Starting phenix.real_space_refine
on Wed Jun  4 12:57:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hzb_35087/06_2025/8hzb_35087.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hzb_35087/06_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_35087/06_2025/8hzb_35087.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hzb_35087/06_2025/8hzb_35087.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hzb_35087/06_2025/8hzb_35087.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hzb_35087/06_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-5710/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: 2.19, per 1000 atoms: 0.74
  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: 0.71
  Conformation dependent library (CDL) restraints added in 407.1 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: 0.40
  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: 0.64

  Time building geometry restraints manager: 0.86 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:             1.990
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.990
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.180
-------------------------------------------------------------------------------
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  : 0.309 
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: 0.1911
  time to fit residues: 5.4949
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  : 0.292 
-------------------------------------------------------------------------------
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: 3.48 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  : 0.291 
Fit side-chains
REVERT: E   45 LYS cc_start: 0.7633 (tttt) cc_final: 0.7047 (tttm)
REVERT: B   45 LYS cc_start: 0.7457 (tttt) cc_final: 0.6914 (tttm)
  outliers start: 6
  outliers final: 6
  residues processed: 23
  average time/residue: 0.1132
  time to fit residues: 3.6769
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  : 0.296 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 31 optimal weight:    8.9990
   chunk 29 optimal weight:    0.7980
   chunk 7 optimal weight:   20.0000
   chunk 24 optimal weight:    1.9990
   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:    0.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.5055 r_free = 0.5055 target = 0.256365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4744 r_free = 0.4744 target = 0.220897 restraints weight = 3279.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.4736 rms_B_bonded: 2.80
r_work: 0.4641 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.4641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6986
moved from start:          0.1973

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= 0.114
  Angle     :  0.553   4.778   4026  Z= 0.297
  Chirality :  0.050   0.129    534
  Planarity :  0.002   0.012    498
  Dihedral  :  5.663  20.358    426
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 5.41
  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: -3.07 (0.37), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.33 (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   0.009   0.002   TYR A  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01808 (   54)
  hydrogen bonds       : angle       5.72434 (  162)
  covalent geometry    : bond        0.00227 ( 2982)
  covalent geometry    : angle       0.55347 ( 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
  29 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 17
  time to evaluate  : 0.292 
Fit side-chains
REVERT: D   39 TYR cc_start: 0.6862 (m-80) cc_final: 0.6639 (m-80)
REVERT: C   39 TYR cc_start: 0.6941 (m-80) cc_final: 0.6543 (m-80)
REVERT: C   44 THR cc_start: 0.6622 (OUTLIER) cc_final: 0.6406 (t)
REVERT: E   44 THR cc_start: 0.6744 (OUTLIER) cc_final: 0.6539 (t)
REVERT: E   45 LYS cc_start: 0.7660 (tttt) cc_final: 0.7107 (tttm)
REVERT: F   44 THR cc_start: 0.6494 (OUTLIER) cc_final: 0.6180 (t)
REVERT: A   39 TYR cc_start: 0.6859 (m-80) cc_final: 0.6387 (m-80)
REVERT: A   44 THR cc_start: 0.6745 (OUTLIER) cc_final: 0.6480 (t)
REVERT: B   44 THR cc_start: 0.6680 (OUTLIER) cc_final: 0.6477 (t)
REVERT: B   45 LYS cc_start: 0.7508 (tttt) cc_final: 0.7014 (tttm)
  outliers start: 12
  outliers final: 6
  residues processed: 29
  average time/residue: 0.0923
  time to fit residues: 3.8327
Evaluate side-chains
  28 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 17
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
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 E residue   44 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 B residue   37 VAL
Chi-restraints excluded: chain B residue   44 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    0.0060
   chunk 6 optimal weight:    9.9990
   chunk 39 optimal weight:    0.8980
   chunk 17 optimal weight:    6.9990
   chunk 36 optimal weight:    5.9990
   chunk 15 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0270
   overall best weight:    1.3858

