Starting phenix.real_space_refine
on Fri Aug 22 12:58:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zwj_60529/08_2025/8zwj_60529.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zwj_60529/08_2025/8zwj_60529.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zwj_60529/08_2025/8zwj_60529.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zwj_60529/08_2025/8zwj_60529.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zwj_60529/08_2025/8zwj_60529.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zwj_60529/08_2025/8zwj_60529.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     C    1704      2.51       5
     N     486      2.21       5
     O     564      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2760
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "G"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 438
          Classifications: {'peptide': 63}
          Link IDs: {'TRANS': 62}
    Chain: "Q"
      Number of atoms: 66
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 66
          Classifications: {'RNA': 3}
          Modifications used: {'rna3p_pur': 3}
          Link IDs: {'rna3p': 2}
  Restraints were copied for chains:
    C, D, E, A, B, F
  Time building chain proxies: 0.64, per 1000 atoms: 0.23
  Number of scatterers: 2760
  At special positions: 0
  Unit cell: (83.83, 103.75, 31.54, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     P       6     15.00
     O     564      8.00
     N     486      7.00
     C    1704      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: 0.16
  Conformation dependent library (CDL) restraints added in 86.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  648

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 6 sheets defined
      0.0% alpha, 46.0% beta
      0 base pairs and 2 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 46 through 58
      removed outlier: 7.446A  pdb=" N   GLY G  47 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 10.167A  pdb=" N   HIS C  50 " --> pdb=" O   GLY G  47 " (cutoff:3.500A)
      removed outlier: 8.906A  pdb=" N   VAL G  49 " --> pdb=" O   HIS C  50 " (cutoff:3.500A)
      removed outlier: 9.252A  pdb=" N   VAL C  52 " --> pdb=" O   VAL G  49 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   GLY G  51 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   THR C  54 " --> pdb=" O   GLY G  51 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ALA G  53 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
      removed outlier: 8.289A  pdb=" N   ALA C  56 " --> pdb=" O   ALA G  53 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   VAL G  55 " --> pdb=" O   ALA C  56 " (cutoff:3.500A)
      removed outlier: 8.000A  pdb=" N   LYS C  58 " --> pdb=" O   VAL G  55 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   GLU G  57 " --> pdb=" O   LYS C  58 " (cutoff:3.500A)
      removed outlier: 8.680A  pdb=" N   GLU G  46 " --> pdb=" O   GLY D  47 " (cutoff:3.500A)
      removed outlier: 8.385A  pdb=" N   VAL D  49 " --> pdb=" O   GLU G  46 " (cutoff:3.500A)
      removed outlier: 9.095A  pdb=" N   VAL G  48 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
      removed outlier: 10.367A  pdb=" N   GLY D  51 " --> pdb=" O   VAL G  48 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   HIS G  50 " --> pdb=" O   GLY D  51 " (cutoff:3.500A)
      removed outlier: 9.000A  pdb=" N   ALA D  53 " --> pdb=" O   HIS G  50 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   VAL G  52 " --> pdb=" O   ALA D  53 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   VAL D  55 " --> pdb=" O   VAL G  52 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   THR G  54 " --> pdb=" O   VAL D  55 " (cutoff:3.500A)
      removed outlier: 8.135A  pdb=" N   GLU D  57 " --> pdb=" O   THR G  54 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   ALA G  56 " --> pdb=" O   GLU D  57 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'C' and resid 62 through 66
      removed outlier: 6.577A  pdb=" N   GLN G  62 " --> pdb=" O   VAL C  63 " (cutoff:3.500A)
      removed outlier: 8.252A  pdb=" N   ASN C  65 " --> pdb=" O   GLN G  62 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   THR G  64 " --> pdb=" O   ASN C  65 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 69 through 82
      removed outlier: 6.917A  pdb=" N   VAL C  74 " --> pdb=" O   GLY G  73 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   THR G  75 " --> pdb=" O   VAL C  74 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   ALA C  76 " --> pdb=" O   THR G  75 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   VAL G  70 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
