Starting phenix.real_space_refine
on Fri May  9 15:45:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hzb_35087/05_2025/8hzb_35087.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hzb_35087/05_2025/8hzb_35087.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hzb_35087/05_2025/8hzb_35087.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hzb_35087/05_2025/8hzb_35087.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hzb_35087/05_2025/8hzb_35087.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hzb_35087/05_2025/8hzb_35087.cif"
  }
  resolution = 3.2
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    1860      2.51       5
     N     516      2.21       5
     O     600      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 2976
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 496
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 496
          Classifications: {'peptide': 72}
          Link IDs: {'TRANS': 71}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 1.85, per 1000 atoms: 0.62
  Number of scatterers: 2976
  At special positions: 0
  Unit cell: (96.28, 121.18, 36.52, 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     600      8.00
     N     516      7.00
     C    1860      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: 0.70
  Conformation dependent library (CDL) restraints added in 468.4 milliseconds
  

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 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 12 sheets defined
      0.0% alpha, 50.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 15 through 21
      removed outlier: 6.545A  pdb=" N   VAL D  16 " --> pdb=" O   ALA E  17 " (cutoff:3.500A)
      removed outlier: 8.570A  pdb=" N   ALA E  19 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   ALA D  18 " --> pdb=" O   ALA E  19 " (cutoff:3.500A)
      removed outlier: 8.317A  pdb=" N   LYS E  21 " --> pdb=" O   ALA D  18 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   GLU D  20 " --> pdb=" O   LYS E  21 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 58
      removed outlier: 6.799A  pdb=" N   GLY C  47 " --> pdb=" O   GLU D  46 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   VAL D  52 " --> pdb=" O   GLY C  51 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   ALA C  53 " --> pdb=" O   VAL D  52 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   THR D  54 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   VAL C  55 " --> pdb=" O   THR D  54 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   ALA D  56 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   GLU C  57 " --> pdb=" O   ALA D  56 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   VAL D  48 " --> pdb=" O   GLY E  47 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   VAL E  49 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   HIS D  50 " --> pdb=" O   VAL E  49 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   GLY E  51 " --> pdb=" O   HIS D  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 62 through 66
      removed outlier: 6.526A  pdb=" N   VAL D  63 " --> pdb=" O   THR E  64 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   VAL E  66 " --> pdb=" O   VAL D  63 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   ASN D  65 " --> pdb=" O   VAL E  66 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 69 through 80
      removed outlier: 9.129A  pdb=" N   VAL D  70 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 10.489A  pdb=" N   GLY C  73 " --> pdb=" O   VAL D  70 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   THR D  72 " --> pdb=" O   GLY C  73 " (cutoff:3.500A)
      removed outlier: 8.673A  pdb=" N   THR C  75 " --> pdb=" O   THR D  72 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   VAL D  74 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 5.899A  pdb=" N   VAL C  77 " --> pdb=" O   VAL D  74 " (cutoff:3.500A)
      removed outlier: 7.399A  pdb=" N   ALA D  76 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
      removed outlier: 10.130A  pdb=" N   GLN C  79 " --> pdb=" O   ALA D  76 " (cutoff:3.500A)
      removed outlier: 8.869A  pdb=" N   ALA D  78 " --> pdb=" O   GLN C  79 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   VAL E  70 " --> pdb=" O   ALA D  69 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   VAL D  71 " --> pdb=" O   VAL E  70 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   THR E  72 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   GLY D  73 " --> pdb=" O   THR E  72 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   VAL D  77 " --> pdb=" O   ALA E  76 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   ALA E  78 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   GLN D  79 " --> pdb=" O   ALA E  78 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   LYS E  80 " --> pdb=" O   GLN D  79 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 91 through 94