-------------------------------------------------------------------------------
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 = 0.5031 r_free = 0.5031 target = 0.252460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4707 r_free = 0.4707 target = 0.216487 restraints weight = 3356.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.4702 rms_B_bonded: 2.87
r_work: 0.4616 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.4616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7009
moved from start:          0.2148

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= 0.124
  Angle     :  0.556   4.645   4026  Z= 0.298
  Chirality :  0.051   0.129    534
  Planarity :  0.002   0.013    498
  Dihedral  :  5.623  19.567    426
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.56 %
    Favored  : 90.44 %
  Rotamer:
    Outliers :  6.00 %
    Allowed  : 23.33 %
    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: -2.92 (0.38), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.22 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS D  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        0.01660 (   54)
  hydrogen bonds       : angle       5.61341 (  162)
  covalent geometry    : bond        0.00253 ( 2982)
  covalent geometry    : angle       0.55568 ( 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
  38 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 20
  time to evaluate  : 0.286 
Fit side-chains
REVERT: C   39 TYR cc_start: 0.6942 (m-80) cc_final: 0.6644 (m-80)
REVERT: E   44 THR cc_start: 0.6819 (OUTLIER) cc_final: 0.6591 (t)
REVERT: E   45 LYS cc_start: 0.7692 (tttt) cc_final: 0.7157 (tttm)
REVERT: A   39 TYR cc_start: 0.6782 (m-80) cc_final: 0.6372 (m-80)
REVERT: B   45 LYS cc_start: 0.7640 (tttt) cc_final: 0.7125 (tttm)
  outliers start: 18
  outliers final: 10
  residues processed: 36
  average time/residue: 0.0968
  time to fit residues: 4.8315
Evaluate side-chains
  30 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 19
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
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 E residue   37 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   64 THR
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:    8.9990
   chunk 27 optimal weight:    5.9990
   chunk 14 optimal weight:   20.0000
   chunk 28 optimal weight:    8.9990
   chunk 25 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 23 optimal weight:    6.9990
   chunk 36 optimal weight:    0.0980
   chunk 3 optimal weight:    7.9990
   chunk 35 optimal weight:   20.0000
   chunk 37 optimal weight:    0.9980
   overall best weight:    2.2184

-------------------------------------------------------------------------------
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 = 0.5034 r_free = 0.5034 target = 0.252296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4702 r_free = 0.4702 target = 0.216287 restraints weight = 3408.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.4667 rms_B_bonded: 2.82
r_work: 0.4572 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.4572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7089
moved from start:          0.2138

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= 0.175
  Angle     :  0.644   5.583   4026  Z= 0.344
  Chirality :  0.052   0.221    534
  Planarity :  0.002   0.013    498
  Dihedral  :  6.178  19.845    426
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  6.00 %
    Allowed  : 23.33 %
    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: -2.99 (0.38), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.27 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.003   HIS D  50 
 PHE   0.011   0.003   PHE B  94 
 TYR   0.014   0.003   TYR C  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01873 (   54)
  hydrogen bonds       : angle       5.64628 (  162)
  covalent geometry    : bond        0.00370 ( 2982)
  covalent geometry    : angle       0.64443 ( 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
  39 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 21
  time to evaluate  : 0.313 
Fit side-chains
REVERT: C   39 TYR cc_start: 0.7086 (m-80) cc_final: 0.6670 (m-80)
REVERT: E   44 THR cc_start: 0.6821 (OUTLIER) cc_final: 0.6549 (t)
REVERT: E   45 LYS cc_start: 0.7726 (tttt) cc_final: 0.7226 (tttm)
REVERT: A   39 TYR cc_start: 0.7109 (m-80) cc_final: 0.6572 (m-80)
REVERT: B   45 LYS cc_start: 0.7660 (tttt) cc_final: 0.7178 (tttm)
  outliers start: 18
  outliers final: 14
  residues processed: 35
  average time/residue: 0.0869
  time to fit residues: 4.3560
Evaluate side-chains
  36 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 21
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
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 E residue   44 THR
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain A residue   37 VAL
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 21 optimal weight:   20.0000
   chunk 22 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 20 optimal weight:    0.2980
   chunk 12 optimal weight:    6.9990
   chunk 28 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 14 optimal weight:   20.0000
   chunk 31 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   overall best weight:    2.0586

