Starting phenix.real_space_refine
on Tue Aug  4 12:28:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9w08_65497/08_2026/9w08_65497.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9w08_65497/08_2026/9w08_65497.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9w08_65497/08_2026/9w08_65497.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9w08_65497/08_2026/9w08_65497.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9w08_65497/08_2026/9w08_65497.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9w08_65497/08_2026/9w08_65497.map"
  }
  resolution = 2.87
  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    1680      2.51       5
     N     462      2.21       5
     O     534      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 2676
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "D"
      Number of atoms: 446
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 446
          Classifications: {'peptide': 64}
          Link IDs: {'TRANS': 63}
  Restraints were copied for chains:
    E, F, G, H, I
  Time building chain proxies: 0.36, per 1000 atoms: 0.13
  Number of scatterers: 2676
  At special positions: 0
  Unit cell: (87.98, 110.39, 35.69, 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     534      8.00
     N     462      7.00
     C    1680      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.11
  Conformation dependent library (CDL) restraints added in 61.3 milliseconds
  

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  660

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 46.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 49 through 57
      removed outlier: 6.849A  pdb=" N   HIS D  50 " --> pdb=" O   VAL F  49 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   GLY F  51 " --> pdb=" O   HIS D  50 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   HIS F  50 " --> pdb=" O   VAL H  49 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   GLY H  51 " --> pdb=" O   HIS F  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 63 through 65
      removed outlier: 6.922A  pdb=" N   VAL D  63 " --> pdb=" O   THR F  64 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   VAL F  63 " --> pdb=" O   THR H  64 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'D' and resid 69 through 82
      removed outlier: 9.297A  pdb=" N   ALA D  69 " --> pdb=" O   VAL F  70 " (cutoff:3.500A)
      removed outlier: 10.333A  pdb=" N   THR F  72 " --> pdb=" O   ALA D  69 " (cutoff:3.500A)
      removed outlier: 9.414A  pdb=" N   VAL D  71 " --> pdb=" O   THR F  72 " (cutoff:3.500A)
      removed outlier: 10.390A  pdb=" N   VAL F  74 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
      removed outlier: 8.607A  pdb=" N   GLY D  73 " --> pdb=" O   VAL F  74 " (cutoff:3.500A)
      removed outlier: 10.125A  pdb=" N   ALA F  76 " --> pdb=" O   GLY D  73 " (cutoff:3.500A)
      removed outlier: 9.138A  pdb=" N   THR D  75 " --> pdb=" O   ALA F  76 " (cutoff:3.500A)
      removed outlier: 10.050A  pdb=" N   ALA F  78 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 8.857A  pdb=" N   VAL D  77 " --> pdb=" O   ALA F  78 " (cutoff:3.500A)
      removed outlier: 10.272A  pdb=" N   LYS F  80 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   GLN D  79 " --> pdb=" O   LYS F  80 " (cutoff:3.500A)
      removed outlier: 7.733A  pdb=" N   VAL F  82 " --> pdb=" O   GLN D  79 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   THR D  81 " --> pdb=" O   VAL F  82 " (cutoff:3.500A)
      removed outlier: 9.304A  pdb=" N   ALA F  69 " --> pdb=" O   VAL H  70 " (cutoff:3.500A)
      removed outlier: 10.342A  pdb=" N   THR H  72 " --> pdb=" O   ALA F  69 " (cutoff:3.500A)
      removed outlier: 9.424A  pdb=" N   VAL F  71 " --> pdb=" O   THR H  72 " (cutoff:3.500A)
      removed outlier: 10.401A  pdb=" N   VAL H  74 " --> pdb=" O   VAL F  71 " (cutoff:3.500A)
      removed outlier: 8.618A  pdb=" N   GLY F  73 " --> pdb=" O   VAL H  74 " (cutoff:3.500A)
      removed outlier: 10.136A  pdb=" N   ALA H  76 " --> pdb=" O   GLY F  73 " (cutoff:3.500A)
      removed outlier: 9.152A  pdb=" N   THR F  75 " --> pdb=" O   ALA H  76 " (cutoff:3.500A)