      removed outlier: 6.784A  pdb=" N   PHE C  94 " --> pdb=" O   GLY D  93 " (cutoff:3.500A)
      removed outlier: 8.820A  pdb=" N   THR D  92 " --> pdb=" O   GLY E  93 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 97 through 98
      removed outlier: 6.906A  pdb=" N   LYS D  97 " --> pdb=" O   ASP E  98 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 15 through 21
      removed outlier: 6.526A  pdb=" N   VAL F  16 " --> pdb=" O   ALA B  17 " (cutoff:3.500A)
      removed outlier: 8.542A  pdb=" N   ALA B  19 " --> pdb=" O   VAL F  16 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ALA F  18 " --> pdb=" O   ALA B  19 " (cutoff:3.500A)
      removed outlier: 8.280A  pdb=" N   LYS B  21 " --> pdb=" O   ALA F  18 " (cutoff:3.500A)
      removed outlier: 6.113A  pdb=" N   GLU F  20 " --> pdb=" O   LYS B  21 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 46 through 58
      removed outlier: 6.821A  pdb=" N   GLY A  47 " --> pdb=" O   GLU F  46 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   VAL F  52 " --> pdb=" O   GLY A  51 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   ALA A  53 " --> pdb=" O   VAL F  52 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   THR F  54 " --> pdb=" O   ALA A  53 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   VAL A  55 " --> pdb=" O   THR F  54 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   ALA F  56 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   GLU A  57 " --> pdb=" O   ALA F  56 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   VAL F  48 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   VAL B  49 " --> pdb=" O   VAL F  48 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   HIS F  50 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   GLY B  51 " --> pdb=" O   HIS F  50 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 62 through 66
      removed outlier: 6.572A  pdb=" N   VAL F  63 " --> pdb=" O   THR B  64 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   VAL B  66 " --> pdb=" O   VAL F  63 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   ASN F  65 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 69 through 80
      removed outlier: 9.115A  pdb=" N   VAL F  70 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
      removed outlier: 10.470A  pdb=" N   GLY A  73 " --> pdb=" O   VAL F  70 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   THR F  72 " --> pdb=" O   GLY A  73 " (cutoff:3.500A)
      removed outlier: 8.658A  pdb=" N   THR A  75 " --> pdb=" O   THR F  72 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   VAL F  74 " --> pdb=" O   THR A  75 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   VAL A  77 " --> pdb=" O   VAL F  74 " (cutoff:3.500A)
      removed outlier: 7.392A  pdb=" N   ALA F  76 " --> pdb=" O   VAL A  77 " (cutoff:3.500A)
      removed outlier: 10.132A  pdb=" N   GLN A  79 " --> pdb=" O   ALA F  76 " (cutoff:3.500A)
      removed outlier: 8.877A  pdb=" N   ALA F  78 " --> pdb=" O   GLN A  79 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   VAL B  70 " --> pdb=" O   ALA F  69 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   VAL F  71 " --> pdb=" O   VAL B  70 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   THR B  72 " --> pdb=" O   VAL F  71 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   GLY F  73 " --> pdb=" O   THR B  72 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   VAL F  77 " --> pdb=" O   ALA B  76 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   ALA B  78 " --> pdb=" O   VAL F  77 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   GLN F  79 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   LYS B  80 " --> pdb=" O   GLN F  79 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 91 through 94
      removed outlier: 6.805A  pdb=" N   PHE A  94 " --> pdb=" O   GLY F  93 " (cutoff:3.500A)
      removed outlier: 8.807A  pdb=" N   THR F  92 " --> pdb=" O   GLY B  93 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 97 through 98
      removed outlier: 6.896A  pdb=" N   LYS F  97 " --> pdb=" O   ASP B  98 " (cutoff:3.500A)

    54 hydrogen bonds defined for protein.
