Starting phenix.real_space_refine
on Fri Aug 22 12:39:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ynt_33971/08_2025/7ynt_33971.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ynt_33971/08_2025/7ynt_33971.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ynt_33971/08_2025/7ynt_33971.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ynt_33971/08_2025/7ynt_33971.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ynt_33971/08_2025/7ynt_33971.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ynt_33971/08_2025/7ynt_33971.cif"
  }
  resolution = 3.1
  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=   0.001 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    1470      2.51       5
     N     420      2.21       5
     O     474      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2364
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "F"
      Number of atoms: 394
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 394
          Classifications: {'peptide': 58}
          Link IDs: {'TRANS': 57}
  Restraints were copied for chains:
    A, B, C, D, E
  Time building chain proxies: 0.60, per 1000 atoms: 0.25
  Number of scatterers: 2364
  At special positions: 0
  Unit cell: (85.86, 107.06, 32.86, 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     474      8.00
     N     420      7.00
     C    1470      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: 0.20
  Conformation dependent library (CDL) restraints added in 111.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  588

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 49.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'F' and resid 44 through 55
      removed outlier: 6.928A  pdb=" N   LYS F  45 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   GLU A  46 " --> pdb=" O   LYS F  45 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   GLY F  47 " --> pdb=" O   GLU A  46 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   VAL A  52 " --> pdb=" O   GLY F  51 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   ALA F  53 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   THR A  54 " --> pdb=" O   ALA F  53 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   VAL F  55 " --> pdb=" O   THR A  54 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   LYS A  45 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   GLU B  46 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   GLY A  47 " --> pdb=" O   GLU B  46 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   VAL B  52 " --> pdb=" O   GLY A  51 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   ALA A  53 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   THR B  54 " --> pdb=" O   ALA A  53 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   VAL A  55 " --> pdb=" O   THR B  54 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'F' and resid 58 through 66
      removed outlier: 6.084A  pdb=" N   THR F  59 " --> pdb=" O   LYS A  60 " (cutoff:3.500A)
      removed outlier: 7.908A  pdb=" N   GLN A  62 " --> pdb=" O   THR F  59 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   GLU F  61 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   THR A  64 " --> pdb=" O   GLU F  61 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   VAL F  63 " --> pdb=" O   THR A  64 " (cutoff:3.500A)
      removed outlier: 7.638A  pdb=" N   VAL A  66 " --> pdb=" O   VAL F  63 " (cutoff:3.500A)
      removed outlier: 6.998A  pdb=" N   ASN F  65 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 6.060A  pdb=" N   THR A  59 " --> pdb=" O   LYS B  60 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   GLN B  62 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   GLU A  61 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   THR B  64 " --> pdb=" O   GLU A  61 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   VAL A  63 " --> pdb=" O   THR B  64 " (cutoff:3.500A)
      removed outlier: 7.642A  pdb=" N   VAL B  66 " --> pdb=" O   VAL A  63 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   ASN A  65 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'F' and resid 69 through 75
      removed outlier: 6.857A  pdb=" N   VAL A  70 " --> pdb=" O   ALA F  69 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   VAL F  71 " --> pdb=" O   VAL A  70 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   THR A  72 " --> pdb=" O   VAL F  71 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   VAL B  70 " --> pdb=" O   ALA A  69 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   VAL A  71 " --> pdb=" O   VAL B  70 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   THR B  72 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'F' and resid 78 through 79