-------------------------------------------------------------------------------
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 = 0.5002 r_free = 0.5002 target = 0.246892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4668 r_free = 0.4668 target = 0.211078 restraints weight = 3405.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.4675 rms_B_bonded: 2.87
r_work: 0.4583 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.4583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7073
moved from start:          0.2360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2982  Z= 0.164
  Angle     :  0.627   5.931   4026  Z= 0.335
  Chirality :  0.052   0.185    534
  Planarity :  0.002   0.013    498
  Dihedral  :  6.050  19.466    426
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.54 %
    Favored  : 89.46 %
  Rotamer:
    Outliers :  6.33 %
    Allowed  : 22.33 %
    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: -2.97 (0.37), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.26 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   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        0.01861 (   54)
  hydrogen bonds       : angle       5.69529 (  162)
  covalent geometry    : bond        0.00344 ( 2982)
  covalent geometry    : angle       0.62690 ( 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
  39 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 20
  time to evaluate  : 0.290 
Fit side-chains
REVERT: C   39 TYR cc_start: 0.6981 (m-80) cc_final: 0.6605 (m-80)
REVERT: E   44 THR cc_start: 0.6709 (OUTLIER) cc_final: 0.6447 (t)
REVERT: E   45 LYS cc_start: 0.7733 (tttt) cc_final: 0.7217 (tttm)
REVERT: A   39 TYR cc_start: 0.6984 (m-80) cc_final: 0.6447 (m-80)
REVERT: B   45 LYS cc_start: 0.7677 (tttt) cc_final: 0.7262 (tttm)
  outliers start: 19
  outliers final: 15
  residues processed: 36
  average time/residue: 0.0817
  time to fit residues: 4.2515
Evaluate side-chains
  36 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 20
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
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   75 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain F residue   37 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:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 23 optimal weight:    7.9990
   chunk 41 optimal weight:    9.9990
   chunk 40 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 7 optimal weight:   20.0000
   chunk 17 optimal weight:    6.9990
   overall best weight:    2.1988

-------------------------------------------------------------------------------
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 = 0.5033 r_free = 0.5033 target = 0.251916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4700 r_free = 0.4700 target = 0.216143 restraints weight = 3373.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.4677 rms_B_bonded: 2.75
r_work: 0.4583 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.4583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
moved from start:          0.2548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   2982  Z= 0.175
  Angle     :  0.651   5.909   4026  Z= 0.347
  Chirality :  0.052   0.148    534
  Planarity :  0.002   0.013    498
  Dihedral  :  6.329  19.827    426
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.01 %
    Favored  : 87.99 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 22.67 %
    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: -2.93 (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   0.003   HIS D  50 
 PHE   0.010   0.003   PHE B  94 
 TYR   0.014   0.003   TYR A  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01919 (   54)
  hydrogen bonds       : angle       5.64366 (  162)
  covalent geometry    : bond        0.00368 ( 2982)
  covalent geometry    : angle       0.65078 ( 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
  38 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 21
  time to evaluate  : 0.375 
Fit side-chains
REVERT: C   39 TYR cc_start: 0.6981 (m-80) cc_final: 0.6554 (m-80)
REVERT: E   44 THR cc_start: 0.6722 (OUTLIER) cc_final: 0.6486 (t)
REVERT: E   45 LYS cc_start: 0.7733 (tttt) cc_final: 0.7250 (tttm)
REVERT: A   39 TYR cc_start: 0.7013 (m-80) cc_final: 0.6536 (m-80)
REVERT: B   45 LYS cc_start: 0.7648 (tttt) cc_final: 0.7216 (tttm)
  outliers start: 17
  outliers final: 14
  residues processed: 35
  average time/residue: 0.0972
  time to fit residues: 4.9129
Evaluate side-chains
  36 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 21
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
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 E residue   44 THR
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   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:    6.9990
   chunk 6 optimal weight:    7.9990
   chunk 12 optimal weight:    1.9990
   chunk 41 optimal weight:    7.9990
   chunk 21 optimal weight:   30.0000
   chunk 16 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   overall best weight:    1.5588

