Starting phenix.real_space_refine
on Tue Feb  3 12:56:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jc3_61355/02_2026/9jc3_61355.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jc3_61355/02_2026/9jc3_61355.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.39
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jc3_61355/02_2026/9jc3_61355.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jc3_61355/02_2026/9jc3_61355.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jc3_61355/02_2026/9jc3_61355.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jc3_61355/02_2026/9jc3_61355.map"
  }
  resolution = 2.39
  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=   0.004
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    1632      2.51       5
     N     444      2.21       5
     O     534      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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2610
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "D"
      Number of atoms: 435
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 435
          Classifications: {'peptide': 62}
          Link IDs: {'TRANS': 61}
  Restraints were copied for chains:
    F, E, G, H, I
  Time building chain proxies: 0.43, per 1000 atoms: 0.16
  Number of scatterers: 2610
  At special positions: 0
  Unit cell: (98.77, 92.13, 32.37, 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     444      7.00
     C    1632      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: 0.19
  Conformation dependent library (CDL) restraints added in 105.4 milliseconds
  

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  648

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 61.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 39 through 40
      removed outlier: 6.575A  pdb=" N   TYR E  39 " --> pdb=" O   VAL H  40 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 43 through 44
      removed outlier: 6.575A  pdb=" N   LYS D  43 " --> pdb=" O   THR H  44 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 48 through 66
      removed outlier: 6.796A  pdb=" N   VAL D  49 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   HIS H  50 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   ASP D  51 " --> pdb=" O   HIS H  50 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   THR D  59 " --> pdb=" O   LYS H  58 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   LYS H  60 " --> pdb=" O   THR D  59 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   GLU D  61 " --> pdb=" O   LYS H  60 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   GLN H  62 " --> pdb=" O   GLU D  61 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   VAL D  63 " --> pdb=" O   GLN H  62 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   THR H  64 " --> pdb=" O   VAL D  63 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   ASN D  65 " --> pdb=" O   THR H  64 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   VAL H  66 " --> pdb=" O   ASN D  65 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   VAL H  49 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   HIS E  50 " --> pdb=" O   VAL H  49 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   ASP H  51 " --> pdb=" O   HIS E  50 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   THR H  59 " --> pdb=" O   LYS E  58 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   LYS E  60 " --> pdb=" O   THR H  59 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   GLU H  61 " --> pdb=" O   LYS E  60 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   GLN E  62 " --> pdb=" O   GLU H  61 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   VAL H  63 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   THR E  64 " --> pdb=" O   VAL H  63 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   ASN H  65 " --> pdb=" O   THR E  64 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   VAL E  66 " --> pdb=" O   ASN H  65 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 69 through 71
      removed outlier: 6.620A  pdb=" N   VAL E  70 " --> pdb=" O   VAL H  71 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 75 through 83
      removed outlier: 6.816A  pdb=" N   THR D  81 " --> pdb=" O   LYS H  80 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   VAL H  82 " --> pdb=" O   THR D  81 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   GLU D  83 " --> pdb=" O   VAL H  82 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   ALA E  76 " --> pdb=" O   VAL H  77 " (cutoff:3.500A)
      removed outlier: 8.210A  pdb=" N   GLN H  79 " --> pdb=" O   ALA E  76 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   ALA E  78 " --> pdb=" O   GLN H  79 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   THR H  81 " --> pdb=" O   ALA E  78 " (cutoff:3.500A)
      removed outlier: 7.502A  pdb=" N   LYS E  80 " --> pdb=" O   THR H  81 " (cutoff:3.500A)