      removed outlier: 10.063A  pdb=" N   ALA H  78 " --> pdb=" O   THR F  75 " (cutoff:3.500A)
      removed outlier: 8.870A  pdb=" N   VAL F  77 " --> pdb=" O   ALA H  78 " (cutoff:3.500A)
      removed outlier: 10.285A  pdb=" N   LYS H  80 " --> pdb=" O   VAL F  77 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   GLN F  79 " --> pdb=" O   LYS H  80 " (cutoff:3.500A)
      removed outlier: 7.750A  pdb=" N   VAL H  82 " --> pdb=" O   GLN F  79 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   THR F  81 " --> pdb=" O   VAL H  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'D' and resid 86 through 89
      removed outlier: 6.386A  pdb=" N   SER D  87 " --> pdb=" O   ILE F  88 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   SER F  87 " --> pdb=" O   ILE H  88 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'D' and resid 92 through 96
      removed outlier: 6.366A  pdb=" N   GLY D  93 " --> pdb=" O   PHE F  94 " (cutoff:3.500A)
      removed outlier: 7.771A  pdb=" N   LYS F  96 " --> pdb=" O   GLY D  93 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   VAL D  95 " --> pdb=" O   LYS F  96 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   GLY F  93 " --> pdb=" O   PHE H  94 " (cutoff:3.500A)
      removed outlier: 7.764A  pdb=" N   LYS H  96 " --> pdb=" O   GLY F  93 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   VAL F  95 " --> pdb=" O   LYS H  96 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 49 through 57
      removed outlier: 6.842A  pdb=" N   HIS E  50 " --> pdb=" O   VAL G  49 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   GLY G  51 " --> pdb=" O   HIS E  50 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   HIS G  50 " --> pdb=" O   VAL I  49 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   GLY I  51 " --> pdb=" O   HIS G  50 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 63 through 65
      removed outlier: 6.916A  pdb=" N   VAL E  63 " --> pdb=" O   THR G  64 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   VAL G  63 " --> pdb=" O   THR I  64 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 69 through 82
      removed outlier: 9.243A  pdb=" N   ALA E  69 " --> pdb=" O   VAL G  70 " (cutoff:3.500A)
      removed outlier: 10.288A  pdb=" N   THR G  72 " --> pdb=" O   ALA E  69 " (cutoff:3.500A)
      removed outlier: 9.371A  pdb=" N   VAL E  71 " --> pdb=" O   THR G  72 " (cutoff:3.500A)
      removed outlier: 10.364A  pdb=" N   VAL G  74 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
      removed outlier: 8.590A  pdb=" N   GLY E  73 " --> pdb=" O   VAL G  74 " (cutoff:3.500A)
      removed outlier: 10.112A  pdb=" N   ALA G  76 " --> pdb=" O   GLY E  73 " (cutoff:3.500A)
      removed outlier: 9.120A  pdb=" N   THR E  75 " --> pdb=" O   ALA G  76 " (cutoff:3.500A)
      removed outlier: 10.038A  pdb=" N   ALA G  78 " --> pdb=" O   THR E  75 " (cutoff:3.500A)
      removed outlier: 8.845A  pdb=" N   VAL E  77 " --> pdb=" O   ALA G  78 " (cutoff:3.500A)
      removed outlier: 10.262A  pdb=" N   LYS G  80 " --> pdb=" O   VAL E  77 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   GLN E  79 " --> pdb=" O   LYS G  80 " (cutoff:3.500A)
      removed outlier: 7.731A  pdb=" N   VAL G  82 " --> pdb=" O   GLN E  79 " (cutoff:3.500A)
      removed outlier: 6.026A  pdb=" N   THR E  81 " --> pdb=" O   VAL G  82 " (cutoff:3.500A)
      removed outlier: 9.301A  pdb=" N   ALA G  69 " --> pdb=" O   VAL I  70 " (cutoff:3.500A)
      removed outlier: 10.337A  pdb=" N   THR I  72 " --> pdb=" O   ALA G  69 " (cutoff:3.500A)
      removed outlier: 9.421A  pdb=" N   VAL G  71 " --> pdb=" O   THR I  72 " (cutoff:3.500A)
      removed outlier: 10.396A  pdb=" N   VAL I  74 " --> pdb=" O   VAL G  71 " (cutoff:3.500A)
      removed outlier: 8.617A  pdb=" N   GLY G  73 " --> pdb=" O   VAL I  74 " (cutoff:3.500A)
      removed outlier: 10.133A  pdb=" N   ALA I  76 " --> pdb=" O   GLY G  73 " (cutoff:3.500A)
      removed outlier: 9.149A  pdb=" N   THR G  75 " --> pdb=" O   ALA I  76 " (cutoff:3.500A)
      removed outlier: 10.059A  pdb=" N   ALA I  78 " --> pdb=" O   THR G  75 " (cutoff:3.500A)
      removed outlier: 8.867A  pdb=" N   VAL G  77 " --> pdb=" O   ALA I  78 " (cutoff:3.500A)