    162 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: 0.66

  Time building geometry restraints manager: 0.82 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 528
        1.29 -     1.35: 460
        1.35 -     1.42: 102
        1.42 -     1.48: 501
        1.48 -     1.55: 1391
  Bond restraints: 2982
  Sorted by residual:
  bond pdb=" CA  LYS A  58 "
       pdb=" C   LYS A  58 "
    ideal  model  delta    sigma   weight residual
    1.526  1.510  0.016 1.08e-02 8.57e+03 2.16e+00
  bond pdb=" CA  LYS E  58 "
       pdb=" C   LYS E  58 "
    ideal  model  delta    sigma   weight residual
    1.526  1.510  0.016 1.08e-02 8.57e+03 2.07e+00
  bond pdb=" CA  LYS C  58 "
       pdb=" C   LYS C  58 "
    ideal  model  delta    sigma   weight residual
    1.526  1.511  0.015 1.08e-02 8.57e+03 1.95e+00
  bond pdb=" CA  LYS B  58 "
       pdb=" C   LYS B  58 "
    ideal  model  delta    sigma   weight residual
    1.526  1.511  0.015 1.08e-02 8.57e+03 1.94e+00
  bond pdb=" CA  LYS D  58 "
       pdb=" C   LYS D  58 "
    ideal  model  delta    sigma   weight residual
    1.526  1.511  0.015 1.08e-02 8.57e+03 1.92e+00
  ... (remaining 2977 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.14: 3486
        1.14 -     2.28: 412
        2.28 -     3.42: 93
        3.42 -     4.56: 23
        4.56 -     5.70: 12
  Bond angle restraints: 4026
  Sorted by residual:
  angle pdb=" C   GLY E  41 "
        pdb=" N   SER E  42 "
        pdb=" CA  SER E  42 "
      ideal   model   delta    sigma   weight residual
     122.42  117.96    4.46 1.55e+00 4.16e-01 8.26e+00
  angle pdb=" C   GLY A  41 "
        pdb=" N   SER A  42 "
        pdb=" CA  SER A  42 "
      ideal   model   delta    sigma   weight residual
     122.42  117.97    4.45 1.55e+00 4.16e-01 8.24e+00
  angle pdb=" C   GLY B  41 "
        pdb=" N   SER B  42 "
        pdb=" CA  SER B  42 "
      ideal   model   delta    sigma   weight residual
     122.42  117.97    4.45 1.55e+00 4.16e-01 8.23e+00
  angle pdb=" C   GLY D  41 "
        pdb=" N   SER D  42 "
        pdb=" CA  SER D  42 "
      ideal   model   delta    sigma   weight residual
     122.42  117.97    4.45 1.55e+00 4.16e-01 8.23e+00
  angle pdb=" C   GLY C  41 "
        pdb=" N   SER C  42 "
        pdb=" CA  SER C  42 "
      ideal   model   delta    sigma   weight residual
     122.42  118.01    4.41 1.55e+00 4.16e-01 8.11e+00
  ... (remaining 4021 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.62: 1524
       17.62 -    35.24: 186
       35.24 -    52.85: 30
       52.85 -    70.47: 0
       70.47 -    88.09: 12
  Dihedral angle restraints: 1752
    sinusoidal: 582
      harmonic: 1170
  Sorted by residual:
  dihedral pdb=" CA  VAL A  40 "
           pdb=" C   VAL A  40 "
           pdb=" N   GLY A  41 "
           pdb=" CA  GLY A  41 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.42   23.58     0      5.00e+00 4.00e-02 2.22e+01
  dihedral pdb=" CA  VAL D  40 "
           pdb=" C   VAL D  40 "
           pdb=" N   GLY D  41 "
           pdb=" CA  GLY D  41 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.44   23.56     0      5.00e+00 4.00e-02 2.22e+01
  dihedral pdb=" CA  VAL F  40 "
           pdb=" C   VAL F  40 "
           pdb=" N   GLY F  41 "
           pdb=" CA  GLY F  41 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.45   23.55     0      5.00e+00 4.00e-02 2.22e+01
  ... (remaining 1749 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 148
       0.026 -    0.051: 160
       0.051 -    0.077: 99
       0.077 -    0.102: 71
       0.102 -    0.128: 56
  Chirality restraints: 534
  Sorted by residual:
  chirality pdb=" CA  VAL A  49 "
            pdb=" N   VAL A  49 "
            pdb=" C   VAL A  49 "
            pdb=" CB  VAL A  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.08e-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   -0.12 2.00e-01 2.50e+01 3.90e-01
  chirality pdb=" CA  VAL E  49 "
            pdb=" N   VAL E  49 "
            pdb=" C   VAL E  49 "
            pdb=" CB  VAL E  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.89e-01
  ... (remaining 531 not shown)

  Planarity restraints: 498
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C  66 "    0.007 2.00e-02 2.50e+03   1.37e-02 1.88e+00
        pdb=" C   VAL C  66 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   VAL C  66 "    0.009 2.00e-02 2.50e+03
        pdb=" N   GLY C  67 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL E  66 "    0.007 2.00e-02 2.50e+03   1.37e-02 1.86e+00
        pdb=" C   VAL E  66 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   VAL E  66 "    0.009 2.00e-02 2.50e+03
        pdb=" N   GLY E  67 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B  66 "   -0.007 2.00e-02 2.50e+03   1.35e-02 1.81e+00
        pdb=" C   VAL B  66 "    0.023 2.00e-02 2.50e+03
        pdb=" O   VAL B  66 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   GLY B  67 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 495 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 154
        2.71 -     3.26: 2853