      removed outlier: 9.913A  pdb=" N   GLU H  83 " --> pdb=" O   LYS E  80 " (cutoff:3.500A)
      removed outlier: 8.655A  pdb=" N   VAL E  82 " --> pdb=" O   GLU H  83 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 88 through 96
      removed outlier: 7.972A  pdb=" N   ALA D  89 " --> pdb=" O   ALA H  90 " (cutoff:3.500A)
      removed outlier: 7.779A  pdb=" N   THR H  92 " --> pdb=" O   ALA D  89 " (cutoff:3.500A)
      removed outlier: 9.408A  pdb=" N   ALA D  91 " --> pdb=" O   THR H  92 " (cutoff:3.500A)
      removed outlier: 8.736A  pdb=" N   PHE H  94 " --> pdb=" O   ALA D  91 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   GLY D  93 " --> pdb=" O   PHE H  94 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   LYS H  96 " --> pdb=" O   GLY D  93 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   VAL D  95 " --> pdb=" O   LYS H  96 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   ALA H  91 " --> pdb=" O   ALA E  90 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   THR E  92 " --> pdb=" O   ALA H  91 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   GLY H  93 " --> pdb=" O   THR E  92 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 39 through 40
      removed outlier: 6.522A  pdb=" N   TYR G  39 " --> pdb=" O   VAL I  40 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 43 through 44
      removed outlier: 6.634A  pdb=" N   LYS F  43 " --> pdb=" O   THR I  44 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 48 through 66
      removed outlier: 9.041A  pdb=" N   VAL F  49 " --> pdb=" O   HIS I  50 " (cutoff:3.500A)
      removed outlier: 9.344A  pdb=" N   VAL I  52 " --> pdb=" O   VAL F  49 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   ASP F  51 " --> pdb=" O   VAL I  52 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   THR I  54 " --> pdb=" O   ASP F  51 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   THR F  53 " --> pdb=" O   THR I  54 " (cutoff:3.500A)
      removed outlier: 7.860A  pdb=" N   ALA I  56 " --> pdb=" O   THR F  53 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   VAL F  55 " --> pdb=" O   ALA I  56 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   LYS I  58 " --> pdb=" O   VAL F  55 " (cutoff:3.500A)
      removed outlier: 8.316A  pdb=" N   GLU F  57 " --> pdb=" O   LYS I  58 " (cutoff:3.500A)
      removed outlier: 7.782A  pdb=" N   LYS I  60 " --> pdb=" O   GLU F  57 " (cutoff:3.500A)
      removed outlier: 8.833A  pdb=" N   THR F  59 " --> pdb=" O   LYS I  60 " (cutoff:3.500A)
      removed outlier: 10.041A  pdb=" N   GLN I  62 " --> pdb=" O   THR F  59 " (cutoff:3.500A)
      removed outlier: 8.661A  pdb=" N   GLU F  61 " --> pdb=" O   GLN I  62 " (cutoff:3.500A)
      removed outlier: 10.077A  pdb=" N   THR I  64 " --> pdb=" O   GLU F  61 " (cutoff:3.500A)
      removed outlier: 8.835A  pdb=" N   VAL F  63 " --> pdb=" O   THR I  64 " (cutoff:3.500A)
      removed outlier: 10.031A  pdb=" N   VAL I  66 " --> pdb=" O   VAL F  63 " (cutoff:3.500A)
      removed outlier: 9.086A  pdb=" N   ASN F  65 " --> pdb=" O   VAL I  66 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   VAL I  49 " --> pdb=" O   VAL G  48 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   HIS G  50 " --> pdb=" O   VAL I  49 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ASP I  51 " --> pdb=" O   HIS G  50 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   THR I  59 " --> pdb=" O   LYS G  58 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   LYS G  60 " --> pdb=" O   THR I  59 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   GLU I  61 " --> pdb=" O   LYS G  60 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   GLN G  62 " --> pdb=" O   GLU I  61 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   VAL I  63 " --> pdb=" O   GLN G  62 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   THR G  64 " --> pdb=" O   VAL I  63 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   ASN I  65 " --> pdb=" O   THR G  64 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   VAL G  66 " --> pdb=" O   ASN I  65 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 69 through 71
      removed outlier: 6.620A  pdb=" N   VAL G  70 " --> pdb=" O   VAL I  71 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 75 through 83
      removed outlier: 6.949A  pdb=" N   THR F  81 " --> pdb=" O   LYS I  80 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   VAL I  82 " --> pdb=" O   THR F  81 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   GLU F  83 " --> pdb=" O   VAL I  82 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   ALA G  76 " --> pdb=" O   VAL I  77 " (cutoff:3.500A)
      removed outlier: 8.182A  pdb=" N   GLN I  79 " --> pdb=" O   ALA G  76 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   ALA G  78 " --> pdb=" O   GLN I  79 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   THR I  81 " --> pdb=" O   ALA G  78 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   LYS G  80 " --> pdb=" O   THR I  81 " (cutoff:3.500A)