      removed outlier: 10.280A  pdb=" N   LYS I  80 " --> pdb=" O   VAL G  77 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   GLN G  79 " --> pdb=" O   LYS I  80 " (cutoff:3.500A)
      removed outlier: 7.748A  pdb=" N   VAL I  82 " --> pdb=" O   GLN G  79 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   THR G  81 " --> pdb=" O   VAL I  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'E' and resid 86 through 89
      removed outlier: 6.360A  pdb=" N   SER E  87 " --> pdb=" O   ILE G  88 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   SER G  87 " --> pdb=" O   ILE I  88 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'E' and resid 92 through 96
      removed outlier: 6.350A  pdb=" N   GLY E  93 " --> pdb=" O   PHE G  94 " (cutoff:3.500A)
      removed outlier: 7.763A  pdb=" N   LYS G  96 " --> pdb=" O   GLY E  93 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   VAL E  95 " --> pdb=" O   LYS G  96 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   GLY G  93 " --> pdb=" O   PHE I  94 " (cutoff:3.500A)
      removed outlier: 7.768A  pdb=" N   LYS I  96 " --> pdb=" O   GLY G  93 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   VAL G  95 " --> pdb=" O   LYS I  96 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1

    24 hydrogen bonds defined for protein.
    72 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: 0.35

  Time building geometry restraints manager: 0.15 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 468
        1.29 -     1.35: 420
        1.35 -     1.42: 102
        1.42 -     1.48: 434
        1.48 -     1.54: 1264
  Bond restraints: 2688
  Sorted by residual:
  bond pdb=" CB  VAL G  52 "
       pdb=" CG1 VAL G  52 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.06e+00
  bond pdb=" CB  VAL H  52 "
       pdb=" CG1 VAL H  52 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.05e+00
  bond pdb=" CB  VAL I  52 "
       pdb=" CG1 VAL I  52 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.05e+00
  bond pdb=" CB  VAL F  52 "
       pdb=" CG1 VAL F  52 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.04e+00
  bond pdb=" CB  VAL D  52 "
       pdb=" CG1 VAL D  52 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.04e+00
  ... (remaining 2683 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.58: 2575
        0.58 -     1.15: 698
        1.15 -     1.73: 243
        1.73 -     2.30: 78
        2.30 -     2.88: 42
  Bond angle restraints: 3636
  Sorted by residual:
  angle pdb=" N   SER F  42 "
        pdb=" CA  SER F  42 "
        pdb=" C   SER F  42 "
      ideal   model   delta    sigma   weight residual
     111.96  114.74   -2.78 1.41e+00 5.03e-01 3.90e+00
  angle pdb=" N   SER I  42 "
        pdb=" CA  SER I  42 "
        pdb=" C   SER I  42 "
      ideal   model   delta    sigma   weight residual
     111.96  114.72   -2.76 1.41e+00 5.03e-01 3.84e+00
  angle pdb=" N   SER E  42 "
        pdb=" CA  SER E  42 "
        pdb=" C   SER E  42 "
      ideal   model   delta    sigma   weight residual
     111.96  114.72   -2.76 1.41e+00 5.03e-01 3.83e+00
  angle pdb=" N   SER G  42 "
        pdb=" CA  SER G  42 "
        pdb=" C   SER G  42 "
      ideal   model   delta    sigma   weight residual
     111.96  114.71   -2.75 1.41e+00 5.03e-01 3.79e+00
  angle pdb=" N   SER H  42 "
        pdb=" CA  SER H  42 "
        pdb=" C   SER H  42 "
      ideal   model   delta    sigma   weight residual
     111.96  114.71   -2.75 1.41e+00 5.03e-01 3.79e+00
  ... (remaining 3631 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.42: 1377
       11.42 -    22.84: 129
       22.84 -    34.26: 48
       34.26 -    45.68: 12
       45.68 -    57.10: 12
  Dihedral angle restraints: 1578
    sinusoidal: 534
      harmonic: 1044
  Sorted by residual:
  dihedral pdb=" CA  LYS D  45 "
           pdb=" C   LYS D  45 "
           pdb=" N   GLU D  46 "
           pdb=" CA  GLU D  46 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.95   18.05     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" CA  LYS I  45 "
           pdb=" C   LYS I  45 "
           pdb=" N   GLU I  46 "
