Starting phenix.real_space_refine
on Fri Aug 22 14:08:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gf7_29980/08_2025/8gf7_29980.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gf7_29980/08_2025/8gf7_29980.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gf7_29980/08_2025/8gf7_29980.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gf7_29980/08_2025/8gf7_29980.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gf7_29980/08_2025/8gf7_29980.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gf7_29980/08_2025/8gf7_29980.map"
  }
  resolution = 4.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    2346      2.51       5
     N     654      2.21       5
     O     774      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3774
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 615
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 615
          Classifications: {'peptide': 90}
          Link IDs: {'TRANS': 89}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Restraints were copied for chains:
    B, C, D, E, F
  Time building chain proxies: 0.69, per 1000 atoms: 0.18
  Number of scatterers: 3774
  At special positions: 0
  Unit cell: (103.2, 116.1, 32.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     774      8.00
     N     654      7.00
     C    2346      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=6, symmetry=0
  Links applied
    NAG-SER
      " NAG A 101 " - " SER A  87 "
      " NAG B 101 " - " SER B  87 "
      " NAG C 101 " - " SER C  87 "
      " NAG D 101 " - " SER D  87 "
      " NAG E 101 " - " SER E  87 "
      " NAG F 101 " - " SER F  87 "
  Number of additional bonds: simple=6, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.56
  Conformation dependent library (CDL) restraints added in 156.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  912