-------------------------------------------------------------------------------
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 = 0.5060 r_free = 0.5060 target = 0.255699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4729 r_free = 0.4729 target = 0.219925 restraints weight = 3319.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.4681 rms_B_bonded: 2.80
r_work: 0.4583 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.4583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7047
moved from start:          0.2785

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= 0.133
  Angle     :  0.584   5.260   4026  Z= 0.312
  Chirality :  0.051   0.149    534
  Planarity :  0.002   0.013    498
  Dihedral  :  5.846  19.141    426
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.54 %
    Favored  : 89.46 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 23.00 %
    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: -2.87 (0.38), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.18 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS D  50 
 PHE   0.007   0.002   PHE B  94 
 TYR   0.011   0.002   TYR C  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01712 (   54)
  hydrogen bonds       : angle       5.60164 (  162)
  covalent geometry    : bond        0.00273 ( 2982)
  covalent geometry    : angle       0.58368 ( 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
  36 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 19
  time to evaluate  : 0.287 
Fit side-chains
REVERT: C   39 TYR cc_start: 0.6808 (m-80) cc_final: 0.6461 (m-80)
REVERT: E   44 THR cc_start: 0.6732 (OUTLIER) cc_final: 0.6522 (t)
REVERT: E   45 LYS cc_start: 0.7737 (tttt) cc_final: 0.7209 (tttm)
REVERT: A   39 TYR cc_start: 0.6850 (m-80) cc_final: 0.6422 (m-80)
REVERT: B   45 LYS cc_start: 0.7662 (tttt) cc_final: 0.7229 (tttm)
  outliers start: 17
  outliers final: 16
  residues processed: 34
  average time/residue: 0.1016
  time to fit residues: 4.7048
Evaluate side-chains
  34 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 17
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
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   75 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain F residue   37 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   66 VAL
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:   10.0000
   chunk 29 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 6 optimal weight:    9.9990
   chunk 1 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 4 optimal weight:    0.0670
   chunk 31 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 7 optimal weight:   20.0000
   overall best weight:    2.1924

-------------------------------------------------------------------------------
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 = 0.5036 r_free = 0.5036 target = 0.252865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4701 r_free = 0.4701 target = 0.216836 restraints weight = 3305.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.4660 rms_B_bonded: 2.71
r_work: 0.4573 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.4573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7106
moved from start:          0.2817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   2982  Z= 0.171
  Angle     :  0.638   5.927   4026  Z= 0.341
  Chirality :  0.052   0.134    534
  Planarity :  0.002   0.014    498
  Dihedral  :  6.239  19.668    426
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.76 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  6.33 %
    Allowed  : 22.00 %
    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: -2.84 (0.37), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.16 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS D  50 
 PHE   0.010   0.003   PHE B  94 
 TYR   0.014   0.003   TYR C  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01901 (   54)
  hydrogen bonds       : angle       5.59987 (  162)
  covalent geometry    : bond        0.00358 ( 2982)
  covalent geometry    : angle       0.63848 ( 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
  38 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 19
  time to evaluate  : 0.330 
Fit side-chains
REVERT: C   39 TYR cc_start: 0.6973 (m-80) cc_final: 0.6648 (m-80)
REVERT: E   44 THR cc_start: 0.6718 (OUTLIER) cc_final: 0.6487 (t)
REVERT: E   45 LYS cc_start: 0.7701 (tttt) cc_final: 0.7215 (tttm)
REVERT: A   39 TYR cc_start: 0.6954 (m-80) cc_final: 0.6570 (m-80)
REVERT: B   45 LYS cc_start: 0.7700 (tttt) cc_final: 0.7238 (tttm)
  outliers start: 19
  outliers final: 16
  residues processed: 36
  average time/residue: 0.0947
  time to fit residues: 4.8451
Evaluate side-chains
  36 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 19
  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   44 THR
Chi-restraints excluded: chain E residue   66 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   66 VAL
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:    6.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 20 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9980
   chunk 14 optimal weight:    7.9990
   chunk 38 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 8 optimal weight:    9.9990
   chunk 41 optimal weight:    7.9990
   overall best weight:    1.9988