           pdb=" CA  GLU I  46 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.95   18.05     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" CA  LYS H  45 "
           pdb=" C   LYS H  45 "
           pdb=" N   GLU H  46 "
           pdb=" CA  GLU H  46 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.96   18.04     0      5.00e+00 4.00e-02 1.30e+01
  ... (remaining 1575 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 133
       0.024 -    0.048: 189
       0.048 -    0.073: 68
       0.073 -    0.097: 48
       0.097 -    0.121: 42
  Chirality restraints: 480
  Sorted by residual:
  chirality pdb=" CA  VAL D  82 "
            pdb=" N   VAL D  82 "
            pdb=" C   VAL D  82 "
            pdb=" CB  VAL D  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.65e-01
  chirality pdb=" CA  VAL E  82 "
            pdb=" N   VAL E  82 "
            pdb=" C   VAL E  82 "
            pdb=" CB  VAL E  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.55e-01
  chirality pdb=" CA  VAL G  82 "
            pdb=" N   VAL G  82 "
            pdb=" C   VAL G  82 "
            pdb=" CB  VAL G  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.51e-01
  ... (remaining 477 not shown)

  Planarity restraints: 450
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E  39 "    0.005 2.00e-02 2.50e+03   4.04e-03 3.27e-01
        pdb=" CG  TYR E  39 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD1 TYR E  39 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR E  39 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR E  39 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR E  39 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR E  39 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR E  39 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR H  39 "   -0.005 2.00e-02 2.50e+03   4.03e-03 3.25e-01
        pdb=" CG  TYR H  39 "    0.009 2.00e-02 2.50e+03
        pdb=" CD1 TYR H  39 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR H  39 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR H  39 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR H  39 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR H  39 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR H  39 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  39 "    0.005 2.00e-02 2.50e+03   3.93e-03 3.10e-01
        pdb=" CG  TYR D  39 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  39 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  39 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  39 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  39 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  39 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR D  39 "    0.001 2.00e-02 2.50e+03
  ... (remaining 447 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 620
        2.80 -     3.32: 2143
        3.32 -     3.85: 4183
        3.85 -     4.37: 4890
        4.37 -     4.90: 9162
  Nonbonded interactions: 20998
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS H  45 "
            pdb=" OE2 GLU I  83 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" OE2 GLU F  83 "
            pdb=" NZ  LYS I  45 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" NZ  LYS F  45 "
            pdb=" OE2 GLU G  83 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" NZ  LYS D  45 "
            pdb=" OE2 GLU E  83 "
     model   vdw
     2.281 3.120
  nonbonded pdb=" OE2 GLU D  83 "
            pdb=" NZ  LYS G  45 "
     model   vdw
     2.303 3.120
  ... (remaining 20993 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 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.450
  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:          0.050
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     3.860
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8834
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      :  0.008   0.034   2688  Z= 0.356
  Angle     :  0.690   2.878   3636  Z= 0.418
  Chirality :  0.053   0.121    480
  Planarity :  0.002   0.005    450
  Dihedral  : 12.839  57.103    918
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  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 are not related in a simple way.