      removed outlier: 9.821A  pdb=" N   GLU I  83 " --> pdb=" O   LYS G  80 " (cutoff:3.500A)
      removed outlier: 8.541A  pdb=" N   VAL G  82 " --> pdb=" O   GLU I  83 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 88 through 96
      removed outlier: 8.052A  pdb=" N   ALA F  89 " --> pdb=" O   ALA I  90 " (cutoff:3.500A)
      removed outlier: 7.836A  pdb=" N   THR I  92 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
      removed outlier: 9.472A  pdb=" N   ALA F  91 " --> pdb=" O   THR I  92 " (cutoff:3.500A)
      removed outlier: 8.802A  pdb=" N   PHE I  94 " --> pdb=" O   ALA F  91 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   GLY F  93 " --> pdb=" O   PHE I  94 " (cutoff:3.500A)
      removed outlier: 7.873A  pdb=" N   LYS I  96 " --> pdb=" O   GLY F  93 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   VAL F  95 " --> pdb=" O   LYS I  96 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   ALA I  91 " --> pdb=" O   ALA G  90 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   THR G  92 " --> pdb=" O   ALA I  91 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   GLY I  93 " --> pdb=" O   THR G  92 " (cutoff:3.500A)

    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: 0.33

  Time building geometry restraints manager: 0.27 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: 462
        1.29 -     1.35: 396
        1.35 -     1.41: 108
        1.41 -     1.48: 426
        1.48 -     1.54: 1230
  Bond restraints: 2622
  Sorted by residual:
  bond pdb=" CG  GLN E  79 "
       pdb=" CD  GLN E  79 "
    ideal  model  delta    sigma   weight residual
    1.516  1.495  0.021 2.50e-02 1.60e+03 6.80e-01
  bond pdb=" CG  GLN F  79 "
       pdb=" CD  GLN F  79 "
    ideal  model  delta    sigma   weight residual
    1.516  1.496  0.020 2.50e-02 1.60e+03 6.67e-01
  bond pdb=" CG  GLN G  79 "
       pdb=" CD  GLN G  79 "
    ideal  model  delta    sigma   weight residual
    1.516  1.496  0.020 2.50e-02 1.60e+03 6.66e-01
  bond pdb=" CG  GLN I  79 "
       pdb=" CD  GLN I  79 "
    ideal  model  delta    sigma   weight residual
    1.516  1.496  0.020 2.50e-02 1.60e+03 6.65e-01
  bond pdb=" CG  GLN D  79 "
       pdb=" CD  GLN D  79 "
    ideal  model  delta    sigma   weight residual
    1.516  1.496  0.020 2.50e-02 1.60e+03 6.49e-01
  ... (remaining 2617 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.17: 3311
        1.17 -     2.34: 199
        2.34 -     3.52: 24
        3.52 -     4.69: 12
        4.69 -     5.86: 6
  Bond angle restraints: 3552
  Sorted by residual:
  angle pdb=" C   VAL G  49 "
        pdb=" N   HIS G  50 "
        pdb=" CA  HIS G  50 "
      ideal   model   delta    sigma   weight residual
     121.75  117.74    4.01 1.73e+00 3.34e-01 5.38e+00
  angle pdb=" C   VAL E  49 "
        pdb=" N   HIS E  50 "
        pdb=" CA  HIS E  50 "
      ideal   model   delta    sigma   weight residual
     121.75  117.75    4.00 1.73e+00 3.34e-01 5.35e+00
  angle pdb=" C   VAL D  49 "
        pdb=" N   HIS D  50 "
        pdb=" CA  HIS D  50 "
      ideal   model   delta    sigma   weight residual
     121.75  117.75    4.00 1.73e+00 3.34e-01 5.34e+00
  angle pdb=" C   VAL I  49 "
        pdb=" N   HIS I  50 "
        pdb=" CA  HIS I  50 "
      ideal   model   delta    sigma   weight residual
     121.75  117.77    3.98 1.73e+00 3.34e-01 5.28e+00
  angle pdb=" C   VAL H  49 "
        pdb=" N   HIS H  50 "
        pdb=" CA  HIS H  50 "
      ideal   model   delta    sigma   weight residual
     121.75  117.78    3.97 1.73e+00 3.34e-01 5.27e+00
  ... (remaining 3547 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     7.00: 1194
        7.00 -    14.00: 186
       14.00 -    21.00: 84
       21.00 -    27.99: 30
       27.99 -    34.99: 48
  Dihedral angle restraints: 1542
    sinusoidal: 522
      harmonic: 1020
  Sorted by residual:
  dihedral pdb=" CA  THR D  59 "
           pdb=" C   THR D  59 "
           pdb=" N   LYS D  60 "
           pdb=" CA  LYS D  60 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  166.40   13.60     0      5.00e+00 4.00e-02 7.39e+00
  dihedral pdb=" CA  THR E  59 "
           pdb=" C   THR E  59 "
           pdb=" N   LYS E  60 "
           pdb=" CA  LYS E  60 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  166.43   13.57     0      5.00e+00 4.00e-02 7.37e+00
  dihedral pdb=" CA  THR H  59 "
           pdb=" C   THR H  59 "
           pdb=" N   LYS H  60 "
           pdb=" CA  LYS H  60 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  166.45   13.55     0      5.00e+00 4.00e-02 7.35e+00
  ... (remaining 1539 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 206
       0.033 -    0.065: 165
       0.065 -    0.098: 48
       0.098 -    0.130: 43
       0.130 -    0.163: 12
  Chirality restraints: 474
  Sorted by residual:
  chirality pdb=" CA  VAL E  49 "
            pdb=" N   VAL E  49 "