      removed outlier: 6.708A  pdb=" N   ALA F  78 " --> pdb=" O   GLN A  79 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ALA A  78 " --> pdb=" O   GLN B  79 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'F' and resid 94 through 95
      removed outlier: 5.979A  pdb=" N   PHE F  94 " --> pdb=" O   VAL A  95 " (cutoff:3.500A)
      removed outlier: 5.995A  pdb=" N   PHE A  94 " --> pdb=" O   VAL B  95 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 87 through 89
      removed outlier: 5.723A  pdb=" N   ILE A  88 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'C' and resid 44 through 55
      removed outlier: 6.953A  pdb=" N   LYS C  45 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   GLU D  46 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   GLY C  47 " --> pdb=" O   GLU D  46 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   VAL D  52 " --> pdb=" O   GLY C  51 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   ALA C  53 " --> pdb=" O   VAL D  52 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   THR D  54 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   VAL C  55 " --> pdb=" O   THR D  54 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   LYS D  45 " --> pdb=" O   THR E  44 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   GLU E  46 " --> pdb=" O   LYS D  45 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   GLY D  47 " --> pdb=" O   GLU E  46 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   VAL E  52 " --> pdb=" O   GLY D  51 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   ALA D  53 " --> pdb=" O   VAL E  52 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   THR E  54 " --> pdb=" O   ALA D  53 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   VAL D  55 " --> pdb=" O   THR E  54 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 58 through 66
      removed outlier: 6.068A  pdb=" N   THR C  59 " --> pdb=" O   LYS D  60 " (cutoff:3.500A)
      removed outlier: 7.901A  pdb=" N   GLN D  62 " --> pdb=" O   THR C  59 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   GLU C  61 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
      removed outlier: 7.814A  pdb=" N   THR D  64 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   VAL C  63 " --> pdb=" O   THR D  64 " (cutoff:3.500A)
      removed outlier: 7.635A  pdb=" N   VAL D  66 " --> pdb=" O   VAL C  63 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   ASN C  65 " --> pdb=" O   VAL D  66 " (cutoff:3.500A)
      removed outlier: 6.073A  pdb=" N   THR D  59 " --> pdb=" O   LYS E  60 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   GLN E  62 " --> pdb=" O   THR D  59 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   GLU D  61 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   THR E  64 " --> pdb=" O   GLU D  61 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   VAL D  63 " --> pdb=" O   THR E  64 " (cutoff:3.500A)
      removed outlier: 7.662A  pdb=" N   VAL E  66 " --> pdb=" O   VAL D  63 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   ASN D  65 " --> pdb=" O   VAL E  66 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'C' and resid 69 through 75
      removed outlier: 6.855A  pdb=" N   VAL D  70 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   VAL C  71 " --> pdb=" O   VAL D  70 " (cutoff:3.500A)
      removed outlier: 6.959A  pdb=" N   THR D  72 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   VAL E  70 " --> pdb=" O   ALA D  69 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   VAL D  71 " --> pdb=" O   VAL E  70 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   THR E  72 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 78 through 79
      removed outlier: 6.720A  pdb=" N   ALA C  78 " --> pdb=" O   GLN D  79 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   ALA D  78 " --> pdb=" O   GLN E  79 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'C' and resid 87 through 89
      removed outlier: 5.718A  pdb=" N   ILE C  88 " --> pdb=" O   ALA D  89 " (cutoff:3.500A)
      removed outlier: 5.721A  pdb=" N   ILE D  88 " --> pdb=" O   ALA E  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'C' and resid 94 through 95
      removed outlier: 5.981A  pdb=" N   PHE C  94 " --> pdb=" O   VAL D  95 " (cutoff:3.500A)
      removed outlier: 6.006A  pdb=" N   PHE D  94 " --> pdb=" O   VAL E  95 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3