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 24 sheets defined
      0.0% alpha, 46.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 8 through 9
      removed outlier: 6.538A  pdb=" N   LEU A   8 " --> pdb=" O   SER C   9 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 23
      removed outlier: 8.203A  pdb=" N   GLY A  14 " --> pdb=" O   VAL B  15 " (cutoff:3.500A)
      removed outlier: 10.576A  pdb=" N   ALA B  17 " --> pdb=" O   GLY A  14 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   VAL A  16 " --> pdb=" O   ALA B  17 " (cutoff:3.500A)
      removed outlier: 8.505A  pdb=" N   ALA B  19 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   ALA A  18 " --> pdb=" O   ALA B  19 " (cutoff:3.500A)
      removed outlier: 8.620A  pdb=" N   LYS B  21 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   GLU A  20 " --> pdb=" O   LYS B  21 " (cutoff:3.500A)
      removed outlier: 8.520A  pdb=" N   LYS B  23 " --> pdb=" O   GLU A  20 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   THR A  22 " --> pdb=" O   LYS B  23 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   GLY A  14 " --> pdb=" O   GLU C  13 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   ALA A  18 " --> pdb=" O   ALA C  17 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   ALA C  19 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   GLU A  20 " --> pdb=" O   ALA C  19 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   LYS C  21 " --> pdb=" O   GLU A  20 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   THR A  22 " --> pdb=" O   LYS C  21 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   LYS C  23 " --> pdb=" O   THR A  22 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 26 through 31
      removed outlier: 6.856A  pdb=" N   ALA A  27 " --> pdb=" O   VAL B  26 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   GLU B  28 " --> pdb=" O   ALA A  27 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   ALA A  29 " --> pdb=" O   GLU B  28 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   ALA B  30 " --> pdb=" O   ALA A  29 " (cutoff:3.500A)
      removed outlier: 8.282A  pdb=" N   VAL A  26 " --> pdb=" O   ALA C  27 " (cutoff:3.500A)
      removed outlier: 10.665A  pdb=" N   ALA C  29 " --> pdb=" O   VAL A  26 " (cutoff:3.500A)
      removed outlier: 9.234A  pdb=" N   GLU A  28 " --> pdb=" O   ALA C  29 " (cutoff:3.500A)
      removed outlier: 9.901A  pdb=" N   GLY C  31 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
      removed outlier: 5.923A  pdb=" N   ALA A  30 " --> pdb=" O   GLY C  31 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 38 through 43
      removed outlier: 6.339A  pdb=" N   TYR A  39 " --> pdb=" O   VAL B  40 " (cutoff:3.500A)
      removed outlier: 7.197A  pdb=" N   SER B  42 " --> pdb=" O   TYR A  39 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   GLY A  41 " --> pdb=" O   SER B  42 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 49
      removed outlier: 6.628A  pdb=" N   VAL A  48 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 54
      removed outlier: 6.691A  pdb=" N   VAL A  52 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 66
      removed outlier: 6.833A  pdb=" N   GLU A  61 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
      removed outlier: 8.415A  pdb=" N   THR B  64 " --> pdb=" O   GLU A  61 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   VAL A  63 " --> pdb=" O   THR B  64 " (cutoff:3.500A)
      removed outlier: 8.001A  pdb=" N   VAL B  66 " --> pdb=" O   VAL A  63 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ASN A  65 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   LYS A  60 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
      removed outlier: 8.347A  pdb=" N   VAL C  63 " --> pdb=" O   LYS A  60 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   GLN A  62 " --> pdb=" O   VAL C  63 " (cutoff:3.500A)
      removed outlier: 8.339A  pdb=" N   ASN C  65 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   THR A  64 " --> pdb=" O   ASN C  65 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 70 through 77
      removed outlier: 7.094A  pdb=" N   VAL B  74 " --> pdb=" O   GLY A  73 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   THR A  75 " --> pdb=" O   VAL B  74 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   ALA B  76 " --> pdb=" O   THR A  75 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   VAL A  77 " --> pdb=" O   ALA B  76 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   VAL A  70 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 8.243A  pdb=" N   GLY C  73 " --> pdb=" O   VAL A  70 " (cutoff:3.500A)
      removed outlier: 8.565A  pdb=" N   THR A  72 " --> pdb=" O   GLY C  73 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   THR C  75 " --> pdb=" O   THR A  72 " (cutoff:3.500A)
      removed outlier: 8.701A  pdb=" N   VAL A  74 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 10.462A  pdb=" N   VAL C  77 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
      removed outlier: 9.054A  pdb=" N   ALA A  76 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 80 through 81
      removed outlier: 6.730A  pdb=" N   LYS A  80 " --> pdb=" O   THR B  81 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 85 through 86
      removed outlier: 7.059A  pdb=" N   ALA A  85 " --> pdb=" O   GLY B  86 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 89 through 90
      removed outlier: 6.660A  pdb=" N   ALA A  89 " --> pdb=" O   ALA B  90 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 93 through 95
      removed outlier: 6.221A  pdb=" N   PHE A  94 " --> pdb=" O   VAL B  95 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 8 through 9
    Processing sheet with id=AB5, first strand: chain 'D' and resid 13 through 23
      removed outlier: 8.125A  pdb=" N   GLY D  14 " --> pdb=" O   VAL E  15 " (cutoff:3.500A)
      removed outlier: 10.515A  pdb=" N   ALA E  17 " --> pdb=" O   GLY D  14 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   VAL D  16 " --> pdb=" O   ALA E  17 " (cutoff:3.500A)
      removed outlier: 8.491A  pdb=" N   ALA E  19 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   ALA D  18 " --> pdb=" O   ALA E  19 " (cutoff:3.500A)
      removed outlier: 8.662A  pdb=" N   LYS E  21 " --> pdb=" O   ALA D  18 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   GLU D  20 " --> pdb=" O   LYS E  21 " (cutoff:3.500A)
      removed outlier: 8.562A  pdb=" N   LYS E  23 " --> pdb=" O   GLU D  20 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   THR D  22 " --> pdb=" O   LYS E  23 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   GLY E  14 " --> pdb=" O   VAL F  15 " (cutoff:3.500A)
      removed outlier: 10.516A  pdb=" N   ALA F  17 " --> pdb=" O   GLY E  14 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   VAL E  16 " --> pdb=" O   ALA F  17 " (cutoff:3.500A)
      removed outlier: 8.492A  pdb=" N   ALA F  19 " --> pdb=" O   VAL E  16 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   ALA E  18 " --> pdb=" O   ALA F  19 " (cutoff:3.500A)
      removed outlier: 8.662A  pdb=" N   LYS F  21 " --> pdb=" O   ALA E  18 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   GLU E  20 " --> pdb=" O   LYS F  21 " (cutoff:3.500A)
      removed outlier: 8.562A  pdb=" N   LYS F  23 " --> pdb=" O   GLU E  20 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   THR E  22 " --> pdb=" O   LYS F  23 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'D' and resid 26 through 31
      removed outlier: 6.840A  pdb=" N   ALA D  27 " --> pdb=" O   VAL E  26 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   GLU E  28 " --> pdb=" O   ALA D  27 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   ALA D  29 " --> pdb=" O   GLU E  28 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   ALA E  30 " --> pdb=" O   ALA D  29 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   ALA E  27 " --> pdb=" O   VAL F  26 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   GLU F  28 " --> pdb=" O   ALA E  27 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   ALA E  29 " --> pdb=" O   GLU F  28 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   ALA F  30 " --> pdb=" O   ALA E  29 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 38 through 43
      removed outlier: 6.256A  pdb=" N   TYR D  39 " --> pdb=" O   VAL E  40 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   SER E  42 " --> pdb=" O   TYR D  39 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   GLY D  41 " --> pdb=" O   SER E  42 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   TYR E  39 " --> pdb=" O   VAL F  40 " (cutoff:3.500A)
      removed outlier: 7.162A  pdb=" N   SER F  42 " --> pdb=" O   TYR E  39 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   GLY E  41 " --> pdb=" O   SER F  42 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'D' and resid 48 through 49
    Processing sheet with id=AB9, first strand: chain 'D' and resid 52 through 54
    Processing sheet with id=AC1, first strand: chain 'D' and resid 60 through 66
    Processing sheet with id=AC2, first strand: chain 'D' and resid 70 through 77
      removed outlier: 7.072A  pdb=" N   VAL E  74 " --> pdb=" O   GLY D  73 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   THR D  75 " --> pdb=" O   VAL E  74 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   ALA E  76 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   VAL D  77 " --> pdb=" O   ALA E  76 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   VAL F  74 " --> pdb=" O   GLY E  73 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   THR E  75 " --> pdb=" O   VAL F  74 " (cutoff:3.500A)
      removed outlier: 7.024A  pdb=" N   ALA F  76 " --> pdb=" O   THR E  75 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   VAL E  77 " --> pdb=" O   ALA F  76 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 80 through 81
      removed outlier: 6.672A  pdb=" N   LYS D  80 " --> pdb=" O   THR E  81 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   LYS E  80 " --> pdb=" O   THR F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC3
    Processing sheet with id=AC4, first strand: chain 'D' and resid 85 through 86
      removed outlier: 7.083A  pdb=" N   ALA D  85 " --> pdb=" O   GLY E  86 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   ALA E  85 " --> pdb=" O   GLY F  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC4
    Processing sheet with id=AC5, first strand: chain 'D' and resid 89 through 90
      removed outlier: 6.684A  pdb=" N   ALA D  89 " --> pdb=" O   ALA E  90 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   ALA E  89 " --> pdb=" O   ALA F  90 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC5
    Processing sheet with id=AC6, first strand: chain 'D' and resid 93 through 95
      removed outlier: 6.254A  pdb=" N   PHE D  94 " --> pdb=" O   VAL E  95 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   PHE E  94 " --> pdb=" O   VAL F  95 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC6