        3.26 -     3.80: 4388
        3.80 -     4.35: 5053
        4.35 -     4.90: 10336
  Nonbonded interactions: 22784
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU F  46 "
            pdb=" NZ  LYS F  80 "
     model   vdw
     2.162 3.120
  nonbonded pdb=" OE2 GLU C  46 "
            pdb=" NZ  LYS C  80 "
     model   vdw
     2.162 3.120
  nonbonded pdb=" OE2 GLU E  46 "
            pdb=" NZ  LYS E  80 "
     model   vdw
     2.162 3.120
  nonbonded pdb=" OE2 GLU B  46 "
            pdb=" NZ  LYS B  80 "
     model   vdw
     2.162 3.120
  nonbonded pdb=" OE2 GLU A  46 "
            pdb=" NZ  LYS A  80 "
     model   vdw
     2.162 3.120
  ... (remaining 22779 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:             1.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.480
  Find NCS groups from input model:        0.070
  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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7055
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.044   2982  Z= 0.398
  Angle     :  0.920   5.699   4026  Z= 0.518
  Chirality :  0.059   0.128    534
  Planarity :  0.004   0.014    498
  Dihedral  : 16.623  88.088   1008
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 16.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.29 %
    Favored  : 89.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 20.00 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.16 (0.28), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.17 (0.22), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.003   HIS A  50 
 PHE   0.019   0.006   PHE C  94 
 TYR   0.019   0.005   TYR F  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18721 (   54)
  hydrogen bonds       : angle       8.50467 (  162)
  covalent geometry    : bond        0.00807 ( 2982)
  covalent geometry    : angle       0.92012 ( 4026)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.322 
Fit side-chains
REVERT: C   45 LYS cc_start: 0.7387 (tttt) cc_final: 0.7140 (tttm)
REVERT: E   45 LYS cc_start: 0.7543 (tttt) cc_final: 0.7095 (tttm)
REVERT: F   45 LYS cc_start: 0.7570 (tttt) cc_final: 0.7092 (tttm)
REVERT: A   45 LYS cc_start: 0.7425 (tttt) cc_final: 0.7175 (tttm)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.1779
  time to fit residues: 5.0998
Evaluate side-chains
  23 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
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:    0.0470
   chunk 31 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 21 optimal weight:   20.0000
   chunk 32 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.9882

-------------------------------------------------------------------------------
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 = 0.5093 r_free = 0.5093 target = 0.262155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4807 r_free = 0.4807 target = 0.227753 restraints weight = 3297.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.4769 rms_B_bonded: 2.93
r_work: 0.4652 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.4652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6962
moved from start:          0.1739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   2982  Z= 0.114
  Angle     :  0.570   4.699   4026  Z= 0.309
  Chirality :  0.051   0.133    534
  Planarity :  0.002   0.012    498
  Dihedral  :  5.979  21.996    426
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.82 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 24.67 %
    Favored  : 73.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.37 (0.35), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.56 (0.27), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS F  50 
 PHE   0.006   0.002   PHE B  94 
 TYR   0.007   0.001   TYR A  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01892 (   54)
  hydrogen bonds       : angle       6.17404 (  162)
  covalent geometry    : bond        0.00217 ( 2982)
  covalent geometry    : angle       0.57035 ( 4026)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 17
  time to evaluate  : 0.321 
Fit side-chains
REVERT: E   45 LYS cc_start: 0.7630 (tttt) cc_final: 0.7045 (tttm)
REVERT: B   45 LYS cc_start: 0.7460 (tttt) cc_final: 0.6917 (tttm)
  outliers start: 6
  outliers final: 6
  residues processed: 23
  average time/residue: 0.1115
  time to fit residues: 3.6383
Evaluate side-chains
  23 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 17
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain B residue   37 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 18 optimal weight:    0.5980
   chunk 31 optimal weight:    8.9990
   chunk 29 optimal weight:    0.8980
   chunk 7 optimal weight:   20.0000
   chunk 24 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 14 optimal weight:   20.0000
   chunk 12 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    1.0784

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5048 r_free = 0.5048 target = 0.255400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4739 r_free = 0.4739 target = 0.220050 restraints weight = 3276.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.4770 rms_B_bonded: 2.82