            pdb=" C   VAL E  49 "
            pdb=" CB  VAL E  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.62e-01
  chirality pdb=" CA  VAL D  49 "
            pdb=" N   VAL D  49 "
            pdb=" C   VAL D  49 "
            pdb=" CB  VAL D  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.45e-01
  chirality pdb=" CA  VAL G  49 "
            pdb=" N   VAL G  49 "
            pdb=" C   VAL G  49 "
            pdb=" CB  VAL G  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.43e-01
  ... (remaining 471 not shown)

  Planarity restraints: 438
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS G  50 "   -0.007 2.00e-02 2.50e+03   6.60e-03 6.54e-01
        pdb=" CG  HIS G  50 "    0.014 2.00e-02 2.50e+03
        pdb=" ND1 HIS G  50 "   -0.000 2.00e-02 2.50e+03
        pdb=" CD2 HIS G  50 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 HIS G  50 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE2 HIS G  50 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS I  50 "   -0.007 2.00e-02 2.50e+03   6.57e-03 6.47e-01
        pdb=" CG  HIS I  50 "    0.014 2.00e-02 2.50e+03
        pdb=" ND1 HIS I  50 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 HIS I  50 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 HIS I  50 "   -0.004 2.00e-02 2.50e+03
        pdb=" NE2 HIS I  50 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS F  50 "   -0.007 2.00e-02 2.50e+03   6.53e-03 6.39e-01
        pdb=" CG  HIS F  50 "    0.014 2.00e-02 2.50e+03
        pdb=" ND1 HIS F  50 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 HIS F  50 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 HIS F  50 "   -0.004 2.00e-02 2.50e+03
        pdb=" NE2 HIS F  50 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 435 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 589
        2.80 -     3.33: 2218
        3.33 -     3.85: 4207
        3.85 -     4.38: 4416
        4.38 -     4.90: 8898
  Nonbonded interactions: 20328
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS G  80 "
            pdb=" OE1 GLU I  46 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" OE1 GLU D  46 "
            pdb=" NZ  LYS H  80 "
     model   vdw
     2.281 3.120
  nonbonded pdb=" NZ  LYS E  80 "
            pdb=" OE1 GLU H  46 "
     model   vdw
     2.349 3.120
  nonbonded pdb=" ND2 ASN D  65 "
            pdb=" O   GLY D  68 "
     model   vdw
     2.382 3.120
  nonbonded pdb=" ND2 ASN H  65 "
            pdb=" O   GLY H  68 "
     model   vdw
     2.382 3.120
  ... (remaining 20323 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 'F'
  selection = chain 'E'
  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:             1.540
  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:                     4.230
  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:6.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
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      :  0.006   0.025   2622  Z= 0.271
  Angle     :  0.686   5.860   3552  Z= 0.381
  Chirality :  0.057   0.163    474
  Planarity :  0.002   0.008    438
  Dihedral  : 11.594  34.991    894
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.06 %
    Favored  : 90.94 %
  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: -3.48 (0.30), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.64 (0.23), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.002   TYR E  39 
 PHE   0.003   0.001   PHE D  94 
 HIS   0.006   0.004   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00607 ( 2622)
  covalent geometry    : angle       0.68586 ( 3552)
  hydrogen bonds       : bond        0.11427 (   49)
  hydrogen bonds       : angle       7.21293 (  147)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.099 
Fit side-chains
REVERT: E   58 LYS cc_start: 0.8353 (mttt) cc_final: 0.6408 (pptt)
REVERT: G   58 LYS cc_start: 0.8320 (mttt) cc_final: 0.6468 (pptt)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.4260
  time to fit residues: 20.9362
Evaluate side-chains
  31 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    8.9990
   chunk 22 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   overall best weight:    3.3388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4714 r_free = 0.4714 target = 0.191540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4609 r_free = 0.4609 target = 0.176907 restraints weight = 3171.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.4613 rms_B_bonded: 2.38
r_work: 0.4546 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.4453 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.4453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.1202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.020   2622  Z= 0.207
  Angle     :  0.663   8.477   3552  Z= 0.340
  Chirality :  0.055   0.156    474
  Planarity :  0.002   0.007    438
  Dihedral  :  5.148  13.835    372
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.78 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 20.29 %