    49 hydrogen bonds defined for protein.
    147 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.50

  Time building geometry restraints manager: 0.44 seconds

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

  Histogram of bond lengths:
        1.21 -     1.28: 666
        1.28 -     1.35: 576
        1.35 -     1.42: 102
        1.42 -     1.49: 648
        1.49 -     1.55: 1794
  Bond restraints: 3786
  Sorted by residual:
  bond pdb=" C3  NAG E 101 "
       pdb=" O3  NAG E 101 "
    ideal  model  delta    sigma   weight residual
    1.403  1.430 -0.027 2.00e-02 2.50e+03 1.79e+00
  bond pdb=" C2  NAG F 101 "
       pdb=" N2  NAG F 101 "
    ideal  model  delta    sigma   weight residual
    1.439  1.465 -0.026 2.00e-02 2.50e+03 1.72e+00
  bond pdb=" C3  NAG F 101 "
       pdb=" O3  NAG F 101 "
    ideal  model  delta    sigma   weight residual
    1.403  1.429 -0.026 2.00e-02 2.50e+03 1.69e+00
  bond pdb=" C3  NAG B 101 "
       pdb=" O3  NAG B 101 "
    ideal  model  delta    sigma   weight residual
    1.403  1.429 -0.026 2.00e-02 2.50e+03 1.69e+00
  bond pdb=" C3  NAG A 101 "
       pdb=" O3  NAG A 101 "
    ideal  model  delta    sigma   weight residual
    1.403  1.429 -0.026 2.00e-02 2.50e+03 1.68e+00
  ... (remaining 3781 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.99: 4633
        0.99 -     1.99: 344
        1.99 -     2.98: 81
        2.98 -     3.98: 18
        3.98 -     4.97: 18
  Bond angle restraints: 5094
  Sorted by residual:
  angle pdb=" C   ALA C  11 "
        pdb=" N   LYS C  12 "
        pdb=" CA  LYS C  12 "
      ideal   model   delta    sigma   weight residual
     122.56  118.91    3.65 1.50e+00 4.44e-01 5.93e+00
  angle pdb=" C   ALA F  11 "
        pdb=" N   LYS F  12 "
        pdb=" CA  LYS F  12 "
      ideal   model   delta    sigma   weight residual
     122.56  118.92    3.64 1.50e+00 4.44e-01 5.90e+00
  angle pdb=" C   ALA D  11 "
        pdb=" N   LYS D  12 "
        pdb=" CA  LYS D  12 "
      ideal   model   delta    sigma   weight residual
     122.56  118.92    3.64 1.50e+00 4.44e-01 5.88e+00
  angle pdb=" C   ALA B  11 "
        pdb=" N   LYS B  12 "
        pdb=" CA  LYS B  12 "
      ideal   model   delta    sigma   weight residual
     122.56  118.93    3.63 1.50e+00 4.44e-01 5.87e+00
  angle pdb=" C   ALA A  11 "
        pdb=" N   LYS A  12 "
        pdb=" CA  LYS A  12 "
      ideal   model   delta    sigma   weight residual
     122.56  118.94    3.62 1.50e+00 4.44e-01 5.82e+00
  ... (remaining 5089 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.15: 2070
       10.15 -    20.30: 168
       20.30 -    30.44: 60
       30.44 -    40.59: 12
       40.59 -    50.74: 18
  Dihedral angle restraints: 2328
    sinusoidal: 876
      harmonic: 1452
  Sorted by residual:
  dihedral pdb=" CA  LYS D  32 "
           pdb=" C   LYS D  32 "
           pdb=" N   THR D  33 "
           pdb=" CA  THR D  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.97   19.03     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CA  LYS A  32 "
           pdb=" C   LYS A  32 "
           pdb=" N   THR A  33 "
           pdb=" CA  THR A  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.99   19.01     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CA  LYS C  32 "
           pdb=" C   LYS C  32 "
           pdb=" N   THR C  33 "
           pdb=" CA  THR C  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.00   19.00     0      5.00e+00 4.00e-02 1.44e+01
  ... (remaining 2325 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 423
       0.035 -    0.071: 87
       0.071 -    0.106: 84
       0.106 -    0.142: 48
       0.142 -    0.177: 18
  Chirality restraints: 660
  Sorted by residual:
  chirality pdb=" C5  NAG F 101 "
            pdb=" C4  NAG F 101 "
            pdb=" C6  NAG F 101 "
            pdb=" O5  NAG F 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.41   -2.59    0.18 2.00e-01 2.50e+01 7.83e-01
  chirality pdb=" C5  NAG B 101 "
            pdb=" C4  NAG B 101 "
            pdb=" C6  NAG B 101 "
            pdb=" O5  NAG B 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.41   -2.58    0.17 2.00e-01 2.50e+01 7.64e-01
  chirality pdb=" C5  NAG A 101 "
            pdb=" C4  NAG A 101 "
            pdb=" C6  NAG A 101 "
            pdb=" O5  NAG A 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.41   -2.58    0.17 2.00e-01 2.50e+01 7.47e-01
  ... (remaining 657 not shown)