  whole: -5.40 (0.23), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.11 (0.18), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.003   TYR E  39 
 PHE   0.003   0.002   PHE G  94 
 HIS   0.005   0.003   HIS I  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00791 /  0.36 ( 2688)
  covalent geometry    : angle       0.68976 /  0.42 ( 3636)
  hydrogen bonds       : bond        0.22702 / 12.91 (   24)
  hydrogen bonds       : angle       6.82608 /  4.50 (   72)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.066 
Fit side-chains
REVERT: E   87 SER cc_start: 0.8991 (t) cc_final: 0.8619 (m)
REVERT: E   96 LYS cc_start: 0.8298 (tttp) cc_final: 0.7977 (ttmt)
REVERT: F   43 LYS cc_start: 0.8170 (mtpt) cc_final: 0.7847 (mtpt)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.6759
  time to fit residues: 22.7043
Evaluate side-chains
  23 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  50 HIS
D  62 GLN
D  65 ASN
D  99 GLN
E  50 HIS
E  62 GLN
E  65 ASN
E  99 GLN
F  50 HIS
F  62 GLN
F  65 ASN
F  99 GLN
G  50 HIS
G  62 GLN
G  65 ASN
G  99 GLN
H  50 HIS
H  62 GLN
H  65 ASN
H  99 GLN
I  50 HIS
I  62 GLN
I  65 ASN
I  99 GLN

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.150822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.115551 restraints weight = 2801.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3675 rms_B_bonded: 2.55
r_work: 0.3560 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3437 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8887
moved from start:          0.1548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2688  Z= 0.129
  Angle     :  0.481   3.013   3636  Z= 0.284
  Chirality :  0.050   0.128    480
  Planarity :  0.001   0.004    450
  Dihedral  :  5.815  18.012    384
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  9.42 %
    Favored  : 90.22 %
  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 are not related in a simple way.
  whole: -5.04 (0.25), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.83 (0.19), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR D  39 
 PHE   0.002   0.001   PHE G  94 
 HIS   0.003   0.002   HIS D  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.13 ( 2688)
  covalent geometry    : angle       0.48101 /  0.28 ( 3636)
  hydrogen bonds       : bond        0.02591 /  1.48 (   24)
  hydrogen bonds       : angle       3.94590 /  2.44 (   72)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 26
  time to evaluate  : 0.099 
Fit side-chains
REVERT: D   58 LYS cc_start: 0.8492 (ptpp) cc_final: 0.8239 (pttm)
REVERT: E   87 SER cc_start: 0.9067 (t) cc_final: 0.8707 (m)
REVERT: I   43 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7924 (mtmt)
  outliers start: 1
  outliers final: 0
  residues processed: 26
  average time/residue: 0.6782
  time to fit residues: 18.0017
Evaluate side-chains
  26 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   43 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 20 optimal weight:    8.9990
   chunk 19 optimal weight:    7.9990
   chunk 2 optimal weight:    8.9990
   chunk 0 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 10 optimal weight:    7.9990
   chunk 17 optimal weight:    5.9990
   chunk 12 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   overall best weight:    3.1186

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.145886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.109661 restraints weight = 2768.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 2.53
r_work: 0.3473 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3350 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8926
moved from start:          0.1584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.025   2688  Z= 0.229
  Angle     :  0.557   2.835   3636  Z= 0.331
  Chirality :  0.051   0.129    480
  Planarity :  0.002   0.006    450
  Dihedral  :  6.239  18.805    384
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 10.14 %
    Favored  : 86.96 %
  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 are not related in a simple way.