-------------------------------------------------------------------------------
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 = 0.5048 r_free = 0.5048 target = 0.253782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4716 r_free = 0.4716 target = 0.217921 restraints weight = 3272.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.4669 rms_B_bonded: 2.70
r_work: 0.4574 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.4574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7074
moved from start:          0.2990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   2982  Z= 0.160
  Angle     :  0.619   5.742   4026  Z= 0.330
  Chirality :  0.052   0.138    534
  Planarity :  0.002   0.013    498
  Dihedral  :  6.110  19.547    426
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 22.67 %
    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: -2.83 (0.38), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.15 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS D  50 
 PHE   0.009   0.003   PHE B  94 
 TYR   0.013   0.002   TYR A  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01844 (   54)
  hydrogen bonds       : angle       5.57845 (  162)
  covalent geometry    : bond        0.00335 ( 2982)
  covalent geometry    : angle       0.61852 ( 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
  36 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 19
  time to evaluate  : 0.340 
Fit side-chains
REVERT: C   39 TYR cc_start: 0.6888 (m-80) cc_final: 0.6605 (m-80)
REVERT: E   44 THR cc_start: 0.6547 (OUTLIER) cc_final: 0.6304 (t)
REVERT: E   45 LYS cc_start: 0.7713 (tttt) cc_final: 0.7259 (tttm)
REVERT: A   39 TYR cc_start: 0.6881 (m-80) cc_final: 0.6498 (m-80)
REVERT: B   45 LYS cc_start: 0.7635 (tttt) cc_final: 0.7149 (tttm)
  outliers start: 17
  outliers final: 16
  residues processed: 33
  average time/residue: 0.1120
  time to fit residues: 5.0152
Evaluate side-chains
  35 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 18
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
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   44 THR
Chi-restraints excluded: chain E residue   66 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   66 VAL
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:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 14 optimal weight:   20.0000
   chunk 12 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 35 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   chunk 41 optimal weight:    7.9990
   chunk 22 optimal weight:    2.9990
   chunk 38 optimal weight:    0.1980
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.5085 r_free = 0.5085 target = 0.258568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4797 r_free = 0.4797 target = 0.224393 restraints weight = 3294.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.4800 rms_B_bonded: 2.65
r_work: 0.4709 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.4709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6999
moved from start:          0.3388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   2982  Z= 0.090
  Angle     :  0.504   3.956   4026  Z= 0.273
  Chirality :  0.050   0.144    534
  Planarity :  0.002   0.012    498
  Dihedral  :  5.165  17.455    426
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.05 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 26.00 %
    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: -2.70 (0.39), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.05 (0.29), residues: 408

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01545 (   54)
  hydrogen bonds       : angle       5.48046 (  162)
  covalent geometry    : bond        0.00179 ( 2982)
  covalent geometry    : angle       0.50443 ( 4026)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1959.84 seconds
wall clock time: 34 minutes 18.95 seconds (2058.95 seconds total)