  Planarity restraints: 630
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL F  15 "   -0.002 2.00e-02 2.50e+03   4.18e-03 1.75e-01
        pdb=" C   VAL F  15 "    0.007 2.00e-02 2.50e+03
        pdb=" O   VAL F  15 "   -0.003 2.00e-02 2.50e+03
        pdb=" N   VAL F  16 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D  15 "   -0.002 2.00e-02 2.50e+03   4.11e-03 1.69e-01
        pdb=" C   VAL D  15 "    0.007 2.00e-02 2.50e+03
        pdb=" O   VAL D  15 "   -0.003 2.00e-02 2.50e+03
        pdb=" N   VAL D  16 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR E  59 "    0.002 2.00e-02 2.50e+03   4.05e-03 1.64e-01
        pdb=" C   THR E  59 "   -0.007 2.00e-02 2.50e+03
        pdb=" O   THR E  59 "    0.003 2.00e-02 2.50e+03
        pdb=" N   LYS E  60 "    0.002 2.00e-02 2.50e+03
  ... (remaining 627 not shown)

  Histogram of nonbonded interaction distances:
        1.68 -     2.32: 35
        2.32 -     2.97: 1747
        2.97 -     3.61: 5076
        3.61 -     4.26: 7164
        4.26 -     4.90: 11983
  Nonbonded interactions: 26005
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A  20 "
            pdb=" NZ  LYS C  80 "
     model   vdw
     1.681 3.120
  nonbonded pdb=" CE  LYS A  10 "
            pdb=" OE2 GLU C  35 "
     model   vdw
     1.695 3.440
  nonbonded pdb=" OE2 GLU D  35 "
            pdb=" CE  LYS E  10 "
     model   vdw
     1.730 3.440
  nonbonded pdb=" OE2 GLU E  35 "
            pdb=" CE  LYS F  10 "
     model   vdw
     1.730 3.440
  nonbonded pdb=" OE2 GLU A  35 "
            pdb=" CE  LYS B  10 "
     model   vdw
     1.730 3.440
  ... (remaining 26000 not shown)

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

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}
Set refine NCS operators
  NCS operators will be refined.
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 group one per residue
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:             2.290
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.170
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5169
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      :  0.016   0.390   3798  Z= 1.558
  Angle     :  0.680   4.970   5106  Z= 0.368
  Chirality :  0.058   0.177    660
  Planarity :  0.001   0.004    630
  Dihedral  : 10.147  50.740   1416
  Min Nonbonded Distance : 1.681

Molprobity Statistics.
  All-atom Clashscore : 53.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.23 %
    Favored  : 89.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.11 (0.27), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.13 (0.21), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.001   TYR B  39 
 PHE   0.004   0.001   PHE B  94 
 HIS   0.002   0.001   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 3786)
  covalent geometry    : angle       0.67609 ( 5094)
  hydrogen bonds       : bond        0.24446 (   49)
  hydrogen bonds       : angle       8.53897 (  147)
  Misc. bond           : bond        0.38959 (    6)
  link_NAG-SER         : bond        0.03628 (    6)
  link_NAG-SER         : angle       1.62480 (   12)