    Favored  : 77.90 %
  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: -2.91 (0.33), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.21 (0.25), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.002   TYR E  39 
 PHE   0.003   0.001   PHE I  94 
 HIS   0.007   0.003   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 ( 2622)
  covalent geometry    : angle       0.66323 ( 3552)
  hydrogen bonds       : bond        0.02345 (   49)
  hydrogen bonds       : angle       5.35951 (  147)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.101 
Fit side-chains
  outliers start: 5
  outliers final: 5
  residues processed: 37
  average time/residue: 0.4429
  time to fit residues: 16.8872
Evaluate side-chains
  33 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 28
  time to evaluate  : 0.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain G residue   46 GLU
Chi-restraints excluded: chain H residue   54 THR
Chi-restraints excluded: chain I residue   43 LYS
Chi-restraints excluded: chain I residue   54 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 23 optimal weight:    9.9990
   chunk 12 optimal weight:    8.9990
   chunk 34 optimal weight:    8.9990
   chunk 3 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   chunk 32 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 10 optimal weight:    0.8980
   chunk 31 optimal weight:    8.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    2.1788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4736 r_free = 0.4736 target = 0.194104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4636 r_free = 0.4636 target = 0.179701 restraints weight = 3164.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.4633 rms_B_bonded: 2.40
r_work: 0.4565 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.4471 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.4471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.015   2622  Z= 0.142
  Angle     :  0.607   8.440   3552  Z= 0.303
  Chirality :  0.053   0.147    474
  Planarity :  0.002   0.007    438
  Dihedral  :  4.791  12.723    372
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 26.45 %
    Favored  : 72.46 %
  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: -2.67 (0.34), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.03 (0.26), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR E  39 
 PHE   0.002   0.001   PHE I  94 
 HIS   0.005   0.002   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 2622)
  covalent geometry    : angle       0.60658 ( 3552)
  hydrogen bonds       : bond        0.01820 (   49)
  hydrogen bonds       : angle       5.06599 (  147)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 37
  time to evaluate  : 0.060 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 38
  average time/residue: 0.3585
  time to fit residues: 14.0813
Evaluate side-chains
  34 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 32
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain E residue   46 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 33 optimal weight:    9.9990
   chunk 14 optimal weight:    9.9990
   chunk 13 optimal weight:   10.0000
   chunk 32 optimal weight:   10.0000
   chunk 25 optimal weight:    5.9990
   chunk 31 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 34 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    2.5186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4721 r_free = 0.4721 target = 0.193326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4624 r_free = 0.4624 target = 0.179061 restraints weight = 3114.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.4626 rms_B_bonded: 2.35
r_work: 0.4555 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.4460 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.4460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.1504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.016   2622  Z= 0.160
  Angle     :  0.626   8.845   3552  Z= 0.309
  Chirality :  0.053   0.148    474
  Planarity :  0.002   0.006    438
  Dihedral  :  4.798  13.032    372
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 25.72 %
    Favored  : 71.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.51 (0.35), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.90 (0.27), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR E  39 
 PHE   0.002   0.001   PHE I  94 
 HIS   0.005   0.002   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 2622)
  covalent geometry    : angle       0.62561 ( 3552)
  hydrogen bonds       : bond        0.01800 (   49)
  hydrogen bonds       : angle       5.04352 (  147)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 0.062 
Fit side-chains
  outliers start: 8
  outliers final: 6
  residues processed: 38
  average time/residue: 0.3500
  time to fit residues: 13.7319
Evaluate side-chains
  38 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain G residue   46 GLU