  whole: -4.90 (0.25), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.72 (0.19), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.002   TYR F  39 
 PHE   0.003   0.001   PHE D  94 
 HIS   0.002   0.001   HIS E  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00511 /  0.23 ( 2688)
  covalent geometry    : angle       0.55713 /  0.33 ( 3636)
  hydrogen bonds       : bond        0.03225 /  1.81 (   24)
  hydrogen bonds       : angle       4.03239 /  2.49 (   72)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 26
  time to evaluate  : 0.058 
Fit side-chains
   revert: symmetry clash
REVERT: F   43 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7894 (mtmt)
  outliers start: 8
  outliers final: 3
  residues processed: 31
  average time/residue: 0.5218
  time to fit residues: 16.5710
Evaluate side-chains
  29 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 25
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   43 LYS
Chi-restraints excluded: chain I residue   38 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 29 optimal weight:    7.9990
   chunk 11 optimal weight:    5.9990
   chunk 7 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 18 optimal weight:    7.9990
   chunk 6 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   overall best weight:    1.3584

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.152559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.116827 restraints weight = 2696.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 2.54
r_work: 0.3570 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3442 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8897
moved from start:          0.1845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   2688  Z= 0.111
  Angle     :  0.444   2.423   3636  Z= 0.264
  Chirality :  0.050   0.130    480
  Planarity :  0.001   0.004    450
  Dihedral  :  5.679  18.125    384
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 10.87 %
    Favored  : 86.59 %
  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 are not related in a simple way.
  whole: -4.63 (0.28), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.52 (0.21), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR F  39 
 PHE   0.002   0.001   PHE G  94 
 HIS   0.002   0.001   HIS E  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.11 ( 2688)
  covalent geometry    : angle       0.44364 /  0.26 ( 3636)
  hydrogen bonds       : bond        0.02209 /  1.25 (   24)
  hydrogen bonds       : angle       4.07936 /  2.55 (   72)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 27
  time to evaluate  : 0.066 
Fit side-chains
   revert: symmetry clash
REVERT: E   58 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8188 (ptmt)
  outliers start: 7
  outliers final: 3
  residues processed: 29
  average time/residue: 0.4779
  time to fit residues: 14.1859
Evaluate side-chains
  31 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 27
  time to evaluate  : 0.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   58 LYS
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain G residue   38 LEU
Chi-restraints excluded: chain I residue   38 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 21 optimal weight:   10.0000
   chunk 6 optimal weight:    6.9990
   chunk 13 optimal weight:    8.9990
   chunk 30 optimal weight:    7.9990
   chunk 19 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:   10.0000
   chunk 4 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 35 optimal weight:    0.8980
   overall best weight:    2.5788

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.146403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.110221 restraints weight = 2728.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 2.53
r_work: 0.3507 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3380 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8921
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   2688  Z= 0.192
  Angle     :  0.508   2.626   3636  Z= 0.302
  Chirality :  0.050   0.127    480
  Planarity :  0.002   0.006    450
  Dihedral  :  6.035  18.575    384
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 11.59 %
    Favored  : 85.87 %
  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 are not related in a simple way.
  whole: -4.56 (0.28), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.47 (0.21), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.002   TYR G  39 
 PHE   0.003   0.001   PHE D  94 
 HIS   0.002   0.001   HIS G  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00429 /  0.19 ( 2688)
  covalent geometry    : angle       0.50767 /  0.30 ( 3636)
  hydrogen bonds       : bond        0.02645 /  1.47 (   24)
  hydrogen bonds       : angle       4.26073 /  2.70 (   72)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 28
  time to evaluate  : 0.075 
Fit side-chains
   revert: symmetry clash
  outliers start: 7
  outliers final: 3
  residues processed: 31
  average time/residue: 0.5707
  time to fit residues: 18.0785
Evaluate side-chains
  31 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 28
  time to evaluate  : 0.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain G residue   38 LEU
Chi-restraints excluded: chain I residue   38 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 35 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9980
   chunk 15 optimal weight:    9.9990
   chunk 31 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9980
   chunk 14 optimal weight:    6.9990
   chunk 28 optimal weight:    0.0870
   chunk 0 optimal weight:    6.9990
   chunk 8 optimal weight:    7.9990
   chunk 2 optimal weight:    0.7980
   overall best weight:    1.7760

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.149415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.113471 restraints weight = 2724.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 2.54
r_work: 0.3549 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3421 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8901
moved from start:          0.1917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   2688  Z= 0.137
  Angle     :  0.461   2.660   3636  Z= 0.275
  Chirality :  0.050   0.128    480
  Planarity :  0.001   0.005    450
  Dihedral  :  5.766  18.439    384
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 2.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 12.68 %
    Favored  : 85.51 %
  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 are not related in a simple way.