*********************** 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.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.028 
Fit side-chains
REVERT: A   22 THR cc_start: 0.8470 (m) cc_final: 0.8055 (p)
REVERT: A   62 GLN cc_start: 0.8701 (mt0) cc_final: 0.8076 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.0688
  time to fit residues: 1.6875
Evaluate side-chains
  13 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 48 optimal weight:    0.0070
   chunk 26 optimal weight:    8.9990
   chunk 2 optimal weight:    8.9990
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    7.9990
   chunk 25 optimal weight:   20.0000
   chunk 50 optimal weight:    0.0770
   chunk 53 optimal weight:    0.0980
   chunk 19 optimal weight:    0.0270
   overall best weight:    0.2414
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  50 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.141889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.120307 restraints weight = 2358.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.122221 restraints weight = 1753.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.123623 restraints weight = 1406.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.124671 restraints weight = 1185.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.125473 restraints weight = 1039.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5491
moved from start:          0.3868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3798  Z= 0.152
  Angle     :  0.956   7.264   5106  Z= 0.511
  Chirality :  0.067   0.316    660
  Planarity :  0.002   0.010    630
  Dihedral  :  8.872  52.435    666
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 15.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.64 %
    Favored  : 86.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.90 (0.27), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.97 (0.21), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.001   TYR E  39 
 PHE   0.000   0.000   PHE E  94 
 HIS   0.001   0.000   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 3786)
  covalent geometry    : angle       0.95627 ( 5094)
  hydrogen bonds       : bond        0.14353 (   49)
  hydrogen bonds       : angle       6.78074 (  147)
  Misc. bond           : bond        0.00072 (    6)
  link_NAG-SER         : bond        0.00166 (    6)
  link_NAG-SER         : angle       0.98267 (   12)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.014 
Fit side-chains
REVERT: B   20 GLU cc_start: 0.7175 (tp30) cc_final: 0.6678 (pp20)
REVERT: B   62 GLN cc_start: 0.8649 (mt0) cc_final: 0.8044 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 17
  average time/residue: 0.0612
  time to fit residues: 1.1090
Evaluate side-chains
  14 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 38 optimal weight:    0.1980
   chunk 39 optimal weight:   10.0000
   chunk 8 optimal weight:    0.0970
   chunk 40 optimal weight:   20.0000
   chunk 20 optimal weight:    5.9990
   chunk 6 optimal weight:    8.9990
   chunk 44 optimal weight:    5.9990
   chunk 35 optimal weight:    0.0870
   chunk 41 optimal weight:    0.8980
   chunk 22 optimal weight:   30.0000
   chunk 12 optimal weight:   10.0000
   overall best weight:    1.4558
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.143377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.123019 restraints weight = 2349.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.124750 restraints weight = 1754.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.126104 restraints weight = 1414.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.126998 restraints weight = 1197.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.127723 restraints weight = 1057.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5479
moved from start:          0.4350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3798  Z= 0.133
  Angle     :  0.795   8.228   5106  Z= 0.430
  Chirality :  0.059   0.252    660
  Planarity :  0.002   0.006    630
  Dihedral  :  9.732  59.863    666
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 15.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.50 %
    Favored  : 87.50 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  5.00 %
    Favored  : 93.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.89 (0.29), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.96 (0.22), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR F  39 
 PHE   0.002   0.000   PHE A  94 
 HIS   0.001   0.000   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 3786)
  covalent geometry    : angle       0.79559 ( 5094)
  hydrogen bonds       : bond        0.12086 (   49)
  hydrogen bonds       : angle       6.74397 (  147)
  Misc. bond           : bond        0.00000 (    6)
  link_NAG-SER         : bond        0.00218 (    6)
  link_NAG-SER         : angle       0.25002 (   12)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 17
  time to evaluate  : 0.025 
Fit side-chains
REVERT: B   20 GLU cc_start: 0.7382 (tp30) cc_final: 0.6778 (pp20)
REVERT: B   32 LYS cc_start: 0.3654 (mmmt) cc_final: 0.3423 (mmmt)
REVERT: B   62 GLN cc_start: 0.8652 (mt0) cc_final: 0.8109 (tt0)
  outliers start: 1
  outliers final: 0
  residues processed: 17
  average time/residue: 0.0580
  time to fit residues: 1.0658
Evaluate side-chains
  13 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 38 optimal weight:    0.0070
   chunk 22 optimal weight:    0.0470
   chunk 31 optimal weight:    0.0030
   chunk 29 optimal weight:    0.9980
   chunk 19 optimal weight:   20.0000
   chunk 0 optimal weight:    9.9990
   chunk 14 optimal weight:    0.2980
   chunk 35 optimal weight:    0.0070
   chunk 41 optimal weight:    0.8980
   chunk 10 optimal weight:   20.0000
   chunk 42 optimal weight:   30.0000
   overall best weight:    0.0724
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.157813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.136201 restraints weight = 2263.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.138066 restraints weight = 1679.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.139586 restraints weight = 1356.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.140701 restraints weight = 1150.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.141624 restraints weight = 1014.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.4065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4870
moved from start:          0.4938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3798  Z= 0.133
  Angle     :  0.837   9.163   5106  Z= 0.448
  Chirality :  0.060   0.242    660
  Planarity :  0.002   0.012    630
  Dihedral  :  9.469  58.032    666
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.64 %
    Favored  : 86.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.84 (0.29), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.92 (0.22), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.016   0.005   TYR D  39 
 PHE   0.000   0.000   PHE E  94 
 HIS   0.000   0.000   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 3786)
  covalent geometry    : angle       0.83522 ( 5094)
  hydrogen bonds       : bond        0.10407 (   49)
  hydrogen bonds       : angle       6.95029 (  147)
  Misc. bond           : bond        0.00002 (    6)
  link_NAG-SER         : bond        0.00329 (    6)
  link_NAG-SER         : angle       1.27247 (   12)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.029 
Fit side-chains
REVERT: B   20 GLU cc_start: 0.7502 (tp30) cc_final: 0.6733 (pp20)
REVERT: B   21 LYS cc_start: 0.8545 (ptmt) cc_final: 0.8282 (ptmt)
REVERT: B   62 GLN cc_start: 0.8764 (mt0) cc_final: 0.8095 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.0639
  time to fit residues: 1.3814
Evaluate side-chains
  13 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 6 optimal weight:    0.0570
   chunk 27 optimal weight:    9.9990
   chunk 15 optimal weight:    0.0570
   chunk 30 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 14 optimal weight:    0.7980
   chunk 25 optimal weight:    7.9990
   chunk 41 optimal weight:    0.4980
   chunk 37 optimal weight:    8.9990
   chunk 4 optimal weight:   20.0000
   chunk 53 optimal weight:    0.0570
   overall best weight:    0.2534
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.152878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.141778 restraints weight = 2901.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.142839 restraints weight = 2227.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.143677 restraints weight = 1855.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.144333 restraints weight = 1621.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.144614 restraints weight = 1456.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.4072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5435
moved from start:          0.5418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3798  Z= 0.155
  Angle     :  1.088  15.362   5106  Z= 0.559
  Chirality :  0.059   0.220    660
  Planarity :  0.002   0.010    630
  Dihedral  :  9.583  59.166    666
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 16.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.05 %
    Favored  : 82.95 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  6.67 %
    Favored  : 91.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.90 (0.30), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.97 (0.23), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.000   TYR D  39 
 PHE   0.001   0.000   PHE E  94 
 HIS   0.000   0.000   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 3786)
  covalent geometry    : angle       1.08937 ( 5094)
  hydrogen bonds       : bond        0.09898 (   49)
  hydrogen bonds       : angle       6.98410 (  147)
  Misc. bond           : bond        0.00011 (    6)
  link_NAG-SER         : bond        0.00231 (    6)
  link_NAG-SER         : angle       0.26110 (   12)