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain I residue   54 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 31 optimal weight:   10.0000
   chunk 16 optimal weight:    8.9990
   chunk 8 optimal weight:    9.9990
   chunk 5 optimal weight:    9.9990
   chunk 7 optimal weight:    0.9990
   chunk 12 optimal weight:    8.9990
   chunk 32 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0980
   chunk 14 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9990
   chunk 6 optimal weight:    7.9990
   overall best weight:    2.0188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4730 r_free = 0.4730 target = 0.195070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4635 r_free = 0.4635 target = 0.180890 restraints weight = 3079.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.4638 rms_B_bonded: 2.33
r_work: 0.4567 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.4474 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.4474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.1655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.013   2622  Z= 0.132
  Angle     :  0.591   8.641   3552  Z= 0.290
  Chirality :  0.052   0.144    474
  Planarity :  0.001   0.005    438
  Dihedral  :  4.584  12.458    372
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 25.00 %
    Favored  : 70.65 %
  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: -2.40 (0.36), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.82 (0.27), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR E  39 
 PHE   0.003   0.001   PHE H  94 
 HIS   0.005   0.002   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 2622)
  covalent geometry    : angle       0.59136 ( 3552)
  hydrogen bonds       : bond        0.01586 (   49)
  hydrogen bonds       : angle       4.93251 (  147)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 36
  time to evaluate  : 0.061 
Fit side-chains
  outliers start: 12
  outliers final: 7
  residues processed: 43
  average time/residue: 0.3175
  time to fit residues: 14.0954
Evaluate side-chains
  39 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain G residue   46 GLU
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   54 THR
Chi-restraints excluded: chain I residue   54 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 17 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   chunk 28 optimal weight:    7.9990
   chunk 11 optimal weight:    8.9990
   chunk 31 optimal weight:   10.0000
   chunk 12 optimal weight:    8.9990
   chunk 4 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 20 optimal weight:   10.0000
   chunk 24 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    2.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4713 r_free = 0.4713 target = 0.192044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4620 r_free = 0.4620 target = 0.177960 restraints weight = 3169.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.4624 rms_B_bonded: 2.29
r_work: 0.4555 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.4464 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.4464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.1599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.019   2622  Z= 0.186
  Angle     :  0.654   9.405   3552  Z= 0.322
  Chirality :  0.053   0.150    474
  Planarity :  0.002   0.008    438
  Dihedral  :  4.832  12.984    372
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 24.28 %
    Favored  : 71.01 %
  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: -2.38 (0.36), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.28), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.002   TYR E  39 
 PHE   0.003   0.001   PHE I  94 
 HIS   0.006   0.003   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 2622)
  covalent geometry    : angle       0.65412 ( 3552)
  hydrogen bonds       : bond        0.01783 (   49)
  hydrogen bonds       : angle       5.08709 (  147)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 32
  time to evaluate  : 0.112 
Fit side-chains
  outliers start: 13
  outliers final: 9
  residues processed: 40
  average time/residue: 0.4234
  time to fit residues: 17.4863
Evaluate side-chains
  40 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   43 LYS
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain G residue   46 GLU
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   54 THR
Chi-restraints excluded: chain I residue   43 LYS
Chi-restraints excluded: chain I residue   54 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 12 optimal weight:    8.9990
   chunk 4 optimal weight:    6.9990
   chunk 32 optimal weight:    9.9990
   chunk 13 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 34 optimal weight:   10.0000
   chunk 25 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   chunk 7 optimal weight:    7.9990
   chunk 27 optimal weight:    9.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
E  50 HIS