r_work: 0.4675 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.4675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6973
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   0.015   2982  Z= 0.112
  Angle     :  0.548   4.714   4026  Z= 0.295
  Chirality :  0.050   0.131    534
  Planarity :  0.002   0.012    498
  Dihedral  :  5.622  20.491    426
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.56 %
    Favored  : 90.44 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 23.67 %
    Favored  : 72.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.05 (0.37), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.32 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS F  50 
 PHE   0.005   0.002   PHE B  94 
 TYR   0.008   0.002   TYR A  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01740 (   54)
  hydrogen bonds       : angle       5.69814 (  162)
  covalent geometry    : bond        0.00220 ( 2982)
  covalent geometry    : angle       0.54795 ( 4026)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 18
  time to evaluate  : 0.337 
Fit side-chains
REVERT: C   39 TYR cc_start: 0.6995 (m-80) cc_final: 0.6599 (m-80)
REVERT: C   44 THR cc_start: 0.6594 (OUTLIER) cc_final: 0.6386 (t)
REVERT: E   45 LYS cc_start: 0.7644 (tttt) cc_final: 0.7089 (tttm)
REVERT: F   44 THR cc_start: 0.6492 (OUTLIER) cc_final: 0.6190 (t)
REVERT: A   39 TYR cc_start: 0.6843 (m-80) cc_final: 0.6383 (m-80)
REVERT: A   44 THR cc_start: 0.6747 (OUTLIER) cc_final: 0.6494 (t)
REVERT: B   45 LYS cc_start: 0.7508 (tttt) cc_final: 0.7010 (tttm)
  outliers start: 12
  outliers final: 6
  residues processed: 30
  average time/residue: 0.1045
  time to fit residues: 4.3317
Evaluate side-chains
  26 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 17
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain B residue   37 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    8.9990
   chunk 6 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 36 optimal weight:    8.9990
   chunk 15 optimal weight:    7.9990
   chunk 38 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   chunk 10 optimal weight:    5.9990
   overall best weight:    3.7990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4983 r_free = 0.4983 target = 0.248199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.211758 restraints weight = 3337.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.4597 rms_B_bonded: 2.82
r_work: 0.4508 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.4508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7166
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035   2982  Z= 0.278
  Angle     :  0.800   7.189   4026  Z= 0.429
  Chirality :  0.056   0.204    534
  Planarity :  0.003   0.014    498
  Dihedral  :  7.120  21.176    426
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.76 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  7.33 %
    Allowed  : 21.00 %
    Favored  : 71.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.22 (0.36), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.44 (0.27), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.003   HIS D  50 
 PHE   0.017   0.005   PHE B  94 
 TYR   0.018   0.005   TYR C  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02417 (   54)
  hydrogen bonds       : angle       5.79806 (  162)
  covalent geometry    : bond        0.00605 ( 2982)
  covalent geometry    : angle       0.79988 ( 4026)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 25
  time to evaluate  : 0.297 
Fit side-chains
REVERT: C   44 THR cc_start: 0.6782 (OUTLIER) cc_final: 0.6569 (t)
REVERT: E   45 LYS cc_start: 0.7792 (tttt) cc_final: 0.7262 (tttm)
REVERT: F   39 TYR cc_start: 0.7091 (m-80) cc_final: 0.6837 (m-80)
REVERT: F   44 THR cc_start: 0.6919 (OUTLIER) cc_final: 0.6536 (t)
REVERT: A   44 THR cc_start: 0.6950 (OUTLIER) cc_final: 0.6654 (t)
REVERT: B   39 TYR cc_start: 0.7236 (m-80) cc_final: 0.7026 (m-80)
REVERT: B   45 LYS cc_start: 0.7695 (tttt) cc_final: 0.7256 (tttm)
  outliers start: 22
  outliers final: 15
  residues processed: 42
  average time/residue: 0.1062
  time to fit residues: 5.9268
Evaluate side-chains
  43 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 25
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   66 VAL
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   75 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:    0.4980
   chunk 27 optimal weight:    4.9990
   chunk 14 optimal weight:   20.0000
   chunk 28 optimal weight:   20.0000
   chunk 25 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 3 optimal weight:    7.9990
   chunk 35 optimal weight:   20.0000
   chunk 37 optimal weight:    0.9980
   overall best weight:    1.4784

-------------------------------------------------------------------------------
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 = 0.5016 r_free = 0.5016 target = 0.250541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4700 r_free = 0.4700 target = 0.215301 restraints weight = 3399.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.4717 rms_B_bonded: 2.82
