Starting phenix.real_space_refine
on Mon Feb 10 22:17:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jey_36203/02_2025/8jey_36203.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jey_36203/02_2025/8jey_36203.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jey_36203/02_2025/8jey_36203.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jey_36203/02_2025/8jey_36203.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jey_36203/02_2025/8jey_36203.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jey_36203/02_2025/8jey_36203.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    1914      2.51       5
     N     528      2.21       5
     O     606      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 3060
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 510
          Classifications: {'peptide': 72}
          Link IDs: {'TRANS': 71}
    Chain: "B"
      Number of atoms: 510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 510
          Classifications: {'peptide': 72}
          Link IDs: {'TRANS': 71}
    Chain: "C"
      Number of atoms: 510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 510
          Classifications: {'peptide': 72}
          Link IDs: {'TRANS': 71}
    Chain: "D"
      Number of atoms: 510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 510
          Classifications: {'peptide': 72}
          Link IDs: {'TRANS': 71}
    Chain: "E"
      Number of atoms: 510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 510
          Classifications: {'peptide': 72}
          Link IDs: {'TRANS': 71}
    Chain: "F"
      Number of atoms: 510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 510
          Classifications: {'peptide': 72}
          Link IDs: {'TRANS': 71}
  Time building chain proxies: 2.61, per 1000 atoms: 0.85
  Number of scatterers: 3060
  At special positions: 0
  Unit cell: (75.53, 107.07, 34.86, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      12     16.00
     O     606      8.00
     N     528      7.00
     C    1914      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: 0.67
  Conformation dependent library (CDL) restraints added in 380.3 milliseconds
  

