
  Planarity :  0.004   0.028    738
  Dihedral  :  5.010  15.809    594
  Min Nonbonded Distance : 2.649

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 19.23 %
    Favored  : 78.85 %
  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: -2.26 (0.34), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.72 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A  79 
 HIS   0.005   0.001   HIS D  31 
 PHE   0.010   0.002   PHE B  64 
 TYR   0.014   0.001   TYR C 114 
 ARG   0.004   0.000   ARG E 104 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5334.31 seconds
wall clock time: 94 minutes 0.07 seconds (5640.07 seconds total)