      removed outlier: 8.230A  pdb=" N   GLY D  73 " --> pdb=" O   VAL G  70 " (cutoff:3.500A)
      removed outlier: 8.716A  pdb=" N   THR G  72 " --> pdb=" O   GLY D  73 " (cutoff:3.500A)
      removed outlier: 7.916A  pdb=" N   THR D  75 " --> pdb=" O   THR G  72 " (cutoff:3.500A)
      removed outlier: 8.985A  pdb=" N   VAL G  74 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 9.274A  pdb=" N   VAL D  77 " --> pdb=" O   VAL G  74 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   ALA G  76 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 8.479A  pdb=" N   GLN D  79 " --> pdb=" O   ALA G  76 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   ALA G  78 " --> pdb=" O   GLN D  79 " (cutoff:3.500A)
      removed outlier: 8.451A  pdb=" N   THR D  81 " --> pdb=" O   ALA G  78 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   LYS G  80 " --> pdb=" O   THR D  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 46 through 58
      removed outlier: 7.446A  pdb=" N   GLY E  47 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 10.167A  pdb=" N   HIS A  50 " --> pdb=" O   GLY E  47 " (cutoff:3.500A)
      removed outlier: 8.906A  pdb=" N   VAL E  49 " --> pdb=" O   HIS A  50 " (cutoff:3.500A)
      removed outlier: 9.252A  pdb=" N   VAL A  52 " --> pdb=" O   VAL E  49 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   GLY E  51 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   THR A  54 " --> pdb=" O   GLY E  51 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ALA E  53 " --> pdb=" O   THR A  54 " (cutoff:3.500A)
      removed outlier: 8.289A  pdb=" N   ALA A  56 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   VAL E  55 " --> pdb=" O   ALA A  56 " (cutoff:3.500A)
      removed outlier: 8.000A  pdb=" N   LYS A  58 " --> pdb=" O   VAL E  55 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   GLU E  57 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
      removed outlier: 8.679A  pdb=" N   GLU E  46 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 8.385A  pdb=" N   VAL B  49 " --> pdb=" O   GLU E  46 " (cutoff:3.500A)
      removed outlier: 9.096A  pdb=" N   VAL E  48 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 10.367A  pdb=" N   GLY B  51 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   HIS E  50 " --> pdb=" O   GLY B  51 " (cutoff:3.500A)
      removed outlier: 9.001A  pdb=" N   ALA B  53 " --> pdb=" O   HIS E  50 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   VAL E  52 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   VAL B  55 " --> pdb=" O   VAL E  52 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   THR E  54 " --> pdb=" O   VAL B  55 " (cutoff:3.500A)
      removed outlier: 8.135A  pdb=" N   GLU B  57 " --> pdb=" O   THR E  54 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   ALA E  56 " --> pdb=" O   GLU B  57 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 62 through 66
      removed outlier: 6.577A  pdb=" N   GLN E  62 " --> pdb=" O   VAL A  63 " (cutoff:3.500A)
      removed outlier: 8.253A  pdb=" N   ASN A  65 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   THR E  64 " --> pdb=" O   ASN A  65 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 82
      removed outlier: 6.917A  pdb=" N   VAL A  74 " --> pdb=" O   GLY E  73 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   THR E  75 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   ALA A  76 " --> pdb=" O   THR E  75 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   VAL E  70 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 8.230A  pdb=" N   GLY B  73 " --> pdb=" O   VAL E  70 " (cutoff:3.500A)
      removed outlier: 8.716A  pdb=" N   THR E  72 " --> pdb=" O   GLY B  73 " (cutoff:3.500A)
      removed outlier: 7.916A  pdb=" N   THR B  75 " --> pdb=" O   THR E  72 " (cutoff:3.500A)
      removed outlier: 8.985A  pdb=" N   VAL E  74 " --> pdb=" O   THR B  75 " (cutoff:3.500A)
      removed outlier: 9.274A  pdb=" N   VAL B  77 " --> pdb=" O   VAL E  74 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   ALA E  76 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 8.478A  pdb=" N   GLN B  79 " --> pdb=" O   ALA E  76 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   ALA E  78 " --> pdb=" O   GLN B  79 " (cutoff:3.500A)
      removed outlier: 8.451A  pdb=" N   THR B  81 " --> pdb=" O   ALA E  78 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   LYS E  80 " --> pdb=" O   THR B  81 " (cutoff:3.500A)