  whole: -4.45 (0.29), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.39 (0.22), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.002   TYR G  39 
 PHE   0.003   0.001   PHE G  94 
 HIS   0.002   0.001   HIS G  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.14 ( 2688)
  covalent geometry    : angle       0.46107 /  0.27 ( 3636)
  hydrogen bonds       : bond        0.02287 /  1.29 (   24)
  hydrogen bonds       : angle       4.32614 /  2.74 (   72)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 26
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 2
  residues processed: 28
  average time/residue: 0.5110
  time to fit residues: 14.6727
Evaluate side-chains
  26 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain I residue   38 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9990
   chunk 28 optimal weight:    8.9990
   chunk 19 optimal weight:    8.9990
   chunk 22 optimal weight:    0.8980
   chunk 34 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0010
   chunk 2 optimal weight:    7.9990
   chunk 14 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    2.1792

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.146854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.110770 restraints weight = 2717.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 2.54
r_work: 0.3528 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3398 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8916
moved from start:          0.1915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.020   2688  Z= 0.165
  Angle     :  0.485   2.966   3636  Z= 0.288
  Chirality :  0.050   0.128    480
  Planarity :  0.001   0.006    450
  Dihedral  :  5.908  18.411    384
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 2.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 12.32 %
    Favored  : 85.51 %
  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 are not related in a simple way.
  whole: -4.42 (0.29), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.36 (0.22), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.008   0.002   TYR F  39 
 PHE   0.003   0.001   PHE G  94 
 HIS   0.003   0.001   HIS G  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00367 /  0.17 ( 2688)
  covalent geometry    : angle       0.48454 /  0.29 ( 3636)
  hydrogen bonds       : bond        0.02441 /  1.35 (   24)
  hydrogen bonds       : angle       4.40312 /  2.79 (   72)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 27
  time to evaluate  : 0.058 
Fit side-chains
   revert: symmetry clash
REVERT: I   43 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.7993 (mtmt)
  outliers start: 6
  outliers final: 3
  residues processed: 30
  average time/residue: 0.4002
  time to fit residues: 12.2960
Evaluate side-chains
  29 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 25
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain G residue   38 LEU
Chi-restraints excluded: chain I residue   38 LEU
Chi-restraints excluded: chain I residue   43 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 2 optimal weight:    7.9990
   chunk 5 optimal weight:    0.0040
   chunk 14 optimal weight:    1.9990
   chunk 31 optimal weight:    7.9990
   chunk 0 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 13 optimal weight:    7.9990
   chunk 17 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 20 optimal weight:    8.9990
   chunk 7 optimal weight:    0.2980
   overall best weight:    1.6598

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.150081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.114110 restraints weight = 2738.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 2.56
r_work: 0.3555 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3428 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8899
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   2688  Z= 0.130
  Angle     :  0.452   2.693   3636  Z= 0.269
  Chirality :  0.049   0.129    480
  Planarity :  0.001   0.005    450
  Dihedral  :  5.697  18.225    384
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 13.41 %
    Favored  : 85.14 %
  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 are not related in a simple way.
  whole: -4.38 (0.30), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.33 (0.23), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR F  39 
 PHE   0.002   0.001   PHE G  94 
 HIS   0.002   0.001   HIS E  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.13 ( 2688)
  covalent geometry    : angle       0.45170 /  0.27 ( 3636)
  hydrogen bonds       : bond        0.02211 /  1.23 (   24)
  hydrogen bonds       : angle       4.38139 /  2.79 (   72)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.087 
Fit side-chains
   revert: symmetry clash
REVERT: I   43 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7867 (mtmt)
  outliers start: 4
  outliers final: 1
  residues processed: 26
  average time/residue: 0.5340
  time to fit residues: 14.2153
Evaluate side-chains
  26 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   38 LEU
Chi-restraints excluded: chain I residue   43 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 20 optimal weight:    7.9990
   chunk 0 optimal weight:    6.9990
   chunk 29 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 16 optimal weight:   10.0000
   chunk 8 optimal weight:    0.7980
   chunk 6 optimal weight:    6.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    2.1184

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.147539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.112235 restraints weight = 2754.036|
|-----------------------------------------------------------------------------|
r_work (start): 0.3663 rms_B_bonded: 2.45
r_work: 0.3534 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3408 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8943
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.019   2688  Z= 0.161
  Angle     :  0.481   2.698   3636  Z= 0.286
  Chirality :  0.050   0.128    480
  Planarity :  0.001   0.006    450
  Dihedral  :  5.881  18.330    384
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 2.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 14.13 %
    Favored  : 84.78 %
  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 are not related in a simple way.