    28 hydrogen bonds defined for protein.
    84 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: 0.32

  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:
        1.23 -     1.29: 414
        1.29 -     1.35: 378
        1.35 -     1.42: 60
        1.42 -     1.48: 396
        1.48 -     1.54: 1122
  Bond restraints: 2370
  Sorted by residual:
  bond pdb=" C   THR D  92 "
       pdb=" N   GLY D  93 "
    ideal  model  delta    sigma   weight residual
    1.332  1.325  0.007 5.00e-03 4.00e+04 2.18e+00
  bond pdb=" C   THR A  92 "
       pdb=" N   GLY A  93 "
    ideal  model  delta    sigma   weight residual
    1.332  1.325  0.007 5.00e-03 4.00e+04 2.16e+00
  bond pdb=" C   THR E  92 "
       pdb=" N   GLY E  93 "
    ideal  model  delta    sigma   weight residual
    1.332  1.325  0.007 5.00e-03 4.00e+04 1.97e+00
  bond pdb=" C   THR C  92 "
       pdb=" N   GLY C  93 "
    ideal  model  delta    sigma   weight residual
    1.332  1.325  0.007 5.00e-03 4.00e+04 1.88e+00
  bond pdb=" C   THR B  92 "
       pdb=" N   GLY B  93 "
    ideal  model  delta    sigma   weight residual
    1.332  1.325  0.007 5.00e-03 4.00e+04 1.85e+00
  ... (remaining 2365 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.04: 2969
        1.04 -     2.07: 199
        2.07 -     3.11: 24
        3.11 -     4.14: 0
        4.14 -     5.18: 6
  Bond angle restraints: 3198
  Sorted by residual:
  angle pdb=" N   PHE A  94 "
        pdb=" CA  PHE A  94 "
        pdb=" C   PHE A  94 "
      ideal   model   delta    sigma   weight residual
     108.24  103.06    5.18 1.81e+00 3.05e-01 8.19e+00
  angle pdb=" N   PHE E  94 "
        pdb=" CA  PHE E  94 "
        pdb=" C   PHE E  94 "
      ideal   model   delta    sigma   weight residual
     108.24  103.08    5.16 1.81e+00 3.05e-01 8.12e+00
  angle pdb=" N   PHE B  94 "
        pdb=" CA  PHE B  94 "
        pdb=" C   PHE B  94 "
      ideal   model   delta    sigma   weight residual
     108.24  103.08    5.16 1.81e+00 3.05e-01 8.12e+00
  angle pdb=" N   PHE D  94 "
        pdb=" CA  PHE D  94 "
        pdb=" C   PHE D  94 "
      ideal   model   delta    sigma   weight residual
     108.24  103.09    5.15 1.81e+00 3.05e-01 8.09e+00
  angle pdb=" N   PHE F  94 "
        pdb=" CA  PHE F  94 "
        pdb=" C   PHE F  94 "
      ideal   model   delta    sigma   weight residual
     108.24  103.10    5.14 1.81e+00 3.05e-01 8.06e+00
  ... (remaining 3193 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     7.95: 1028
        7.95 -    15.90: 268
       15.90 -    23.85: 54
       23.85 -    31.80: 18
       31.80 -    39.75: 24
  Dihedral angle restraints: 1392
    sinusoidal: 462
      harmonic: 930
  Sorted by residual:
  dihedral pdb=" CA  ALA A  91 "
           pdb=" C   ALA A  91 "
           pdb=" N   THR A  92 "
           pdb=" CA  THR A  92 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -166.25  -13.75     0      5.00e+00 4.00e-02 7.57e+00
  dihedral pdb=" CA  ALA D  91 "
           pdb=" C   ALA D  91 "
           pdb=" N   THR D  92 "
           pdb=" CA  THR D  92 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -166.27  -13.73     0      5.00e+00 4.00e-02 7.54e+00
  dihedral pdb=" CA  ALA F  91 "
           pdb=" C   ALA F  91 "
           pdb=" N   THR F  92 "
           pdb=" CA  THR F  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -166.27  -13.73     0      5.00e+00 4.00e-02 7.54e+00
  ... (remaining 1389 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.026: 171
       0.026 -    0.052: 106
       0.052 -    0.078: 72
       0.078 -    0.103: 33
       0.103 -    0.129: 44
  Chirality restraints: 426
  Sorted by residual:
  chirality pdb=" CA  VAL F  71 "
            pdb=" N   VAL F  71 "
            pdb=" C   VAL F  71 "
            pdb=" CB  VAL F  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.16e-01
  chirality pdb=" CA  VAL F  49 "
            pdb=" N   VAL F  49 "
            pdb=" C   VAL F  49 "
            pdb=" CB  VAL F  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.14e-01
  chirality pdb=" CA  VAL B  71 "
            pdb=" N   VAL B  71 "
            pdb=" C   VAL B  71 "
            pdb=" CB  VAL B  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.04e-01
  ... (remaining 423 not shown)