    28 hydrogen bonds defined for protein.
    84 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      2 stacking parallelities
  Total time for adding SS restraints: 0.31

  Time building geometry restraints manager: 0.21 seconds

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

  Histogram of bond lengths:
        1.22 -     1.30: 462
        1.30 -     1.38: 503
        1.38 -     1.46: 317
        1.46 -     1.53: 1397
        1.53 -     1.61: 109
  Bond restraints: 2788
  Sorted by residual:
  bond pdb=" C   THR B  92 "
       pdb=" N   GLY B  93 "
    ideal  model  delta    sigma   weight residual
    1.329  1.309  0.020 1.62e-02 3.81e+03 1.53e+00
  bond pdb=" C   THR D  92 "
       pdb=" N   GLY D  93 "
    ideal  model  delta    sigma   weight residual
    1.329  1.309  0.020 1.62e-02 3.81e+03 1.47e+00
  bond pdb=" C   THR G  92 "
       pdb=" N   GLY G  93 "
    ideal  model  delta    sigma   weight residual
    1.329  1.309  0.019 1.62e-02 3.81e+03 1.45e+00
  bond pdb=" C   THR E  92 "
       pdb=" N   GLY E  93 "
    ideal  model  delta    sigma   weight residual
    1.329  1.309  0.019 1.62e-02 3.81e+03 1.40e+00
  bond pdb=" C   THR A  92 "
       pdb=" N   GLY A  93 "
    ideal  model  delta    sigma   weight residual
    1.329  1.310  0.019 1.62e-02 3.81e+03 1.39e+00
  ... (remaining 2783 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.82: 3184
        0.82 -     1.65: 435
        1.65 -     2.47: 113
        2.47 -     3.29: 27
        3.29 -     4.12: 37
  Bond angle restraints: 3796
  Sorted by residual:
  angle pdb=" C   VAL A  49 "
        pdb=" N   HIS A  50 "
        pdb=" CA  HIS A  50 "
      ideal   model   delta    sigma   weight residual
     121.94  117.82    4.12 1.76e+00 3.23e-01 5.47e+00
  angle pdb=" C   VAL D  49 "
        pdb=" N   HIS D  50 "
        pdb=" CA  HIS D  50 "
      ideal   model   delta    sigma   weight residual
     121.94  117.83    4.11 1.76e+00 3.23e-01 5.46e+00
  angle pdb=" C   VAL G  49 "
        pdb=" N   HIS G  50 "
        pdb=" CA  HIS G  50 "
      ideal   model   delta    sigma   weight residual
     121.94  117.83    4.11 1.76e+00 3.23e-01 5.46e+00
  angle pdb=" C   VAL B  49 "
        pdb=" N   HIS B  50 "
        pdb=" CA  HIS B  50 "
      ideal   model   delta    sigma   weight residual
     121.94  117.83    4.11 1.76e+00 3.23e-01 5.46e+00
  angle pdb=" C   VAL E  49 "
        pdb=" N   HIS E  50 "
        pdb=" CA  HIS E  50 "
      ideal   model   delta    sigma   weight residual
     121.94  117.83    4.11 1.76e+00 3.23e-01 5.44e+00
  ... (remaining 3791 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.39: 1514
       24.39 -    48.77: 94
       48.77 -    73.15: 0
       73.15 -    97.53: 0
       97.53 -   121.91: 6
  Dihedral angle restraints: 1614
    sinusoidal: 588
      harmonic: 1026
  Sorted by residual:
  dihedral pdb=" CA  VAL G  40 "
           pdb=" C   VAL G  40 "
           pdb=" N   GLY G  41 "
           pdb=" CA  GLY G  41 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.06   17.94     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  VAL E  40 "
           pdb=" C   VAL E  40 "
           pdb=" N   GLY E  41 "
           pdb=" CA  GLY E  41 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.07   17.93     0      5.00e+00 4.00e-02 1.29e+01
  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  162.09   17.91     0      5.00e+00 4.00e-02 1.28e+01
  ... (remaining 1611 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 186
       0.028 -    0.055: 190
       0.055 -    0.083: 48
       0.083 -    0.110: 44
       0.110 -    0.138: 30
  Chirality restraints: 498
  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    2.58   -0.14 2.00e-01 2.50e+01 4.73e-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    2.58   -0.13 2.00e-01 2.50e+01 4.52e-01
  chirality pdb=" CA  VAL B  49 "
            pdb=" N   VAL B  49 "
            pdb=" C   VAL B  49 "
            pdb=" CB  VAL B  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.42e-01
  ... (remaining 495 not shown)