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  744

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 18 sheets defined
      0.0% alpha, 47.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7
      removed outlier: 6.215A  pdb=" N   VAL A   3 " --> pdb=" O   PHE B   4 " (cutoff:3.500A)
      removed outlier: 7.952A  pdb=" N   LYS B   6 " --> pdb=" O   VAL A   3 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   MET A   5 " --> pdb=" O   LYS B   6 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 12
      removed outlier: 6.523A  pdb=" N   ALA A  11 " --> pdb=" O   LYS C  12 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 15 through 16
      removed outlier: 6.701A  pdb=" N   VAL A  15 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 23 through 29
      removed outlier: 9.036A  pdb=" N   LYS A  23 " --> pdb=" O   GLN B  24 " (cutoff:3.500A)
      removed outlier: 9.028A  pdb=" N   VAL B  26 " --> pdb=" O   LYS A  23 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   GLY A  25 " --> pdb=" O   VAL B  26 " (cutoff:3.500A)
      removed outlier: 8.302A  pdb=" N   GLU B  28 " --> pdb=" O   GLY A  25 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   ALA A  27 " --> pdb=" O   GLU B  28 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   GLN A  24 " --> pdb=" O   LYS C  23 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   GLY C  25 " --> pdb=" O   GLN A  24 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 35 through 40
      removed outlier: 6.924A  pdb=" N   GLY B  36 " --> pdb=" O   GLU A  35 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   GLY A  36 " --> pdb=" O   VAL C  37 " (cutoff:3.500A)
      removed outlier: 8.092A  pdb=" N   TYR C  39 " --> pdb=" O   GLY A  36 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   LEU A  38 " --> pdb=" O   TYR C  39 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 43 through 44
      removed outlier: 6.586A  pdb=" N   LYS A  43 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 49 through 52
      removed outlier: 5.995A  pdb=" N   VAL A  49 " --> pdb=" O   HIS B  50 " (cutoff:3.500A)
      removed outlier: 7.763A  pdb=" N   VAL B  52 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   GLY A  51 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 55 through 66
      removed outlier: 8.676A  pdb=" N   ALA A  56 " --> pdb=" O   GLU B  57 " (cutoff:3.500A)
      removed outlier: 9.353A  pdb=" N   THR B  59 " --> pdb=" O   ALA A  56 " (cutoff:3.500A)
      removed outlier: 8.738A  pdb=" N   LYS A  58 " --> pdb=" O   THR B  59 " (cutoff:3.500A)
      removed outlier: 10.515A  pdb=" N   GLU B  61 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
      removed outlier: 5.923A  pdb=" N   LYS A  60 " --> pdb=" O   GLU B  61 " (cutoff:3.500A)
      removed outlier: 8.446A  pdb=" N   VAL B  63 " --> pdb=" O   LYS A  60 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   GLN A  62 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
      removed outlier: 7.765A  pdb=" N   ASN B  65 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   THR A  64 " --> pdb=" O   ASN B  65 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   ALA C  56 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   GLU A  57 " --> pdb=" O   ALA C  56 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   LYS C  58 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   THR A  59 " --> pdb=" O   LYS C  58 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   LYS C  60 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   GLU A  61 " --> pdb=" O   LYS C  60 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 69 through 71
      removed outlier: 6.490A  pdb=" N   ALA A  69 " --> pdb=" O   VAL B  70 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   VAL A  70 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7
      removed outlier: 6.215A  pdb=" N   VAL D   3 " --> pdb=" O   PHE E   4 " (cutoff:3.500A)
      removed outlier: 7.951A  pdb=" N   LYS E   6 " --> pdb=" O   VAL D   3 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   MET D   5 " --> pdb=" O   LYS E   6 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12
      removed outlier: 6.524A  pdb=" N   ALA D  11 " --> pdb=" O   LYS F  12 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 15 through 16
      removed outlier: 6.701A  pdb=" N   VAL D  15 " --> pdb=" O   VAL E  16 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 23 through 29
      removed outlier: 9.034A  pdb=" N   LYS D  23 " --> pdb=" O   GLN E  24 " (cutoff:3.500A)
      removed outlier: 9.021A  pdb=" N   VAL E  26 " --> pdb=" O   LYS D  23 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   GLY D  25 " --> pdb=" O   VAL E  26 " (cutoff:3.500A)
      removed outlier: 8.298A  pdb=" N   GLU E  28 " --> pdb=" O   GLY D  25 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   ALA D  27 " --> pdb=" O   GLU E  28 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   GLN D  24 " --> pdb=" O   LYS F  23 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   GLY F  25 " --> pdb=" O   GLN D  24 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 35 through 40
      removed outlier: 6.924A  pdb=" N   GLY E  36 " --> pdb=" O   GLU D  35 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   GLY D  36 " --> pdb=" O   VAL F  37 " (cutoff:3.500A)
      removed outlier: 8.092A  pdb=" N   TYR F  39 " --> pdb=" O   GLY D  36 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   LEU D  38 " --> pdb=" O   TYR F  39 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 43 through 44
      removed outlier: 6.586A  pdb=" N   LYS D  43 " --> pdb=" O   THR F  44 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 49 through 52
      removed outlier: 5.994A  pdb=" N   VAL D  49 " --> pdb=" O   HIS E  50 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   VAL E  52 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   GLY D  51 " --> pdb=" O   VAL E  52 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 55 through 66
      removed outlier: 8.675A  pdb=" N   ALA D  56 " --> pdb=" O   GLU E  57 " (cutoff:3.500A)
      removed outlier: 9.354A  pdb=" N   THR E  59 " --> pdb=" O   ALA D  56 " (cutoff:3.500A)
      removed outlier: 8.705A  pdb=" N   LYS D  58 " --> pdb=" O   THR E  59 " (cutoff:3.500A)
      removed outlier: 10.515A  pdb=" N   GLU E  61 " --> pdb=" O   LYS D  58 " (cutoff:3.500A)
      removed outlier: 5.923A  pdb=" N   LYS D  60 " --> pdb=" O   GLU E  61 " (cutoff:3.500A)
      removed outlier: 8.446A  pdb=" N   VAL E  63 " --> pdb=" O   LYS D  60 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   GLN D  62 " --> pdb=" O   VAL E  63 " (cutoff:3.500A)
      removed outlier: 7.765A  pdb=" N   ASN E  65 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   THR D  64 " --> pdb=" O   ASN E  65 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   ALA F  56 " --> pdb=" O   VAL D  55 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   GLU D  57 " --> pdb=" O   ALA F  56 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   LYS F  58 " --> pdb=" O   GLU D  57 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   THR D  59 " --> pdb=" O   LYS F  58 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   LYS F  60 " --> pdb=" O   THR D  59 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   GLU D  61 " --> pdb=" O   LYS F  60 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 69 through 71
      removed outlier: 6.490A  pdb=" N   ALA D  69 " --> pdb=" O   VAL E  70 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   VAL D  70 " --> pdb=" O   VAL F  71 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB9