  Planarity restraints: 396
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU E  83 "   -0.004 2.00e-02 2.50e+03   7.27e-03 5.28e-01
        pdb=" C   GLU E  83 "    0.013 2.00e-02 2.50e+03
        pdb=" O   GLU E  83 "   -0.005 2.00e-02 2.50e+03
        pdb=" N   GLY E  84 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU F  83 "    0.004 2.00e-02 2.50e+03   7.13e-03 5.09e-01
        pdb=" C   GLU F  83 "   -0.012 2.00e-02 2.50e+03
        pdb=" O   GLU F  83 "    0.005 2.00e-02 2.50e+03
        pdb=" N   GLY F  84 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU D  83 "   -0.004 2.00e-02 2.50e+03   7.10e-03 5.04e-01
        pdb=" C   GLU D  83 "    0.012 2.00e-02 2.50e+03
        pdb=" O   GLU D  83 "   -0.005 2.00e-02 2.50e+03
        pdb=" N   GLY D  84 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 393 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 499
        2.80 -     3.32: 2053
        3.32 -     3.85: 3686
        3.85 -     4.37: 3947
        4.37 -     4.90: 7981
  Nonbonded interactions: 18166
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS E  60 "
            pdb=" OE1 GLN E  62 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" NZ  LYS D  60 "
            pdb=" OE1 GLN D  62 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" NZ  LYS C  60 "
            pdb=" OE1 GLN C  62 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" NZ  LYS B  60 "
            pdb=" OE1 GLN B  62 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" NZ  LYS A  60 "
            pdb=" OE1 GLN A  62 "
     model   vdw
     2.276 3.120
  ... (remaining 18161 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 'F'
  selection = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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:             2.590
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.950
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6714
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   0.019   2370  Z= 0.224
  Angle     :  0.590   5.180   3198  Z= 0.360
  Chirality :  0.056   0.129    426
  Planarity :  0.002   0.007    396
  Dihedral  : 11.350  39.754    804
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.93 %
    Favored  : 91.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.55 (0.24), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.23 (0.18), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.006   0.003   PHE A  94 
 HIS   0.004   0.002   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 2370)
  covalent geometry    : angle       0.58968 ( 3198)
  hydrogen bonds       : bond        0.24907 (   28)
  hydrogen bonds       : angle      11.35624 (   84)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  8 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 8
  time to evaluate  : 0.100 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0493
  time to fit residues: 0.6137
Evaluate side-chains
  3 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 3
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    0.1980
   chunk 12 optimal weight:    9.9990
   chunk 24 optimal weight:    0.0030
   chunk 28 optimal weight:    8.9990
   chunk 13 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   chunk 8 optimal weight:    6.9990
   chunk 16 optimal weight:    0.5980
   chunk 15 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   overall best weight:    1.9594

-------------------------------------------------------------------------------
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 = 0.5374 r_free = 0.5374 target = 0.275343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.5652 r_free = 0.5652 target = 0.241724 restraints weight = 4117.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.5124 rms_B_bonded: 1.64
r_work: 0.5266 rms_B_bonded: 1.68 restraints_weight: 0.5000
r_work: 0.5224 rms_B_bonded: 2.80 restraints_weight: 0.2500
r_work (final): 0.5224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6746
moved from start:          0.1095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   2370  Z= 0.145
  Angle     :  0.479   4.412   3198  Z= 0.285
  Chirality :  0.055   0.126    426
  Planarity :  0.002   0.017    396
  Dihedral  :  4.978  13.530    342
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.08 (0.28), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.87 (0.21), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.003   0.001   PHE D  94 
 HIS   0.010   0.004   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 2370)
  covalent geometry    : angle       0.47911 ( 3198)
  hydrogen bonds       : bond        0.04448 (   28)
  hydrogen bonds       : angle       8.53448 (   84)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  5 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 5
  time to evaluate  : 0.087 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0249
  time to fit residues: 0.3036
Evaluate side-chains
  4 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 4
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 18 optimal weight:    9.9990
   chunk 21 optimal weight:   10.0000
   chunk 10 optimal weight:    7.9990
   chunk 6 optimal weight:    9.9990
   chunk 13 optimal weight:    9.9990
   chunk 16 optimal weight:    9.9990
   chunk 3 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 22 optimal weight:    6.9990
   chunk 29 optimal weight:    0.0770
   chunk 15 optimal weight:   10.0000
   overall best weight:    7.0146