  Planarity restraints: 450
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS G  50 "    0.010 2.00e-02 2.50e+03   8.45e-03 1.07e+00
        pdb=" CG  HIS G  50 "   -0.018 2.00e-02 2.50e+03
        pdb=" ND1 HIS G  50 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 HIS G  50 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 HIS G  50 "    0.002 2.00e-02 2.50e+03
        pdb=" NE2 HIS G  50 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS E  50 "   -0.009 2.00e-02 2.50e+03   8.36e-03 1.05e+00
        pdb=" CG  HIS E  50 "    0.018 2.00e-02 2.50e+03
        pdb=" ND1 HIS E  50 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 HIS E  50 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 HIS E  50 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE2 HIS E  50 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS D  50 "    0.009 2.00e-02 2.50e+03   8.24e-03 1.02e+00
        pdb=" CG  HIS D  50 "   -0.017 2.00e-02 2.50e+03
        pdb=" ND1 HIS D  50 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 HIS D  50 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 HIS D  50 "    0.002 2.00e-02 2.50e+03
        pdb=" NE2 HIS D  50 "    0.004 2.00e-02 2.50e+03
  ... (remaining 447 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 298
        2.75 -     3.29: 2572
        3.29 -     3.83: 4155
        3.83 -     4.36: 4725
        4.36 -     4.90: 9688
  Nonbonded interactions: 21438
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B  46 "
            pdb=" NZ  LYS B  80 "
     model   vdw
     2.218 3.120
  nonbonded pdb=" OE2 GLU A  46 "
            pdb=" NZ  LYS A  80 "
     model   vdw
     2.218 3.120
  nonbonded pdb=" OE2 GLU E  46 "
            pdb=" NZ  LYS E  80 "
     model   vdw
     2.218 3.120
  nonbonded pdb=" OE2 GLU D  46 "
            pdb=" NZ  LYS D  80 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" OE2 GLU G  46 "
            pdb=" NZ  LYS G  80 "
     model   vdw
     2.219 3.120
  ... (remaining 21433 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'G'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'Q'
  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:             2.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.260
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.030   2788  Z= 0.287
  Angle     :  0.737   4.117   3796  Z= 0.412
  Chirality :  0.054   0.138    498
  Planarity :  0.002   0.009    450
  Dihedral  : 15.838 121.909    966
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 14.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.11 %
    Favored  : 89.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 17.78 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.10 (0.30), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.12 (0.23), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.003   TYR C  39 
 PHE   0.013   0.004   PHE A  94 
 HIS   0.007   0.004   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00633 ( 2788)
  covalent geometry    : angle       0.73689 ( 3796)
  hydrogen bonds       : bond        0.19242 (   28)
  hydrogen bonds       : angle       8.54414 (   84)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.104 
Fit side-chains
REVERT: G   60 LYS cc_start: 0.8316 (ttpt) cc_final: 0.7928 (ttmm)
REVERT: G   96 LYS cc_start: 0.6397 (mttt) cc_final: 0.6197 (mttm)
REVERT: C   62 GLN cc_start: 0.7188 (mt0) cc_final: 0.6770 (tt0)
REVERT: C   83 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7321 (tm-30)
REVERT: E   62 GLN cc_start: 0.7018 (mt0) cc_final: 0.6599 (tt0)
REVERT: E   83 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7314 (tm-30)
REVERT: A   60 LYS cc_start: 0.8371 (ttpt) cc_final: 0.8102 (ttmm)
REVERT: A   62 GLN cc_start: 0.7293 (mt0) cc_final: 0.6866 (tt0)
REVERT: A   83 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7423 (tm-30)
REVERT: B   60 LYS cc_start: 0.8311 (ttpt) cc_final: 0.8063 (ttmm)
  outliers start: 0
  outliers final: 0
  residues processed: 30
  average time/residue: 0.0959
  time to fit residues: 3.3275
Evaluate side-chains
  29 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    8.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
G  62 GLN
C  62 GLN
D  62 GLN
E  62 GLN
A  62 GLN
B  62 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.205827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.155956 restraints weight = 2713.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.4046 rms_B_bonded: 2.29
r_work: 0.3945 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3820 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.1458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   2788  Z= 0.100
  Angle     :  0.479   3.263   3796  Z= 0.263
  Chirality :  0.050   0.137    498
  Planarity :  0.002   0.011    450
  Dihedral  : 14.673 107.771    444
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 15.93 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.53 (0.35), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.68 (0.26), residues: 366

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 2788)
  covalent geometry    : angle       0.47911 ( 3796)
  hydrogen bonds       : bond        0.02607 (   28)
  hydrogen bonds       : angle       5.82140 (   84)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 27
  time to evaluate  : 0.106 
Fit side-chains
REVERT: G   60 LYS cc_start: 0.8224 (ttpt) cc_final: 0.7840 (ttmm)
REVERT: G   62 GLN cc_start: 0.7362 (mt0) cc_final: 0.7135 (tt0)
REVERT: C   60 LYS cc_start: 0.8450 (ttmt) cc_final: 0.8199 (tttt)
REVERT: C   62 GLN cc_start: 0.7643 (mt0) cc_final: 0.7366 (tt0)
REVERT: C   83 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7831 (tm-30)
REVERT: E   62 GLN cc_start: 0.7306 (mt0) cc_final: 0.6990 (tt0)
REVERT: A   60 LYS cc_start: 0.8313 (ttpt) cc_final: 0.8079 (ttmm)
REVERT: A   62 GLN cc_start: 0.7652 (mt0) cc_final: 0.7106 (tt0)
REVERT: A   83 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7961 (tm-30)
REVERT: A   87 SER cc_start: 0.8772 (m) cc_final: 0.8534 (p)
REVERT: B   60 LYS cc_start: 0.8337 (ttpt) cc_final: 0.7967 (ttmm)
  outliers start: 2
  outliers final: 2
  residues processed: 27
  average time/residue: 0.1040
  time to fit residues: 3.2285
Evaluate side-chains
  29 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 27
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   62 GLN
Chi-restraints excluded: chain B residue   62 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 6 optimal weight:    0.0980
   chunk 11 optimal weight:    9.9990
   chunk 8 optimal weight:    2.9990
   chunk 28 optimal weight:    0.1980
   chunk 0 optimal weight:    9.9990
   chunk 23 optimal weight:    8.9990
   chunk 33 optimal weight:    7.9990
   chunk 26 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0370
   chunk 31 optimal weight:    3.9990
   overall best weight:    0.8660

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

Flipped N/Q/H residues before XYZ refinement:
D  62 GLN
B  62 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4601 r_free = 0.4601 target = 0.207265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.156678 restraints weight = 2734.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.4038 rms_B_bonded: 2.32
r_work: 0.3932 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3809 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.1687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   2788  Z= 0.085
  Angle     :  0.420   3.393   3796  Z= 0.235
  Chirality :  0.049   0.132    498
  Planarity :  0.001   0.007    450
  Dihedral  : 14.058 104.182    444
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.02 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 15.19 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.22 (0.37), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.44 (0.28), residues: 366