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

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

  704 Ramachandran restraints generated.
    352 Oldfield, 0 Emsley, 352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  704 Ramachandran restraints generated.
    352 Oldfield, 0 Emsley, 352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 19
  time to evaluate  : 0.014 
Fit side-chains
REVERT: C   20 GLU cc_start: 0.7464 (tp30) cc_final: 0.7244 (pp20)
REVERT: C   62 GLN cc_start: 0.8566 (mt0) cc_final: 0.8229 (mp10)
REVERT: C   72 THR cc_start: 0.7555 (p) cc_final: 0.7283 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 19
  average time/residue: 0.0566
  time to fit residues: 1.1472
Evaluate side-chains
  14 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 48 optimal weight:    0.3980
   chunk 23 optimal weight:   10.0000
   chunk 19 optimal weight:    0.6980
   chunk 5 optimal weight:   10.0000
   chunk 47 optimal weight:    7.9990
   chunk 1 optimal weight:    0.6980
   chunk 49 optimal weight:   20.0000
   chunk 51 optimal weight:   10.0000
   chunk 15 optimal weight:    9.9990
   chunk 39 optimal weight:    0.4980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.8582
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.144348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.127768 restraints weight = 2219.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.129695 restraints weight = 1477.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.131053 restraints weight = 1128.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.132091 restraints weight = 923.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.132766 restraints weight = 793.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.4038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4924
moved from start:          0.5920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   3798  Z= 0.153
  Angle     :  0.920   9.209   5106  Z= 0.489
  Chirality :  0.062   0.239    660
  Planarity :  0.002   0.009    630
  Dihedral  :  9.240  55.663    666
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.05 %
    Favored  : 82.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.83 (0.30), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.91 (0.23), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.015   0.005   TYR C  39 
 PHE   0.001   0.000   PHE C  94 
 HIS   0.000   0.000   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 3786)
  covalent geometry    : angle       0.91976 ( 5094)
  hydrogen bonds       : bond        0.09599 (   49)
  hydrogen bonds       : angle       6.87890 (  147)
  Misc. bond           : bond        0.00143 (    6)
  link_NAG-SER         : bond        0.00204 (    6)
  link_NAG-SER         : angle       0.92286 (   12)

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

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

  704 Ramachandran restraints generated.
    352 Oldfield, 0 Emsley, 352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  704 Ramachandran restraints generated.
    352 Oldfield, 0 Emsley, 352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.024 
Fit side-chains
REVERT: B   20 GLU cc_start: 0.7603 (tp30) cc_final: 0.6914 (pp20)
REVERT: B   57 GLU cc_start: 0.8713 (tp30) cc_final: 0.8481 (tp30)
REVERT: B   62 GLN cc_start: 0.8751 (mt0) cc_final: 0.8166 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.0543
  time to fit residues: 1.1715
Evaluate side-chains
  17 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 42 optimal weight:    9.9990
   chunk 46 optimal weight:    0.0000
   chunk 30 optimal weight:    7.9990
   chunk 25 optimal weight:    9.9990
   chunk 37 optimal weight:    0.2980
   chunk 52 optimal weight:   10.0000
   chunk 20 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0970
   chunk 39 optimal weight:    6.9990
   chunk 29 optimal weight:    7.9990
   chunk 32 optimal weight:    9.9990
   overall best weight:    2.2786
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.139377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.124263 restraints weight = 2437.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.125697 restraints weight = 1827.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.126845 restraints weight = 1495.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.127526 restraints weight = 1272.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.127526 restraints weight = 1142.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5218
moved from start:          0.5977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073   3798  Z= 0.210
  Angle     :  0.944  10.276   5106  Z= 0.495
  Chirality :  0.061   0.242    660
  Planarity :  0.002   0.013    630
  Dihedral  :  9.528  56.285    666
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 20.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.77 %
    Favored  : 85.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.64 (0.30), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.77 (0.23), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR C  39 
 PHE   0.002   0.001   PHE E  94 
 HIS   0.001   0.001   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00536 ( 3786)
  covalent geometry    : angle       0.94457 ( 5094)
  hydrogen bonds       : bond        0.09561 (   49)
  hydrogen bonds       : angle       6.62388 (  147)
  Misc. bond           : bond        0.00091 (    6)
  link_NAG-SER         : bond        0.00107 (    6)
  link_NAG-SER         : angle       0.45251 (   12)