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

Flipped N/Q/H residues before XYZ refinement:
A  65 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4906 r_free = 0.4906 target = 0.154245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4692 r_free = 0.4692 target = 0.126048 restraints weight = 3974.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.4723 rms_B_bonded: 3.69
r_work: 0.4649 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.4649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5624
moved from start:          0.2390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.030   2370  Z= 0.328
  Angle     :  0.697   5.421   3198  Z= 0.409
  Chirality :  0.063   0.153    426
  Planarity :  0.004   0.017    396
  Dihedral  :  6.349  16.049    342
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.88 %
    Favored  : 85.12 %
  Rotamer:
    Outliers :  5.42 %
    Allowed  :  3.33 %
    Favored  : 91.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.78 (0.34), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.63 (0.26), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.006   0.002   PHE D  94 
 HIS   0.013   0.006   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00698 ( 2370)
  covalent geometry    : angle       0.69725 ( 3198)
  hydrogen bonds       : bond        0.05434 (   28)
  hydrogen bonds       : angle       7.97238 (   84)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 10
  time to evaluate  : 0.110 
Fit side-chains
  outliers start: 13
  outliers final: 10
  residues processed: 22
  average time/residue: 0.0328
  time to fit residues: 1.0889
Evaluate side-chains
  19 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 9
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain D residue   88 ILE
Chi-restraints excluded: chain E residue   77 VAL
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain E residue   88 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 22 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 5 optimal weight:    9.9990
   chunk 1 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A  65 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4988 r_free = 0.4988 target = 0.163071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4791 r_free = 0.4791 target = 0.133532 restraints weight = 3757.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.4819 rms_B_bonded: 3.69
r_work: 0.4744 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.4744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5465
moved from start:          0.2496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   2370  Z= 0.110
  Angle     :  0.447   3.932   3198  Z= 0.263
  Chirality :  0.054   0.129    426
  Planarity :  0.002   0.010    396
  Dihedral  :  5.008  13.722    342
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.52 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 11.25 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.61 (0.34), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.51 (0.26), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.015   0.002   PHE F  94 
 HIS   0.011   0.004   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 2370)
  covalent geometry    : angle       0.44722 ( 3198)
  hydrogen bonds       : bond        0.03935 (   28)
  hydrogen bonds       : angle       7.66047 (   84)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 11
  time to evaluate  : 0.096 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 14
  average time/residue: 0.0260
  time to fit residues: 0.6459
Evaluate side-chains
  13 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 10
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain E residue   81 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 29 optimal weight:    0.0570
   chunk 9 optimal weight:    7.9990
   chunk 11 optimal weight:    6.9990
   chunk 19 optimal weight:    0.2980
   chunk 1 optimal weight:    8.9990
   chunk 3 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   chunk 14 optimal weight:    7.9990
   chunk 27 optimal weight:    2.9990
   chunk 20 optimal weight:   10.0000
   chunk 17 optimal weight:    2.9990
   overall best weight:    2.0704