    46 hydrogen bonds defined for protein.
    138 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: 0.71

  Time building geometry restraints manager: 0.78 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1002
        1.34 -     1.46: 335
        1.46 -     1.57: 1711
        1.57 -     1.69: 0
        1.69 -     1.80: 24
  Bond restraints: 3072
  Sorted by residual:
  bond pdb=" N   VAL A  26 "
       pdb=" CA  VAL A  26 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.14e-02 7.69e+03 9.48e+00
  bond pdb=" N   VAL E  26 "
       pdb=" CA  VAL E  26 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.035 1.17e-02 7.31e+03 9.06e+00
  bond pdb=" N   VAL D  26 "
       pdb=" CA  VAL D  26 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.035 1.17e-02 7.31e+03 9.06e+00
  bond pdb=" N   VAL C  26 "
       pdb=" CA  VAL C  26 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.17e-02 7.31e+03 8.89e+00
  bond pdb=" N   VAL B  26 "
       pdb=" CA  VAL B  26 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.17e-02 7.31e+03 8.88e+00
  ... (remaining 3067 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.97: 3573
        0.97 -     1.94: 403
        1.94 -     2.91: 92
        2.91 -     3.88: 24
        3.88 -     4.84: 18
  Bond angle restraints: 4110
  Sorted by residual:
  angle pdb=" N   GLU E  13 "
        pdb=" CA  GLU E  13 "
        pdb=" C   GLU E  13 "
      ideal   model   delta    sigma   weight residual
     112.58  108.44    4.14 1.22e+00 6.72e-01 1.15e+01
  angle pdb=" N   GLU D  13 "
        pdb=" CA  GLU D  13 "
        pdb=" C   GLU D  13 "
      ideal   model   delta    sigma   weight residual
     112.58  108.45    4.13 1.22e+00 6.72e-01 1.15e+01
  angle pdb=" N   GLU B  13 "
        pdb=" CA  GLU B  13 "
        pdb=" C   GLU B  13 "
      ideal   model   delta    sigma   weight residual
     112.58  108.46    4.12 1.22e+00 6.72e-01 1.14e+01
  angle pdb=" N   GLU A  13 "
        pdb=" CA  GLU A  13 "
        pdb=" C   GLU A  13 "
      ideal   model   delta    sigma   weight residual
     112.58  108.47    4.11 1.22e+00 6.72e-01 1.14e+01
  angle pdb=" N   GLU F  13 "
        pdb=" CA  GLU F  13 "
        pdb=" C   GLU F  13 "
      ideal   model   delta    sigma   weight residual
     112.58  108.51    4.07 1.22e+00 6.72e-01 1.11e+01
  ... (remaining 4105 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.63: 1508
        9.63 -    19.26: 244
       19.26 -    28.89: 60
       28.89 -    38.52: 36
       38.52 -    48.15: 12
  Dihedral angle restraints: 1860
    sinusoidal: 684
      harmonic: 1176
  Sorted by residual:
  dihedral pdb=" CA  LYS C  58 "
           pdb=" C   LYS C  58 "
           pdb=" N   THR C  59 "
           pdb=" CA  THR C  59 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.06  -16.94     0      5.00e+00 4.00e-02 1.15e+01
  dihedral pdb=" CA  LYS F  58 "
           pdb=" C   LYS F  58 "
           pdb=" N   THR F  59 "
           pdb=" CA  THR F  59 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.07  -16.93     0      5.00e+00 4.00e-02 1.15e+01
  dihedral pdb=" CA  LYS D  58 "
           pdb=" C   LYS D  58 "
           pdb=" N   THR D  59 "
           pdb=" CA  THR D  59 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.09  -16.91     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 1857 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 315
       0.038 -    0.076: 82
       0.076 -    0.114: 93
       0.114 -    0.152: 11
       0.152 -    0.190: 9
  Chirality restraints: 510
  Sorted by residual:
  chirality pdb=" CA  GLU D  20 "
            pdb=" N   GLU D  20 "
            pdb=" C   GLU D  20 "
            pdb=" CB  GLU D  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.03e-01
  chirality pdb=" CA  GLU E  20 "
            pdb=" N   GLU E  20 "
            pdb=" C   GLU E  20 "
            pdb=" CB  GLU E  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.69e-01
  chirality pdb=" CA  GLU A  20 "
            pdb=" N   GLU A  20 "
            pdb=" C   GLU A  20 "
            pdb=" CB  GLU A  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.66e-01
  ... (remaining 507 not shown)