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

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

  704 Ramachandran restraints generated.
    352 Oldfield, 0 Emsley, 352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  704 Ramachandran restraints generated.
    352 Oldfield, 0 Emsley, 352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.014 
Fit side-chains
   revert: symmetry clash
REVERT: B   20 GLU cc_start: 0.7704 (tp30) cc_final: 0.7140 (pp20)
REVERT: B   57 GLU cc_start: 0.8799 (tp30) cc_final: 0.8531 (tp30)
REVERT: B   62 GLN cc_start: 0.8726 (mt0) cc_final: 0.8144 (tt0)
REVERT: B   70 VAL cc_start: 0.8442 (m) cc_final: 0.8197 (t)
REVERT: B   83 GLU cc_start: 0.7957 (pp20) cc_final: 0.7630 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 17
  average time/residue: 0.0401
  time to fit residues: 0.7597
Evaluate side-chains
  16 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 8 optimal weight:    0.0050
   chunk 38 optimal weight:    0.1980
   chunk 31 optimal weight:   30.0000
   chunk 17 optimal weight:    0.0050
   chunk 11 optimal weight:   10.0000
   chunk 44 optimal weight:    0.0170
   chunk 0 optimal weight:   10.0000
   chunk 13 optimal weight:    7.9990
   chunk 21 optimal weight:    5.9990
   chunk 16 optimal weight:   10.0000
   chunk 45 optimal weight:    9.9990
   overall best weight:    1.2448
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.148488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.137405 restraints weight = 2737.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.138735 restraints weight = 2040.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.139706 restraints weight = 1641.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.140510 restraints weight = 1381.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.141110 restraints weight = 1200.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.4047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5321
moved from start:          0.5969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   3798  Z= 0.181
  Angle     :  0.818   7.132   5106  Z= 0.432
  Chirality :  0.061   0.258    660
  Planarity :  0.002   0.011    630
  Dihedral  :  9.090  54.507    666
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 16.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.59 %
    Favored  : 78.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.74 (0.30), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.84 (0.23), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.001   TYR D  39 
 PHE   0.001   0.000   PHE D  94 
 HIS   0.001   0.001   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 3786)
  covalent geometry    : angle       0.81922 ( 5094)
  hydrogen bonds       : bond        0.09581 (   49)
  hydrogen bonds       : angle       6.89962 (  147)
  Misc. bond           : bond        0.00109 (    6)
  link_NAG-SER         : bond        0.00172 (    6)
  link_NAG-SER         : angle       0.35058 (   12)

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

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

  704 Ramachandran restraints generated.
    352 Oldfield, 0 Emsley, 352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  704 Ramachandran restraints generated.
    352 Oldfield, 0 Emsley, 352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.023 
Fit side-chains
   revert: symmetry clash
REVERT: B   20 GLU cc_start: 0.7667 (tp30) cc_final: 0.7160 (pp20)
REVERT: B   57 GLU cc_start: 0.8801 (tp30) cc_final: 0.8514 (tp30)
REVERT: B   62 GLN cc_start: 0.8697 (mt0) cc_final: 0.8199 (mp10)
REVERT: B   70 VAL cc_start: 0.8489 (m) cc_final: 0.8222 (t)
REVERT: B   83 GLU cc_start: 0.8336 (pp20) cc_final: 0.7709 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 0.0377
  time to fit residues: 0.7405
Evaluate side-chains
  16 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 51 optimal weight:   20.0000
   chunk 24 optimal weight:    8.9990
   chunk 34 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0970
   chunk 30 optimal weight:   10.0000
   chunk 33 optimal weight:   30.0000
   chunk 28 optimal weight:    0.0010
   chunk 47 optimal weight:    0.0870
   chunk 46 optimal weight:    0.0030
   chunk 45 optimal weight:    9.9990
   overall best weight:    0.4374
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.151750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.140520 restraints weight = 2704.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.141857 restraints weight = 2017.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.142879 restraints weight = 1623.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.143716 restraints weight = 1359.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.144342 restraints weight = 1173.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.4088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5289
moved from start:          0.6279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   3798  Z= 0.171
  Angle     :  0.826   6.946   5106  Z= 0.434
  Chirality :  0.057   0.197    660
  Planarity :  0.002   0.015    630
  Dihedral  :  9.435  54.520    666
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 14.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 19.32 %
    Favored  : 80.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 1.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.78 (0.30), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.88 (0.23), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR C  39 
 PHE   0.000   0.000   PHE E  94 
 HIS   0.001   0.000   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 3786)
  covalent geometry    : angle       0.82661 ( 5094)
  hydrogen bonds       : bond        0.09626 (   49)
  hydrogen bonds       : angle       6.76951 (  147)
  Misc. bond           : bond        0.00173 (    6)
  link_NAG-SER         : bond        0.00182 (    6)
  link_NAG-SER         : angle       0.62440 (   12)