-------------------------------------------------------------------------------
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 = 0.5055 r_free = 0.5055 target = 0.208512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.5111 r_free = 0.5111 target = 0.182686 restraints weight = 3699.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.4815 rms_B_bonded: 2.45
r_work: 0.4754 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.4673 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.4673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6421
moved from start:          0.2805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2370  Z= 0.122
  Angle     :  0.431   4.165   3198  Z= 0.259
  Chirality :  0.054   0.130    426
  Planarity :  0.002   0.009    396
  Dihedral  :  4.826  12.932    342
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.74 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 11.67 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.34 (0.36), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.30 (0.27), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.013   0.002   PHE F  94 
 HIS   0.009   0.004   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 2370)
  covalent geometry    : angle       0.43087 ( 3198)
  hydrogen bonds       : bond        0.03852 (   28)
  hydrogen bonds       : angle       7.40779 (   84)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 9
  time to evaluate  : 0.090 
Fit side-chains
  outliers start: 6
  outliers final: 4
  residues processed: 15
  average time/residue: 0.0303
  time to fit residues: 0.7400
Evaluate side-chains
  10 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 6
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain E residue   77 VAL
Chi-restraints excluded: chain E residue   81 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 21 optimal weight:    8.9990
   chunk 15 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9990
   chunk 17 optimal weight:    8.9990
   chunk 23 optimal weight:    4.9990
   chunk 25 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 10 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9990
   chunk 3 optimal weight:   10.0000
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  65 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4930 r_free = 0.4930 target = 0.154379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4744 r_free = 0.4744 target = 0.130040 restraints weight = 4308.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.4628 rms_B_bonded: 3.50
r_work: 0.4527 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.4527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6667
moved from start:          0.3095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   2370  Z= 0.201
  Angle     :  0.506   4.761   3198  Z= 0.305
  Chirality :  0.057   0.134    426
  Planarity :  0.002   0.010    396
  Dihedral  :  5.311  13.587    342
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.20 %
    Favored  : 87.80 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 12.08 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.40 (0.37), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.35 (0.29), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.016   0.004   PHE F  94 
 HIS   0.009   0.004   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 ( 2370)
  covalent geometry    : angle       0.50629 ( 3198)
  hydrogen bonds       : bond        0.04313 (   28)
  hydrogen bonds       : angle       7.54163 (   84)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 11
  time to evaluate  : 0.109 
Fit side-chains
  outliers start: 5
  outliers final: 5
  residues processed: 16
  average time/residue: 0.0332
  time to fit residues: 0.8525
Evaluate side-chains
  15 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 10
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain E residue   77 VAL
Chi-restraints excluded: chain E residue   81 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 23 optimal weight:    7.9990
   chunk 19 optimal weight:   10.0000
   chunk 2 optimal weight:    9.9990
   chunk 25 optimal weight:    4.9990
   chunk 24 optimal weight:    8.9990
   chunk 3 optimal weight:    1.9990
   chunk 6 optimal weight:   20.0000
   chunk 22 optimal weight:    0.9990
   chunk 13 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
F  65 ASN
A  65 ASN
C  65 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4952 r_free = 0.4952 target = 0.155301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4764 r_free = 0.4764 target = 0.131206 restraints weight = 4348.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.4760 rms_B_bonded: 3.48
r_work: 0.4673 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.4673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6111
moved from start:          0.3242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2370  Z= 0.158
  Angle     :  0.460   4.344   3198  Z= 0.276
  Chirality :  0.055   0.130    426
  Planarity :  0.002   0.010    396
  Dihedral  :  4.936  13.057    342
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.63 %
    Favored  : 91.37 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 12.50 %
    Favored  : 86.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.25 (0.38), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.23 (0.29), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.010   0.002   PHE F  94 
 HIS   0.010   0.004   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 2370)
  covalent geometry    : angle       0.45972 ( 3198)
  hydrogen bonds       : bond        0.04027 (   28)
  hydrogen bonds       : angle       7.47718 (   84)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 12
  time to evaluate  : 0.097 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 15
  average time/residue: 0.0308
  time to fit residues: 0.7493
Evaluate side-chains
  14 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 11
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain E residue   81 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 29 optimal weight:    0.0470
   chunk 10 optimal weight:    9.9990
   chunk 8 optimal weight:    6.9990
   chunk 28 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 21 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   overall best weight:    2.1884

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

Flipped N/Q/H residues before XYZ refinement:
F  65 ASN
A  65 ASN
C  65 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4974 r_free = 0.4974 target = 0.158808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4791 r_free = 0.4791 target = 0.134012 restraints weight = 4217.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.4863 rms_B_bonded: 3.43
r_work: 0.4778 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.4778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5929
moved from start:          0.3321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   2370  Z= 0.120
  Angle     :  0.422   4.095   3198  Z= 0.253
  Chirality :  0.054   0.129    426
  Planarity :  0.002   0.009    396
  Dihedral  :  4.587  12.422    342
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.04 %
    Favored  : 91.96 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 11.67 %
    Favored  : 86.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.11 (0.39), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.13 (0.30), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.009   0.002   PHE F  94 
 HIS   0.009   0.004   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 2370)
  covalent geometry    : angle       0.42170 ( 3198)
  hydrogen bonds       : bond        0.03630 (   28)
  hydrogen bonds       : angle       7.35920 (   84)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 12
  time to evaluate  : 0.094 
Fit side-chains
  outliers start: 5
  outliers final: 5
  residues processed: 17
  average time/residue: 0.0294
  time to fit residues: 0.8027
Evaluate side-chains
  16 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 11
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain E residue   81 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 20 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 4 optimal weight:    0.0170
   chunk 7 optimal weight:    1.9990
   chunk 26 optimal weight:   10.0000
   chunk 21 optimal weight:    7.9990
   chunk 17 optimal weight:    9.9990
   chunk 24 optimal weight:   10.0000
   chunk 14 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 11 optimal weight:    6.9990
   overall best weight:    4.2026