G  50 HIS
I  50 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4679 r_free = 0.4679 target = 0.188106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4577 r_free = 0.4577 target = 0.173627 restraints weight = 3171.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.4579 rms_B_bonded: 2.29
r_work: 0.4511 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.4418 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.4418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.1678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.032   2622  Z= 0.340
  Angle     :  0.797  10.047   3552  Z= 0.411
  Chirality :  0.059   0.163    474
  Planarity :  0.003   0.011    438
  Dihedral  :  5.438  15.732    372
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.17 %
    Favored  : 90.83 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 24.64 %
    Favored  : 69.93 %
  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: -2.48 (0.36), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.88 (0.28), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.003   TYR E  39 
 PHE   0.005   0.002   PHE G  94 
 HIS   0.009   0.005   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00772 ( 2622)
  covalent geometry    : angle       0.79744 ( 3552)
  hydrogen bonds       : bond        0.02287 (   49)
  hydrogen bonds       : angle       5.38386 (  147)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 31
  time to evaluate  : 0.078 
Fit side-chains
  outliers start: 15
  outliers final: 10
  residues processed: 37
  average time/residue: 0.3333
  time to fit residues: 12.7304
Evaluate side-chains
  40 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 30
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   46 GLU
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain G residue   46 GLU
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   54 THR
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain I residue   54 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 8 optimal weight:    9.9990
   chunk 2 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 12 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    1.7986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4740 r_free = 0.4740 target = 0.195367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4647 r_free = 0.4647 target = 0.181547 restraints weight = 3164.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.4652 rms_B_bonded: 2.28
r_work: 0.4586 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.4496 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.4496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.014   2622  Z= 0.123
  Angle     :  0.598   8.607   3552  Z= 0.296
  Chirality :  0.052   0.144    474
  Planarity :  0.001   0.008    438
  Dihedral  :  4.666  12.236    372
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 27.17 %
    Favored  : 69.93 %
  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: -2.31 (0.37), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.76 (0.28), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR E  39 
 PHE   0.002   0.001   PHE H  94 
 HIS   0.004   0.002   HIS I  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 2622)
  covalent geometry    : angle       0.59837 ( 3552)
  hydrogen bonds       : bond        0.01537 (   49)
  hydrogen bonds       : angle       5.00584 (  147)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 0.068 
Fit side-chains
  outliers start: 8
  outliers final: 8
  residues processed: 39
  average time/residue: 0.3317
  time to fit residues: 13.3326
Evaluate side-chains
  40 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 32
  time to evaluate  : 0.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain G residue   46 GLU
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   54 THR
Chi-restraints excluded: chain I residue   54 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 6 optimal weight:    8.9990
   chunk 26 optimal weight:   10.0000
   chunk 13 optimal weight:    8.9990
   chunk 12 optimal weight:    7.9990
   chunk 29 optimal weight:    8.9990
   chunk 0 optimal weight:    8.9990
   chunk 14 optimal weight:    5.9990
   chunk 11 optimal weight:    8.9990
   chunk 24 optimal weight:    0.8980
   chunk 10 optimal weight:    9.9990
   overall best weight:    5.7788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4676 r_free = 0.4676 target = 0.188096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4578 r_free = 0.4578 target = 0.173908 restraints weight = 3322.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.4579 rms_B_bonded: 2.29
r_work: 0.4510 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.4418 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.4418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.1743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.030   2622  Z= 0.336
  Angle     :  0.801  10.352   3552  Z= 0.410
  Chirality :  0.059   0.164    474