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00186 ( 2788)
  covalent geometry    : angle       0.42045 ( 3796)
  hydrogen bonds       : bond        0.01907 (   28)
  hydrogen bonds       : angle       5.40289 (   84)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 25
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
REVERT: G   60 LYS cc_start: 0.8243 (ttpt) cc_final: 0.7916 (tttt)
REVERT: G   62 GLN cc_start: 0.7351 (mt0) cc_final: 0.7107 (tt0)
REVERT: C   62 GLN cc_start: 0.7687 (mt0) cc_final: 0.7032 (tt0)
REVERT: C   83 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7781 (tm-30)
REVERT: D   60 LYS cc_start: 0.8523 (ttmm) cc_final: 0.8305 (tttm)
REVERT: E   37 VAL cc_start: 0.3836 (OUTLIER) cc_final: 0.3587 (m)
REVERT: E   60 LYS cc_start: 0.8385 (tttt) cc_final: 0.8183 (tttp)
REVERT: A   60 LYS cc_start: 0.8347 (ttpt) cc_final: 0.8081 (ttmm)
REVERT: A   62 GLN cc_start: 0.7739 (mt0) cc_final: 0.7242 (tt0)
REVERT: A   83 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7933 (tm-30)
REVERT: B   60 LYS cc_start: 0.8353 (ttpt) cc_final: 0.7955 (ttmm)
  outliers start: 6
  outliers final: 3
  residues processed: 29
  average time/residue: 0.0926
  time to fit residues: 3.1099
Evaluate side-chains
  28 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain D residue   62 GLN
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain B residue   62 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 3 optimal weight:    0.0070
   chunk 5 optimal weight:   10.0000
   chunk 23 optimal weight:    9.9990
   chunk 14 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 20 optimal weight:    8.9990
   chunk 32 optimal weight:    0.9990
   chunk 15 optimal weight:    5.9990
   overall best weight:    1.2006

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

Flipped N/Q/H residues before XYZ refinement:
D  62 GLN
B  62 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4593 r_free = 0.4593 target = 0.206318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.155264 restraints weight = 2693.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.4017 rms_B_bonded: 2.27
r_work: 0.3917 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3794 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   2788  Z= 0.104
  Angle     :  0.429   3.355   3796  Z= 0.240
  Chirality :  0.049   0.133    498
  Planarity :  0.001   0.007    450
  Dihedral  : 13.560 101.397    444
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 15.19 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.93 (0.38), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.23 (0.29), residues: 366