r_work: 0.4620 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.4620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7062
moved from start:          0.2209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   2982  Z= 0.131
  Angle     :  0.603   5.197   4026  Z= 0.323
  Chirality :  0.052   0.170    534
  Planarity :  0.002   0.013    498
  Dihedral  :  6.042  20.467    426
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.78 %
    Favored  : 89.22 %
  Rotamer:
    Outliers :  6.33 %
    Allowed  : 24.00 %
    Favored  : 69.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.10 (0.37), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.35 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS F  50 
 PHE   0.008   0.002   PHE B  94 
 TYR   0.009   0.002   TYR A  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01785 (   54)
  hydrogen bonds       : angle       5.75558 (  162)
  covalent geometry    : bond        0.00267 ( 2982)
  covalent geometry    : angle       0.60255 ( 4026)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 18
  time to evaluate  : 0.319 
Fit side-chains
REVERT: C   39 TYR cc_start: 0.7078 (m-80) cc_final: 0.6539 (m-80)
REVERT: E   45 LYS cc_start: 0.7693 (tttt) cc_final: 0.7168 (tttm)
REVERT: F   44 THR cc_start: 0.6731 (OUTLIER) cc_final: 0.6494 (t)
REVERT: A   39 TYR cc_start: 0.6997 (m-80) cc_final: 0.6403 (m-80)
REVERT: B   39 TYR cc_start: 0.6891 (m-80) cc_final: 0.6687 (m-80)
REVERT: B   45 LYS cc_start: 0.7699 (tttt) cc_final: 0.7256 (tttm)
  outliers start: 19
  outliers final: 11
  residues processed: 36
  average time/residue: 0.0887
  time to fit residues: 4.5544
Evaluate side-chains
  30 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 18
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   75 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 21 optimal weight:   20.0000
   chunk 22 optimal weight:    0.4980
   chunk 26 optimal weight:    2.9990
   chunk 20 optimal weight:   10.0000
   chunk 12 optimal weight:    4.9990
   chunk 28 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9980
   chunk 14 optimal weight:   20.0000
   chunk 31 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9980
   overall best weight:    2.0984

-------------------------------------------------------------------------------
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 = 0.5026 r_free = 0.5026 target = 0.252095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4711 r_free = 0.4711 target = 0.218229 restraints weight = 3359.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.4668 rms_B_bonded: 2.90
r_work: 0.4554 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.4554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7101
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   2982  Z= 0.168
  Angle     :  0.642   5.665   4026  Z= 0.343
  Chirality :  0.052   0.137    534
  Planarity :  0.002   0.013    498
  Dihedral  :  6.249  19.785    426
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.76 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  6.33 %
    Allowed  : 23.33 %
    Favored  : 70.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.04 (0.37), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.30 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.003   HIS F  50 
 PHE   0.010   0.003   PHE B  94 
 TYR   0.013   0.003   TYR A  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01899 (   54)
  hydrogen bonds       : angle       5.73023 (  162)
  covalent geometry    : bond        0.00358 ( 2982)
  covalent geometry    : angle       0.64227 ( 4026)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 21
  time to evaluate  : 0.326 
Fit side-chains
REVERT: C   39 TYR cc_start: 0.7067 (m-80) cc_final: 0.6609 (m-80)
REVERT: E   45 LYS cc_start: 0.7672 (tttt) cc_final: 0.7174 (tttm)
REVERT: F   44 THR cc_start: 0.6807 (OUTLIER) cc_final: 0.6526 (t)
REVERT: B   45 LYS cc_start: 0.7702 (tttt) cc_final: 0.7320 (tttm)
  outliers start: 19
  outliers final: 15
  residues processed: 37
  average time/residue: 0.1008
  time to fit residues: 5.1279
Evaluate side-chains
  37 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 21
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   75 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 39 optimal weight:    0.8980
   chunk 23 optimal weight:    5.9990
   chunk 41 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 6 optimal weight:    9.9990
   chunk 26 optimal weight:    3.9990
   chunk 7 optimal weight:   20.0000
   chunk 17 optimal weight:    0.0870
   overall best weight:    1.5362

-------------------------------------------------------------------------------
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 = 0.5049 r_free = 0.5049 target = 0.254994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4726 r_free = 0.4726 target = 0.219717 restraints weight = 3361.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.4683 rms_B_bonded: 2.78