  Planarity restraints: 510
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU F   8 "    0.005 2.00e-02 2.50e+03   1.00e-02 1.00e+00
        pdb=" C   LEU F   8 "   -0.017 2.00e-02 2.50e+03
        pdb=" O   LEU F   8 "    0.006 2.00e-02 2.50e+03
        pdb=" N   SER F   9 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C   8 "   -0.005 2.00e-02 2.50e+03   9.97e-03 9.94e-01
        pdb=" C   LEU C   8 "    0.017 2.00e-02 2.50e+03
        pdb=" O   LEU C   8 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   SER C   9 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A   8 "   -0.005 2.00e-02 2.50e+03   9.73e-03 9.48e-01
        pdb=" C   LEU A   8 "    0.017 2.00e-02 2.50e+03
        pdb=" O   LEU A   8 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   SER A   9 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 507 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 935
        2.85 -     3.36: 2546
        3.36 -     3.88: 4675
        3.88 -     4.39: 4989
        4.39 -     4.90: 10500
  Nonbonded interactions: 23645
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS B   6 "
            pdb=" OE2 GLU B  20 "
     model   vdw
     2.339 3.120
  nonbonded pdb=" NZ  LYS F   6 "
            pdb=" OE2 GLU F  20 "
     model   vdw
     2.339 3.120
  nonbonded pdb=" NZ  LYS E   6 "
            pdb=" OE2 GLU E  20 "
     model   vdw
     2.340 3.120
  nonbonded pdb=" NZ  LYS A   6 "
            pdb=" OE2 GLU A  20 "
     model   vdw
     2.340 3.120
  nonbonded pdb=" NZ  LYS C   6 "
            pdb=" OE2 GLU C  20 "
     model   vdw
     2.340 3.120
  ... (remaining 23640 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.900
  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:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.000
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
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      :  0.004   0.035   3072  Z= 0.271
  Angle     :  0.746   4.845   4110  Z= 0.464
  Chirality :  0.058   0.190    510
  Planarity :  0.002   0.010    510
  Dihedral  : 11.672  48.153   1116
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.60 (0.27), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.50 (0.21), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS F  50 
 PHE   0.007   0.002   PHE E   4 
 TYR   0.008   0.002   TYR E  39 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.330 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 1.2912
  time to fit residues: 75.5855
Evaluate side-chains
  52 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 31 optimal weight:    0.0980
   chunk 17 optimal weight:    0.0970
   chunk 10 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 32 optimal weight:   10.0000
   chunk 12 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   chunk 24 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.4476 r_free = 0.4476 target = 0.175777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.161857 restraints weight = 3527.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.4323 rms_B_bonded: 1.60
r_work: 0.4212 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.4107 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.4107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.1452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   3072  Z= 0.123
  Angle     :  0.463   5.078   4110  Z= 0.255
  Chirality :  0.050   0.123    510
  Planarity :  0.002   0.008    510
  Dihedral  :  4.632  16.948    432
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 3.01
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  6.43 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  :  8.65 %
    Favored  : 88.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.12 (0.27), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.13 (0.21), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS B  50 
 PHE   0.004   0.001   PHE A   4 
 TYR   0.008   0.002   TYR D  39 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.334 
Fit side-chains
  outliers start: 10
  outliers final: 0
  residues processed: 61
  average time/residue: 1.1990
  time to fit residues: 75.1857
Evaluate side-chains
  49 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 18 optimal weight:    0.0040
   chunk 13 optimal weight:    4.9990
   chunk 3 optimal weight:    7.9990
   chunk 11 optimal weight:   10.0000
   chunk 14 optimal weight:    6.9990
   chunk 29 optimal weight:    0.0370
   chunk 4 optimal weight:    0.9980
   chunk 15 optimal weight:   10.0000
   chunk 31 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0470
   overall best weight:    0.8170