  whole: -4.39 (0.30), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.34 (0.23), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.002   TYR F  39 
 PHE   0.003   0.001   PHE G  94 
 HIS   0.003   0.001   HIS G  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00358 /  0.16 ( 2688)
  covalent geometry    : angle       0.48148 /  0.29 ( 3636)
  hydrogen bonds       : bond        0.02405 /  1.33 (   24)
  hydrogen bonds       : angle       4.43977 /  2.84 (   72)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
REVERT: I   43 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.7953 (mtmt)
  outliers start: 3
  outliers final: 1
  residues processed: 25
  average time/residue: 0.5867
  time to fit residues: 15.0256
Evaluate side-chains
  26 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   38 LEU
Chi-restraints excluded: chain I residue   43 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 10 optimal weight:    8.9990
   chunk 29 optimal weight:    6.9990
   chunk 20 optimal weight:    5.9990
   chunk 13 optimal weight:    8.9990
   chunk 4 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    2.7990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.145777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.109702 restraints weight = 2770.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 2.55
r_work: 0.3506 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3380 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8921
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.024   2688  Z= 0.207
  Angle     :  0.533   3.245   3636  Z= 0.316
  Chirality :  0.050   0.125    480
  Planarity :  0.002   0.006    450
  Dihedral  :  6.100  18.979    384
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 13.77 %
    Favored  : 85.14 %
  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 are not related in a simple way.
  whole: -4.44 (0.29), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.38 (0.22), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.002   TYR G  39 
 PHE   0.004   0.002   PHE G  94 
 HIS   0.003   0.002   HIS E  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00464 /  0.21 ( 2688)
  covalent geometry    : angle       0.53325 /  0.32 ( 3636)
  hydrogen bonds       : bond        0.02680 /  1.48 (   24)
  hydrogen bonds       : angle       4.48486 /  2.87 (   72)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
REVERT: I   43 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8020 (mtmt)
  outliers start: 3
  outliers final: 2
  residues processed: 26
  average time/residue: 0.6098
  time to fit residues: 16.2019
Evaluate side-chains
  28 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 0.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain I residue   38 LEU
Chi-restraints excluded: chain I residue   43 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 7 optimal weight:    0.0170
   chunk 26 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 21 optimal weight:    9.9990
   chunk 27 optimal weight:    3.9990
   chunk 10 optimal weight:    7.9990
   chunk 18 optimal weight:    6.9990
   chunk 11 optimal weight:    9.9990
   overall best weight:    3.0026

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.145812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.109726 restraints weight = 2783.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 2.55
r_work: 0.3498 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3371 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8927
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.025   2688  Z= 0.221
  Angle     :  0.550   3.429   3636  Z= 0.325
  Chirality :  0.051   0.125    480
  Planarity :  0.002   0.007    450
  Dihedral  :  6.194  19.217    384
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 13.77 %
    Favored  : 85.14 %
  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 are not related in a simple way.
  whole: -4.44 (0.29), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.38 (0.22), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.002   TYR G  39 
 PHE   0.004   0.002   PHE G  94 
 HIS   0.003   0.002   HIS G  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00494 /  0.22 ( 2688)
  covalent geometry    : angle       0.54961 /  0.32 ( 3636)
  hydrogen bonds       : bond        0.02740 /  1.51 (   24)
  hydrogen bonds       : angle       4.52413 /  2.91 (   72)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 971.05 seconds
wall clock time: 17 minutes 17.58 seconds (1037.58 seconds total)