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 2788)
  covalent geometry    : angle       0.42856 ( 3796)
  hydrogen bonds       : bond        0.01853 (   28)
  hydrogen bonds       : angle       5.25921 (   84)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 24
  time to evaluate  : 0.058 
Fit side-chains
REVERT: G   37 VAL cc_start: 0.3583 (OUTLIER) cc_final: 0.3334 (m)
REVERT: G   60 LYS cc_start: 0.8208 (ttpt) cc_final: 0.7874 (ttmm)
REVERT: G   62 GLN cc_start: 0.7375 (mt0) cc_final: 0.6813 (tt0)
REVERT: C   60 LYS cc_start: 0.8553 (ttmt) cc_final: 0.8200 (tttt)
REVERT: C   62 GLN cc_start: 0.7690 (mt0) cc_final: 0.7406 (tt0)
REVERT: C   83 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7709 (tm-30)
REVERT: D   60 LYS cc_start: 0.8516 (ttmm) cc_final: 0.8277 (tttm)
REVERT: E   37 VAL cc_start: 0.3675 (OUTLIER) cc_final: 0.3419 (m)
REVERT: E   60 LYS cc_start: 0.8361 (tttt) cc_final: 0.8099 (tttp)
REVERT: A   37 VAL cc_start: 0.5109 (OUTLIER) cc_final: 0.4871 (m)
REVERT: A   60 LYS cc_start: 0.8427 (ttpt) cc_final: 0.8146 (ttmm)
REVERT: A   62 GLN cc_start: 0.7728 (mt0) cc_final: 0.7237 (tt0)
REVERT: A   83 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7865 (tm-30)
REVERT: B   60 LYS cc_start: 0.8366 (ttpt) cc_final: 0.7954 (ttmm)
  outliers start: 10
  outliers final: 7
  residues processed: 32
  average time/residue: 0.0539
  time to fit residues: 2.0759
Evaluate side-chains
  33 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 23
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   62 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 22 optimal weight:    0.8980
   chunk 21 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 14 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 12 optimal weight:   10.0000
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.188247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.136805 restraints weight = 2820.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3887 rms_B_bonded: 2.37
r_work: 0.3794 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3679 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.1796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   2788  Z= 0.219
  Angle     :  0.569   3.950   3796  Z= 0.316
  Chirality :  0.051   0.141    498
  Planarity :  0.002   0.008    450
  Dihedral  : 13.210  98.331    444
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.84 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 18.89 %
    Favored  : 77.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.76 (0.38), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.10 (0.29), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.012   0.003   TYR G  39 
 PHE   0.013   0.004   PHE A  94 
 HIS   0.007   0.004   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 ( 2788)
  covalent geometry    : angle       0.56948 ( 3796)
  hydrogen bonds       : bond        0.02560 (   28)
  hydrogen bonds       : angle       5.48356 (   84)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 23
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
REVERT: G   60 LYS cc_start: 0.8363 (ttpt) cc_final: 0.7954 (tttt)
REVERT: G   62 GLN cc_start: 0.7498 (mt0) cc_final: 0.7229 (tt0)
REVERT: G   96 LYS cc_start: 0.6310 (mttt) cc_final: 0.5483 (mtmt)
REVERT: C   60 LYS cc_start: 0.8605 (ttmt) cc_final: 0.8252 (tttt)
REVERT: C   83 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7814 (tm-30)
REVERT: E   83 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7505 (tm-30)
REVERT: A   60 LYS cc_start: 0.8497 (ttpt) cc_final: 0.8251 (ttmm)
REVERT: A   62 GLN cc_start: 0.7728 (mt0) cc_final: 0.7241 (tt0)
REVERT: A   83 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7928 (tm-30)
REVERT: B   60 LYS cc_start: 0.8510 (ttpt) cc_final: 0.8111 (ttmm)
REVERT: B   96 LYS cc_start: 0.6517 (mttm) cc_final: 0.5470 (mtmt)
  outliers start: 11
  outliers final: 11
  residues processed: 32
  average time/residue: 0.0870
  time to fit residues: 3.2602
Evaluate side-chains
  34 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 23
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   62 GLN
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain B residue   59 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 14 optimal weight:    7.9990
   chunk 29 optimal weight:    9.9990
   chunk 0 optimal weight:    9.9990
   chunk 25 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 5 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
C  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.194793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.144796 restraints weight = 2828.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3992 rms_B_bonded: 2.35
r_work: 0.3891 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3779 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   2788  Z= 0.083
  Angle     :  0.408   3.589   3796  Z= 0.229
  Chirality :  0.050   0.133    498
  Planarity :  0.001   0.007    450
  Dihedral  : 12.496  95.529    444
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 18.15 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.60 (0.39), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.98 (0.30), residues: 366

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00175 ( 2788)
  covalent geometry    : angle       0.40830 ( 3796)
  hydrogen bonds       : bond        0.01723 (   28)
  hydrogen bonds       : angle       5.13259 (   84)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 24
  time to evaluate  : 0.101 
Fit side-chains
REVERT: G   37 VAL cc_start: 0.4072 (OUTLIER) cc_final: 0.3806 (p)
REVERT: G   60 LYS cc_start: 0.8287 (ttpt) cc_final: 0.7959 (ttmm)
REVERT: G   62 GLN cc_start: 0.7472 (mt0) cc_final: 0.6944 (tt0)
REVERT: C   60 LYS cc_start: 0.8456 (ttmt) cc_final: 0.8039 (tmtt)
REVERT: C   83 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7856 (tm-30)
REVERT: E   37 VAL cc_start: 0.4175 (OUTLIER) cc_final: 0.3911 (p)
REVERT: E   83 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7468 (tm-30)
REVERT: A   60 LYS cc_start: 0.8390 (ttpt) cc_final: 0.8126 (ttmm)
REVERT: A   62 GLN cc_start: 0.7676 (mt0) cc_final: 0.7236 (tt0)
REVERT: A   83 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7941 (tm-30)
REVERT: B   60 LYS cc_start: 0.8443 (ttpt) cc_final: 0.8165 (ttmm)
  outliers start: 11
  outliers final: 9
  residues processed: 32
  average time/residue: 0.0704
  time to fit residues: 2.6927
Evaluate side-chains
  35 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 24
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   62 GLN
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain B residue   59 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 14 optimal weight:    8.9990
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0980
   chunk 24 optimal weight:   10.0000
   chunk 30 optimal weight:    0.2980
   chunk 32 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 11 optimal weight:   10.0000
   chunk 8 optimal weight:    3.9990
   overall best weight:    1.4786