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4510 r_free = 0.4510 target = 0.176629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.162935 restraints weight = 3439.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.4362 rms_B_bonded: 1.62
r_work: 0.4257 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.4151 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.4151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.1782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   3072  Z= 0.128
  Angle     :  0.458   6.136   4110  Z= 0.241
  Chirality :  0.050   0.123    510
  Planarity :  0.002   0.007    510
  Dihedral  :  4.496  15.202    432
  Min Nonbonded Distance : 2.692

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 11.54 %
    Favored  : 85.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.85 (0.29), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.92 (0.22), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A  50 
 PHE   0.004   0.001   PHE D   4 
 TYR   0.007   0.002   TYR D  39 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.272 
Fit side-chains
  outliers start: 9
  outliers final: 3
  residues processed: 57
  average time/residue: 1.2615
  time to fit residues: 73.8207
Evaluate side-chains
  51 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 48
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain D residue    8 LEU
Chi-restraints excluded: chain E residue    8 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 6 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 21 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 7 optimal weight:    8.9990
   chunk 34 optimal weight:    8.9990
   chunk 17 optimal weight:    6.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.4478 r_free = 0.4478 target = 0.174769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.160781 restraints weight = 3353.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.4351 rms_B_bonded: 1.67
r_work: 0.4247 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.4142 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.4142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   3072  Z= 0.154
  Angle     :  0.450   6.116   4110  Z= 0.239
  Chirality :  0.050   0.124    510
  Planarity :  0.002   0.007    510
  Dihedral  :  4.475  16.473    432
  Min Nonbonded Distance : 2.679