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

Flipped N/Q/H residues before XYZ refinement:
F  65 ASN
A  65 ASN
C  65 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4923 r_free = 0.4923 target = 0.153880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4733 r_free = 0.4733 target = 0.129377 restraints weight = 4452.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.4804 rms_B_bonded: 3.53
r_work: 0.4708 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.4708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6058
moved from start:          0.3462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   2370  Z= 0.198
  Angle     :  0.502   4.621   3198  Z= 0.303
  Chirality :  0.056   0.133    426
  Planarity :  0.002   0.009    396
  Dihedral  :  5.084  13.109    342
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.50 %
    Favored  : 87.50 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 10.83 %
    Favored  : 86.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.16 (0.40), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.16 (0.31), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.015   0.003   PHE F  94 
 HIS   0.008   0.004   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 2370)
  covalent geometry    : angle       0.50170 ( 3198)
  hydrogen bonds       : bond        0.04134 (   28)
  hydrogen bonds       : angle       7.48355 (   84)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 12
  time to evaluate  : 0.088 
Fit side-chains
  outliers start: 7
  outliers final: 6
  residues processed: 19
  average time/residue: 0.0288
  time to fit residues: 0.8661
Evaluate side-chains
  17 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 11
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain E residue   81 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 3 optimal weight:    9.9990
   chunk 17 optimal weight:    7.9990
   chunk 19 optimal weight:    0.5980
   chunk 2 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 20 optimal weight:    9.9990
   chunk 28 optimal weight:    6.9990
   chunk 10 optimal weight:    9.9990
   chunk 22 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    2.9188

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

Flipped N/Q/H residues before XYZ refinement:
F  65 ASN
A  65 ASN
C  65 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4955 r_free = 0.4955 target = 0.155909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4761 r_free = 0.4761 target = 0.131283 restraints weight = 4395.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.4761 rms_B_bonded: 3.51
r_work: 0.4675 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.4675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6212
moved from start:          0.3493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2370  Z= 0.149
  Angle     :  0.458   4.295   3198  Z= 0.275
  Chirality :  0.055   0.133    426
  Planarity :  0.002   0.009    396
  Dihedral  :  4.896  13.418    342
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.74 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 12.08 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.13 (0.40), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.14 (0.30), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.011   0.002   PHE F  94 
 HIS   0.009   0.004   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 2370)
  covalent geometry    : angle       0.45778 ( 3198)
  hydrogen bonds       : bond        0.03931 (   28)
  hydrogen bonds       : angle       7.46937 (   84)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 10
  time to evaluate  : 0.081 
Fit side-chains
  outliers start: 5
  outliers final: 5
  residues processed: 15
  average time/residue: 0.0294
  time to fit residues: 0.7076
Evaluate side-chains
  14 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 9
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain E residue   81 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 5 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9980
   chunk 17 optimal weight:    9.9990
   chunk 15 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 27 optimal weight:    9.9990
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
F  65 ASN
A  65 ASN
C  65 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4933 r_free = 0.4933 target = 0.153845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4741 r_free = 0.4741 target = 0.129523 restraints weight = 4454.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.4618 rms_B_bonded: 3.54
r_work: 0.4518 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.4518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6713
moved from start:          0.3607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2370  Z= 0.182
  Angle     :  0.494   4.525   3198  Z= 0.297
  Chirality :  0.056   0.131    426
  Planarity :  0.002   0.009    396
  Dihedral  :  5.103  13.327    342
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.20 %
    Favored  : 87.80 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 11.67 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.13 (0.41), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.14 (0.31), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.014   0.003   PHE F  94 
 HIS   0.009   0.004   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 2370)
  covalent geometry    : angle       0.49412 ( 3198)
  hydrogen bonds       : bond        0.04067 (   28)
  hydrogen bonds       : angle       7.56607 (   84)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 795.96 seconds
wall clock time: 14 minutes 20.01 seconds (860.01 seconds total)