-------------------------------------------------------------------------------
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 = 0.4480 r_free = 0.4480 target = 0.192892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.142117 restraints weight = 2796.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.3938 rms_B_bonded: 2.34
r_work: 0.3839 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3726 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.2285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2788  Z= 0.121
  Angle     :  0.450   3.891   3796  Z= 0.253
  Chirality :  0.049   0.134    498
  Planarity :  0.001   0.007    450
  Dihedral  : 12.048  92.585    444
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.84 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 20.37 %
    Favored  : 75.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.48 (0.40), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.88 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.002   TYR G  39 
 PHE   0.007   0.002   PHE B  94 
 HIS   0.005   0.003   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 2788)
  covalent geometry    : angle       0.45035 ( 3796)
  hydrogen bonds       : bond        0.01856 (   28)
  hydrogen bonds       : angle       5.27155 (   84)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 21
  time to evaluate  : 0.096 
Fit side-chains
REVERT: G   37 VAL cc_start: 0.3948 (OUTLIER) cc_final: 0.3711 (p)
REVERT: G   60 LYS cc_start: 0.8335 (ttpt) cc_final: 0.8005 (ttmt)
REVERT: G   62 GLN cc_start: 0.7481 (mt0) cc_final: 0.6947 (tt0)
REVERT: C   60 LYS cc_start: 0.8486 (ttmt) cc_final: 0.8074 (tmtt)
REVERT: C   83 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7783 (tm-30)
REVERT: E   37 VAL cc_start: 0.4055 (OUTLIER) cc_final: 0.3781 (p)
REVERT: E   60 LYS cc_start: 0.8352 (tttt) cc_final: 0.8141 (tttp)
REVERT: A   60 LYS cc_start: 0.8436 (ttpt) cc_final: 0.8171 (ttmm)
REVERT: A   62 GLN cc_start: 0.7706 (mt0) cc_final: 0.7257 (tt0)
REVERT: A   83 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7875 (tm-30)
REVERT: B   60 LYS cc_start: 0.8452 (ttpt) cc_final: 0.8041 (ttmm)
  outliers start: 12
  outliers final: 10
  residues processed: 29
  average time/residue: 0.0610
  time to fit residues: 2.1456
Evaluate side-chains
  33 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 21
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   62 GLN
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   62 GLN
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain B residue   59 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 19 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0970
   chunk 17 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 35 optimal weight:    0.6980
   chunk 10 optimal weight:    0.4980
   chunk 11 optimal weight:    0.4980
   chunk 3 optimal weight:    6.9990
   chunk 29 optimal weight:    6.9990
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4579 r_free = 0.4579 target = 0.200770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.151187 restraints weight = 2846.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.4066 rms_B_bonded: 2.35
r_work: 0.3971 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3856 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.2764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.015   2788  Z= 0.066
  Angle     :  0.369   3.685   3796  Z= 0.209
  Chirality :  0.050   0.134    498
  Planarity :  0.001   0.007    450
  Dihedral  : 11.503  89.932    444
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 1.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 21.85 %
    Favored  : 75.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.38 (0.41), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.81 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.000   TYR B  39 
 PHE   0.005   0.001   PHE B  94 
 HIS   0.002   0.001   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00137 ( 2788)
  covalent geometry    : angle       0.36929 ( 3796)
  hydrogen bonds       : bond        0.01368 (   28)
  hydrogen bonds       : angle       4.95960 (   84)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 26
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   62 GLN cc_start: 0.7459 (mt0) cc_final: 0.6827 (tt0)
REVERT: C   60 LYS cc_start: 0.8373 (ttmt) cc_final: 0.7970 (tmtt)
REVERT: C   83 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7766 (tm-30)
REVERT: E   60 LYS cc_start: 0.8255 (tttt) cc_final: 0.8044 (tttp)
REVERT: E   62 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.7259 (tt0)
REVERT: A   60 LYS cc_start: 0.8351 (ttpt) cc_final: 0.8086 (ttmm)
REVERT: A   62 GLN cc_start: 0.7719 (mt0) cc_final: 0.7219 (tt0)
REVERT: A   83 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7843 (tm-30)
REVERT: B   60 LYS cc_start: 0.8373 (ttpt) cc_final: 0.8071 (ttmm)
  outliers start: 8
  outliers final: 5
  residues processed: 32
  average time/residue: 0.0835
  time to fit residues: 3.1567
Evaluate side-chains
  30 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 24
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   62 GLN
Chi-restraints excluded: chain E residue   62 GLN
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain B residue   59 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 23 optimal weight:   10.0000
   chunk 34 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 7 optimal weight:    7.9990
   chunk 14 optimal weight:    8.9990
   chunk 29 optimal weight:    0.8980
   chunk 27 optimal weight:    7.9990
   chunk 26 optimal weight:    4.9990
   chunk 18 optimal weight:   10.0000
   chunk 17 optimal weight:    8.9990
   overall best weight:    3.7586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.188592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.137043 restraints weight = 2867.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3864 rms_B_bonded: 2.33
r_work: 0.3756 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3641 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.2444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   2788  Z= 0.275
  Angle     :  0.640   5.867   3796  Z= 0.351
  Chirality :  0.053   0.143    498
  Planarity :  0.003   0.012    450
  Dihedral  : 11.387  87.094    444
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.84 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 21.85 %
    Favored  : 75.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.44 (0.40), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.85 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.015   0.003   TYR E  39 
 PHE   0.015   0.004   PHE B  94 
 HIS   0.008   0.004   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00644 ( 2788)
  covalent geometry    : angle       0.64040 ( 3796)
  hydrogen bonds       : bond        0.02590 (   28)
  hydrogen bonds       : angle       5.57587 (   84)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 30
  time to evaluate  : 0.103 
Fit side-chains
REVERT: G   60 LYS cc_start: 0.8388 (ttpt) cc_final: 0.7961 (tttt)
REVERT: G   62 GLN cc_start: 0.7536 (mt0) cc_final: 0.7288 (tt0)
REVERT: G   96 LYS cc_start: 0.6325 (mttt) cc_final: 0.5507 (mtmt)
REVERT: C   60 LYS cc_start: 0.8521 (ttmt) cc_final: 0.8264 (tttm)
REVERT: C   83 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7818 (tm-30)
REVERT: E   60 LYS cc_start: 0.8386 (tttt) cc_final: 0.8150 (tttp)
REVERT: E   83 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7526 (tm-30)
REVERT: A   60 LYS cc_start: 0.8499 (ttpt) cc_final: 0.8176 (ttmm)
REVERT: A   62 GLN cc_start: 0.7699 (mt0) cc_final: 0.7298 (tt0)
REVERT: A   83 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7915 (tm-30)
REVERT: B   60 LYS cc_start: 0.8524 (ttpt) cc_final: 0.8200 (ttmm)
REVERT: B   96 LYS cc_start: 0.6574 (mttm) cc_final: 0.5252 (mppt)
  outliers start: 8
  outliers final: 6
  residues processed: 35
  average time/residue: 0.0665
  time to fit residues: 2.7526
Evaluate side-chains
  36 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 30
  time to evaluate  : 0.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   62 GLN
Chi-restraints excluded: chain E residue   62 GLN
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain B residue   59 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    5.9990
   chunk 25 optimal weight:    0.0770
   chunk 11 optimal weight:    8.9990
   chunk 6 optimal weight:    0.2980
   chunk 15 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 18 optimal weight:    9.9990
   chunk 35 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.5538