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 12.82 %
    Favored  : 85.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.67 (0.30), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.79 (0.23), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS F  50 
 PHE   0.005   0.001   PHE A   4 
 TYR   0.008   0.002   TYR D  39 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.336 
Fit side-chains
  outliers start: 6
  outliers final: 4
  residues processed: 53
  average time/residue: 1.3706
  time to fit residues: 74.4834
Evaluate side-chains
  52 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 LEU
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain D residue    8 LEU
Chi-restraints excluded: chain E residue    8 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 4 optimal weight:    7.9990
   chunk 29 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 15 optimal weight:    9.9990
   chunk 8 optimal weight:    3.9990
   chunk 41 optimal weight:    9.9990
   chunk 20 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
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 = 0.4388 r_free = 0.4388 target = 0.166376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.153473 restraints weight = 3440.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.4253 rms_B_bonded: 1.57
r_work: 0.4147 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.4048 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.4048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.025   3072  Z= 0.371
  Angle     :  0.582   5.782   4110  Z= 0.321
  Chirality :  0.053   0.159    510
  Planarity :  0.003   0.011    510
  Dihedral  :  5.641  17.297    432
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 1.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 13.46 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.58 (0.30), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.72 (0.23), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D  50 
 PHE   0.008   0.003   PHE D   4 
 TYR   0.019   0.004   TYR C  39 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.362 
Fit side-chains
REVERT: C    5 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7379 (ttt)
REVERT: D    5 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7477 (ttt)
REVERT: F    5 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7578 (ttp)
  outliers start: 8
  outliers final: 3
  residues processed: 58
  average time/residue: 1.3596
  time to fit residues: 80.8347
Evaluate side-chains
  63 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 LEU
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain C residue    5 MET
Chi-restraints excluded: chain D residue    5 MET
Chi-restraints excluded: chain E residue    8 LEU
Chi-restraints excluded: chain F residue    5 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 4 optimal weight:    8.9990
   chunk 17 optimal weight:    0.9990
   chunk 32 optimal weight:    9.9990
   chunk 37 optimal weight:    7.9990
   chunk 13 optimal weight:    7.9990
   chunk 35 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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 = 0.4367 r_free = 0.4367 target = 0.164728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.151976 restraints weight = 3590.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.4215 rms_B_bonded: 1.61
r_work: 0.4116 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.4019 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.4019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.2585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.034   3072  Z= 0.468
  Angle     :  0.647   5.211   4110  Z= 0.356
  Chirality :  0.054   0.191    510
  Planarity :  0.003   0.014    510
  Dihedral  :  6.129  18.487    432
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 1.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 14.74 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.65 (0.29), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.77 (0.22), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D  50 
 PHE   0.008   0.004   PHE E   4 
 TYR   0.020   0.004   TYR F  39 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.328 
Fit side-chains
REVERT: C    5 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7503 (ttt)
REVERT: F    5 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7573 (ttp)
  outliers start: 10
  outliers final: 5
  residues processed: 58
  average time/residue: 1.3391
  time to fit residues: 79.6373
Evaluate side-chains
  63 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 LEU
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain C residue    5 MET
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain E residue    8 LEU
Chi-restraints excluded: chain F residue    5 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 4 optimal weight:    8.9990
   chunk 3 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   chunk 38 optimal weight:    0.4980
   chunk 28 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 27 optimal weight:    9.9990
   chunk 16 optimal weight:    6.9990
   chunk 2 optimal weight:    0.5980
   overall best weight:    2.4186

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.166987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.154444 restraints weight = 3457.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.4266 rms_B_bonded: 1.54
r_work: 0.4158 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.4058 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.4058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.2576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   3072  Z= 0.277
  Angle     :  0.556   6.390   4110  Z= 0.296
  Chirality :  0.052   0.152    510
  Planarity :  0.002   0.010    510
  Dihedral  :  5.712  17.114    432
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 1.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.03 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.56 (0.30), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.71 (0.23), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D  50 
 PHE   0.004   0.002   PHE B   4 
 TYR   0.013   0.003   TYR D  39 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.332 
Fit side-chains
REVERT: C    5 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7390 (ttt)
REVERT: F    5 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7554 (ttp)
  outliers start: 9
  outliers final: 6
  residues processed: 56
  average time/residue: 1.3426
  time to fit residues: 77.0372
Evaluate side-chains
  62 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 LEU
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain C residue    5 MET
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain E residue    8 LEU
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain F residue    5 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 12 optimal weight:    8.9990
   chunk 32 optimal weight:    3.9990
   chunk 6 optimal weight:    8.9990
   chunk 14 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   chunk 38 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 19 optimal weight:    7.9990
   chunk 5 optimal weight:   10.0000
   overall best weight:    2.7586

-------------------------------------------------------------------------------
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 = 0.4391 r_free = 0.4391 target = 0.166421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.153547 restraints weight = 3505.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.4257 rms_B_bonded: 1.57
r_work: 0.4151 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.4048 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.4048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.2648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   3072  Z= 0.308
  Angle     :  0.578   7.509   4110  Z= 0.306
  Chirality :  0.053   0.158    510
  Planarity :  0.002   0.013    510
  Dihedral  :  5.714  17.288    432
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 1.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 15.71 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.55 (0.30), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.70 (0.23), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D  50 
 PHE   0.004   0.002   PHE F   4 
 TYR   0.015   0.003   TYR D  39 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.428 
Fit side-chains
REVERT: C    5 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7424 (ttt)
  outliers start: 11
  outliers final: 6
  residues processed: 59
  average time/residue: 1.2508
  time to fit residues: 75.8326
Evaluate side-chains
  63 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 LEU
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain C residue    5 MET
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain E residue    8 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 29 optimal weight:    0.0060
   chunk 22 optimal weight:    7.9990
   chunk 11 optimal weight:    3.9990
   chunk 21 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9980
   chunk 33 optimal weight:   10.0000
   chunk 8 optimal weight:    6.9990
   chunk 7 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    2.1800