r_work: 0.4588 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.4588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
moved from start:          0.2590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   2982  Z= 0.131
  Angle     :  0.582   5.128   4026  Z= 0.312
  Chirality :  0.051   0.128    534
  Planarity :  0.002   0.013    498
  Dihedral  :  5.834  19.575    426
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.78 %
    Favored  : 89.22 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 23.67 %
    Favored  : 70.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.94 (0.37), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.23 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS F  50 
 PHE   0.007   0.002   PHE B  94 
 TYR   0.009   0.002   TYR A  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01747 (   54)
  hydrogen bonds       : angle       5.64401 (  162)
  covalent geometry    : bond        0.00270 ( 2982)
  covalent geometry    : angle       0.58241 ( 4026)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 20
  time to evaluate  : 0.339 
Fit side-chains
REVERT: C   39 TYR cc_start: 0.7041 (m-80) cc_final: 0.6595 (m-80)
REVERT: E   45 LYS cc_start: 0.7710 (tttt) cc_final: 0.7177 (tttm)
REVERT: F   44 THR cc_start: 0.6661 (OUTLIER) cc_final: 0.6346 (t)
REVERT: A   39 TYR cc_start: 0.7030 (m-80) cc_final: 0.6535 (m-80)
REVERT: B   45 LYS cc_start: 0.7730 (tttt) cc_final: 0.7298 (tttm)
  outliers start: 17
  outliers final: 15
  residues processed: 33
  average time/residue: 0.1342
  time to fit residues: 5.8821
Evaluate side-chains
  33 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 17
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   75 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    8.9990
   chunk 6 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 41 optimal weight:    8.9990
   chunk 21 optimal weight:   20.0000
   chunk 16 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0970
   overall best weight:    1.4184

-------------------------------------------------------------------------------
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 = 0.254828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4726 r_free = 0.4726 target = 0.219404 restraints weight = 3318.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.4722 rms_B_bonded: 2.77
r_work: 0.4642 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.4642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7040
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   2982  Z= 0.125
  Angle     :  0.569   5.120   4026  Z= 0.304
  Chirality :  0.051   0.129    534
  Planarity :  0.002   0.013    498
  Dihedral  :  5.723  18.002    426
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.78 %
    Favored  : 89.22 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 24.33 %
    Favored  : 70.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.81 (0.38), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.13 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS F  50 
 PHE   0.007   0.002   PHE B  94 
 TYR   0.010   0.002   TYR A  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01686 (   54)
  hydrogen bonds       : angle       5.55313 (  162)
  covalent geometry    : bond        0.00258 ( 2982)
  covalent geometry    : angle       0.56915 ( 4026)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 16
  time to evaluate  : 0.311 
Fit side-chains
REVERT: C   39 TYR cc_start: 0.6887 (m-80) cc_final: 0.6593 (m-80)
REVERT: E   45 LYS cc_start: 0.7663 (tttt) cc_final: 0.7180 (tttm)
REVERT: F   44 THR cc_start: 0.6654 (OUTLIER) cc_final: 0.6442 (t)
REVERT: B   45 LYS cc_start: 0.7679 (tttt) cc_final: 0.7209 (tttm)
  outliers start: 16
  outliers final: 15
  residues processed: 30
  average time/residue: 0.0912
  time to fit residues: 3.9207
Evaluate side-chains
  32 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 16
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   75 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 29 optimal weight:    0.7980
   chunk 25 optimal weight:    4.9990
   chunk 6 optimal weight:   10.0000
   chunk 1 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 7 optimal weight:   20.0000
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.5080 r_free = 0.5080 target = 0.257827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4759 r_free = 0.4759 target = 0.222747 restraints weight = 3377.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.4719 rms_B_bonded: 2.77
r_work: 0.4625 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.4625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6965
moved from start:          0.2995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   2982  Z= 0.104
  Angle     :  0.528   4.212   4026  Z= 0.284
  Chirality :  0.050   0.128    534
  Planarity :  0.002   0.012    498
  Dihedral  :  5.365  17.930    426
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.05 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 24.33 %