  Planarity :  0.003   0.010    438
  Dihedral  :  5.449  15.663    372
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.72 %
    Favored  : 90.28 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 25.72 %
    Favored  : 70.29 %
  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: -2.46 (0.36), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.86 (0.28), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.013   0.003   TYR E  39 
 PHE   0.005   0.002   PHE E  94 
 HIS   0.008   0.003   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00763 ( 2622)
  covalent geometry    : angle       0.80130 ( 3552)
  hydrogen bonds       : bond        0.02272 (   49)
  hydrogen bonds       : angle       5.37522 (  147)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 31
  time to evaluate  : 0.062 
Fit side-chains
  outliers start: 11
  outliers final: 9
  residues processed: 38
  average time/residue: 0.4116
  time to fit residues: 16.0544
Evaluate side-chains
  39 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 30
  time to evaluate  : 0.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain G residue   46 GLU
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   54 THR
Chi-restraints excluded: chain I residue   54 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 27 optimal weight:   10.0000
   chunk 29 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   overall best weight:    3.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4713 r_free = 0.4713 target = 0.192037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4612 r_free = 0.4612 target = 0.177625 restraints weight = 3191.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.4616 rms_B_bonded: 2.32
r_work: 0.4548 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.4457 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.4457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.020   2622  Z= 0.196
  Angle     :  0.686   9.783   3552  Z= 0.339
  Chirality :  0.054   0.154    474
  Planarity :  0.002   0.007    438
  Dihedral  :  5.045  13.967    372
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 26.45 %
    Favored  : 70.29 %
  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: -2.37 (0.37), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.28), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.008   0.002   TYR H  39 
 PHE   0.003   0.001   PHE F  94 
 HIS   0.005   0.002   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 2622)
  covalent geometry    : angle       0.68628 ( 3552)
  hydrogen bonds       : bond        0.01862 (   49)
  hydrogen bonds       : angle       5.16630 (  147)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.061 
Fit side-chains
  outliers start: 9
  outliers final: 9
  residues processed: 37
  average time/residue: 0.4065
  time to fit residues: 15.4451
Evaluate side-chains
  40 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain G residue   46 GLU
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   54 THR
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain I residue   54 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 6 optimal weight:    8.9990
   chunk 26 optimal weight:    9.9990
   chunk 0 optimal weight:    8.9990
   chunk 23 optimal weight:    5.9990
   chunk 29 optimal weight:   10.0000
   chunk 10 optimal weight:    6.9990
   chunk 7 optimal weight:    0.5980
   chunk 18 optimal weight:    3.9990
   chunk 12 optimal weight:    8.9990
   chunk 27 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    3.7186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4704 r_free = 0.4704 target = 0.191016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4602 r_free = 0.4602 target = 0.176519 restraints weight = 3172.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.4606 rms_B_bonded: 2.31
r_work: 0.4539 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.4447 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.4447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.021   2622  Z= 0.224
  Angle     :  0.709   9.850   3552  Z= 0.353
  Chirality :  0.055   0.155    474
  Planarity :  0.002   0.008    438
  Dihedral  :  5.160  14.206    372
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.44 %
    Favored  : 90.56 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 26.09 %
    Favored  : 70.29 %
  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: -2.38 (0.37), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.28), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.002   TYR H  39 
 PHE   0.003   0.001   PHE F  94 
 HIS   0.005   0.002   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 ( 2622)
  covalent geometry    : angle       0.70898 ( 3552)
  hydrogen bonds       : bond        0.01946 (   49)
  hydrogen bonds       : angle       5.22506 (  147)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 957.24 seconds
wall clock time: 17 minutes 9.36 seconds (1029.36 seconds total)