-------------------------------------------------------------------------------
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 = 0.4424 r_free = 0.4424 target = 0.169474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.156230 restraints weight = 3488.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.4280 rms_B_bonded: 1.61
r_work: 0.4171 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.4069 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.4069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.2650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.019   3072  Z= 0.252
  Angle     :  0.558   8.525   4110  Z= 0.290
  Chirality :  0.052   0.157    510
  Planarity :  0.002   0.013    510
  Dihedral  :  5.531  16.960    432
  Min Nonbonded Distance : 2.652

Molprobity Statistics.
  All-atom Clashscore : 1.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 16.67 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.51 (0.30), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.66 (0.23), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D  50 
 PHE   0.004   0.002   PHE F   4 
 TYR   0.012   0.003   TYR D  39 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.315 
Fit side-chains
REVERT: C    5 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7404 (ttt)
  outliers start: 8
  outliers final: 6
  residues processed: 60
  average time/residue: 1.1759
  time to fit residues: 72.4819
Evaluate side-chains
  61 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 LEU
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain C residue    5 MET
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain E residue    8 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 41 optimal weight:    7.9990
   chunk 5 optimal weight:    6.9990
   chunk 28 optimal weight:    0.0170
   chunk 23 optimal weight:    0.6980
   chunk 19 optimal weight:    8.9990
   chunk 12 optimal weight:    9.9990
   chunk 40 optimal weight:    8.9990
   chunk 13 optimal weight:    7.9990
   chunk 10 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   overall best weight:    4.1424

-------------------------------------------------------------------------------
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 = 0.4365 r_free = 0.4365 target = 0.164443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.151721 restraints weight = 3416.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.4233 rms_B_bonded: 1.55
r_work: 0.4124 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.4026 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.4026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.031   3072  Z= 0.438
  Angle     :  0.651   7.601   4110  Z= 0.348
  Chirality :  0.055   0.179    510
  Planarity :  0.003   0.014    510
  Dihedral  :  6.033  19.328    432
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 2.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 17.31 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.59 (0.30), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.73 (0.23), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D  50 
 PHE   0.009   0.003   PHE F   4 
 TYR   0.019   0.004   TYR F  39 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.271 
Fit side-chains
REVERT: C    5 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7476 (ttt)
  outliers start: 7
  outliers final: 6
  residues processed: 60
  average time/residue: 1.3151
  time to fit residues: 80.8464
Evaluate side-chains
  64 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 LEU
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain C residue    5 MET
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain E residue    8 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 15 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 19 optimal weight:    8.9990
   chunk 16 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 2 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   chunk 6 optimal weight:   10.0000
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.4457 r_free = 0.4457 target = 0.171690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.158174 restraints weight = 3404.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.4316 rms_B_bonded: 1.67
r_work: 0.4203 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.4100 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.4100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.2706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   3072  Z= 0.133
  Angle     :  0.522   9.523   4110  Z= 0.263
  Chirality :  0.051   0.144    510
  Planarity :  0.002   0.013    510
  Dihedral  :  5.220  16.906    432
  Min Nonbonded Distance : 2.652

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 16.99 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.47 (0.31), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.63 (0.23), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C  50 
 PHE   0.001   0.001   PHE F   4 
 TYR   0.007   0.001   TYR A  39 
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 2660.55 seconds
wall clock time: 47 minutes 42.66 seconds (2862.66 seconds total)