    Favored  : 70.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.74 (0.38), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.08 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS D  50 
 PHE   0.005   0.001   PHE B  94 
 TYR   0.007   0.002   TYR A  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01600 (   54)
  hydrogen bonds       : angle       5.48534 (  162)
  covalent geometry    : bond        0.00213 ( 2982)
  covalent geometry    : angle       0.52834 ( 4026)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 14
  time to evaluate  : 0.333 
Fit side-chains
REVERT: C   39 TYR cc_start: 0.6832 (m-80) cc_final: 0.6571 (m-80)
REVERT: E   45 LYS cc_start: 0.7670 (tttt) cc_final: 0.7150 (tttm)
REVERT: A   39 TYR cc_start: 0.6797 (m-80) cc_final: 0.6446 (m-80)
  outliers start: 15
  outliers final: 14
  residues processed: 28
  average time/residue: 0.0990
  time to fit residues: 3.9908
Evaluate side-chains
  27 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 13
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   75 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 20 optimal weight:    8.9990
   chunk 11 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 41 optimal weight:    6.9990
   overall best weight:    2.5788

-------------------------------------------------------------------------------
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 = 0.5024 r_free = 0.5024 target = 0.250439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4682 r_free = 0.4682 target = 0.214097 restraints weight = 3325.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.4676 rms_B_bonded: 2.74
r_work: 0.4581 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.4581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
moved from start:          0.2822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   2982  Z= 0.193
  Angle     :  0.664   6.323   4026  Z= 0.353
  Chirality :  0.052   0.125    534
  Planarity :  0.002   0.014    498
  Dihedral  :  6.356  18.399    426
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.76 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 23.67 %
    Favored  : 71.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.76 (0.38), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.09 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS D  50 
 PHE   0.012   0.004   PHE B  94 
 TYR   0.014   0.003   TYR C  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02010 (   54)
  hydrogen bonds       : angle       5.58962 (  162)
  covalent geometry    : bond        0.00409 ( 2982)
  covalent geometry    : angle       0.66356 ( 4026)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 22
  time to evaluate  : 0.326 
Fit side-chains
REVERT: C   39 TYR cc_start: 0.7053 (m-80) cc_final: 0.6724 (m-80)
REVERT: E   45 LYS cc_start: 0.7729 (tttt) cc_final: 0.7237 (tttm)
REVERT: A   39 TYR cc_start: 0.7103 (m-80) cc_final: 0.6652 (m-80)
REVERT: B   45 LYS cc_start: 0.7745 (tttt) cc_final: 0.7304 (tttm)
  outliers start: 15
  outliers final: 15
  residues processed: 34
  average time/residue: 0.1126
  time to fit residues: 5.1786
Evaluate side-chains
  37 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 22
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   75 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 14 optimal weight:    7.9990
   chunk 12 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0770
   chunk 33 optimal weight:    3.9990
   chunk 41 optimal weight:    0.3980
   chunk 22 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    1.2740

-------------------------------------------------------------------------------
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 = 0.5067 r_free = 0.5067 target = 0.255802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4745 r_free = 0.4745 target = 0.220968 restraints weight = 3341.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.4705 rms_B_bonded: 2.69
r_work: 0.4614 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.4614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7015
moved from start:          0.3120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   2982  Z= 0.116
  Angle     :  0.555   4.675   4026  Z= 0.297
  Chirality :  0.051   0.129    534
  Planarity :  0.002   0.013    498
  Dihedral  :  5.651  18.687    426
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.29 %
    Favored  : 89.71 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 24.67 %
    Favored  : 71.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.69 (0.38), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.04 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS D  50 
 PHE   0.005   0.002   PHE B  94 
 TYR   0.009   0.002   TYR C  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01660 (   54)
  hydrogen bonds       : angle       5.51179 (  162)
  covalent geometry    : bond        0.00237 ( 2982)
  covalent geometry    : angle       0.55472 ( 4026)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1817.57 seconds
wall clock time: 32 minutes 20.69 seconds (1940.69 seconds total)