-------------------------------------------------------------------------------
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 = 0.4576 r_free = 0.4576 target = 0.198172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.148912 restraints weight = 2815.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.4030 rms_B_bonded: 2.29
r_work: 0.3933 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3819 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.2970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.016   2788  Z= 0.068
  Angle     :  0.398   3.880   3796  Z= 0.223
  Chirality :  0.050   0.135    498
  Planarity :  0.001   0.008    450
  Dihedral  : 10.756  85.928    444
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.47 %
    Favored  : 91.53 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 24.44 %
    Favored  : 73.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.33 (0.42), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.77 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.000   TYR C  39 
 PHE   0.005   0.001   PHE B  94 
 HIS   0.002   0.001   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00139 ( 2788)
  covalent geometry    : angle       0.39800 ( 3796)
  hydrogen bonds       : bond        0.01493 (   28)
  hydrogen bonds       : angle       5.12654 (   84)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 24
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
REVERT: G   60 LYS cc_start: 0.8292 (ttpt) cc_final: 0.7972 (ttmm)
REVERT: G   62 GLN cc_start: 0.7462 (mt0) cc_final: 0.6935 (tt0)
REVERT: C   60 LYS cc_start: 0.8356 (ttmt) cc_final: 0.7974 (tmtt)
REVERT: C   83 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7815 (tm-30)
REVERT: E   60 LYS cc_start: 0.8311 (tttt) cc_final: 0.8071 (tttp)
REVERT: E   83 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7387 (tm-30)
REVERT: A   60 LYS cc_start: 0.8368 (ttpt) cc_final: 0.8103 (ttmm)
REVERT: A   62 GLN cc_start: 0.7667 (mt0) cc_final: 0.7228 (tt0)
REVERT: A   83 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7861 (tm-30)
REVERT: B   60 LYS cc_start: 0.8409 (ttpt) cc_final: 0.8114 (ttmm)
  outliers start: 5
  outliers final: 5
  residues processed: 27
  average time/residue: 0.0854
  time to fit residues: 2.7468
Evaluate side-chains
  29 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 24
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   62 GLN
Chi-restraints excluded: chain E residue   62 GLN
Chi-restraints excluded: chain B residue   59 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   chunk 17 optimal weight:    9.9990
   chunk 10 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   overall best weight:    1.7586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.192396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.141768 restraints weight = 2697.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.3930 rms_B_bonded: 2.28
r_work: 0.3826 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3711 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.2814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2788  Z= 0.141
  Angle     :  0.475   3.915   3796  Z= 0.266
  Chirality :  0.050   0.134    498
  Planarity :  0.002   0.012    450
  Dihedral  : 10.397  82.892    444
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.29 %
    Favored  : 90.71 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 24.07 %
    Favored  : 73.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.26 (0.42), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.71 (0.32), residues: 366

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 2788)
  covalent geometry    : angle       0.47468 ( 3796)
  hydrogen bonds       : bond        0.01787 (   28)
  hydrogen bonds       : angle       5.25897 (   84)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 877.98 seconds
wall clock time: 15 minutes 46.02 seconds (946.02 seconds total)