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

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

  704 Ramachandran restraints generated.
    352 Oldfield, 0 Emsley, 352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  704 Ramachandran restraints generated.
    352 Oldfield, 0 Emsley, 352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.023 
Fit side-chains
REVERT: B   20 GLU cc_start: 0.7629 (tp30) cc_final: 0.7197 (pp20)
REVERT: B   57 GLU cc_start: 0.8813 (tp30) cc_final: 0.8517 (tp30)
REVERT: B   62 GLN cc_start: 0.8659 (mt0) cc_final: 0.8208 (mp10)
REVERT: B   70 VAL cc_start: 0.8391 (m) cc_final: 0.8128 (t)
REVERT: B   83 GLU cc_start: 0.8186 (pp20) cc_final: 0.7434 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 17
  average time/residue: 0.0324
  time to fit residues: 0.6218
Evaluate side-chains
  15 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 36 optimal weight:   10.0000
   chunk 5 optimal weight:    8.9990
   chunk 9 optimal weight:   10.0000
   chunk 23 optimal weight:    8.9990
   chunk 34 optimal weight:    6.9990
   chunk 51 optimal weight:   20.0000
   chunk 50 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:   10.0000
   chunk 21 optimal weight:    3.9990
   chunk 41 optimal weight:    8.9990
   overall best weight:    6.9990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.119086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.107195 restraints weight = 2472.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.108938 restraints weight = 1554.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.110255 restraints weight = 1138.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.111114 restraints weight = 889.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.111143 restraints weight = 748.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5876
moved from start:          0.6440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060   3798  Z= 0.238
  Angle     :  1.028   7.191   5106  Z= 0.553
  Chirality :  0.065   0.238    660
  Planarity :  0.003   0.008    630
  Dihedral  :  9.518  50.987    666
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 24.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.91 %
    Favored  : 84.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.13 (0.28), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.14 (0.21), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.008   0.003   TYR C  39 
 PHE   0.008   0.002   PHE F  94 
 HIS   0.004   0.003   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00557 ( 3786)
  covalent geometry    : angle       1.02883 ( 5094)
  hydrogen bonds       : bond        0.12310 (   49)
  hydrogen bonds       : angle       6.36610 (  147)
  Misc. bond           : bond        0.00597 (    6)
  link_NAG-SER         : bond        0.00029 (    6)
  link_NAG-SER         : angle       0.60934 (   12)

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

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

  704 Ramachandran restraints generated.
    352 Oldfield, 0 Emsley, 352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  704 Ramachandran restraints generated.
    352 Oldfield, 0 Emsley, 352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.024 
Fit side-chains
REVERT: B   20 GLU cc_start: 0.7793 (tp30) cc_final: 0.7339 (pm20)
REVERT: B   23 LYS cc_start: 0.7993 (tmtt) cc_final: 0.7637 (tmtt)
REVERT: B   24 GLN cc_start: 0.7376 (pp30) cc_final: 0.6448 (pp30)
REVERT: B   32 LYS cc_start: 0.4817 (mmmt) cc_final: 0.4565 (mmmt)
REVERT: B   62 GLN cc_start: 0.8582 (mt0) cc_final: 0.8072 (tt0)
REVERT: B   83 GLU cc_start: 0.8321 (pp20) cc_final: 0.7583 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.0634
  time to fit residues: 1.3570
Evaluate side-chains
  17 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 29 optimal weight:    3.9990
   chunk 16 optimal weight:   10.0000
   chunk 13 optimal weight:    9.9990
   chunk 44 optimal weight:    9.9990
   chunk 11 optimal weight:    0.3980
   chunk 6 optimal weight:   30.0000
   chunk 49 optimal weight:    8.9990
   chunk 47 optimal weight:    0.3980
   chunk 25 optimal weight:   10.0000
   chunk 35 optimal weight:   10.0000
   overall best weight:    4.5586
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.125834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.116743 restraints weight = 2765.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.118265 restraints weight = 1766.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.119374 restraints weight = 1290.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.120236 restraints weight = 1005.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.120726 restraints weight = 817.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5907
moved from start:          0.6229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.026   0.499   3798  Z= 0.914
  Angle     :  4.233 111.895   5106  Z= 1.529
  Chirality :  0.080   0.516    660
  Planarity :  0.004   0.021    630
  Dihedral  :  9.928  51.563    666
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 41.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.91 %
    Favored  : 84.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 1.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.28 (0.27), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.26 (0.21), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.032   0.013   TYR E  39 
 PHE   0.005   0.002   PHE B  94 
 HIS   0.000   0.000   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.02606 ( 3786)
  covalent geometry    : angle       4.23755 ( 5094)
  hydrogen bonds       : bond        0.12339 (   49)
  hydrogen bonds       : angle       6.14520 (  147)
  Misc. bond           : bond        0.03872 (    6)
  link_NAG-SER         : bond        0.00077 (    6)
  link_NAG-SER         : angle       0.68301 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 656.05 seconds
wall clock time: 12 minutes 6.99 seconds (726.99 seconds total)