Starting phenix.real_space_refine
on Wed Feb  4 22:00:48 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rzc_54399/02_2026/9rzc_54399.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rzc_54399/02_2026/9rzc_54399.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rzc_54399/02_2026/9rzc_54399.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rzc_54399/02_2026/9rzc_54399.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rzc_54399/02_2026/9rzc_54399.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rzc_54399/02_2026/9rzc_54399.cif"
  }
  resolution = 3.66
  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=   0.002
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: 5
    Type Number    sf(0)   Gaussians
     P     256      5.49       5
     S      32      5.16       5
     C    7495      2.51       5
     N    2462      2.21       5
     O    2990      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13235
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "N"
      Number of atoms: 2662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 2662
          Classifications: {'DNA': 129}
          Link IDs: {'rna3p': 128}
    Chain: "O"
      Number of atoms: 1993
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 1993
          Classifications: {'peptide': 245}
          Link IDs: {'PTRANS': 7, 'TRANS': 237}
    Chain: "T"
      Number of atoms: 2586
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 2586
          Classifications: {'DNA': 127}
          Link IDs: {'rna3p': 126}
    Chain: "a"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 821
          Classifications: {'peptide': 101}
          Link IDs: {'PTRANS': 4, 'TRANS': 96}
    Chain: "b"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "c"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 801
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "d"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 719
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "f"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "g"
      Number of atoms: 796
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 796
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "h"
      Number of atoms: 693
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 693
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 2, 'TRANS': 86}
    Chain: "k"
      Number of atoms: 138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 138
          Classifications: {'peptide': 18}
          Link IDs: {'PTRANS': 1, 'TRANS': 16}
    Chain: "e"
      Number of atoms: 782
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 782
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
  Time building chain proxies: 3.39, per 1000 atoms: 0.26
  Number of scatterers: 13235
  At special positions: 0
  Unit cell: (89.25, 127.05, 131.25, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      32     16.00
     P     256     15.00
     O    2990      8.00
     N    2462      7.00
     C    7495      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: 1.22
  Conformation dependent library (CDL) restraints added in 430.5 milliseconds
  

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1868

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 13 sheets defined
      59.7% alpha, 6.2% beta
      126 base pairs and 220 stacking pairs defined.
    Time for finding SS restraints: 1.99
  Creating SS restraints...
    Processing helix  chain 'O' and resid 1630 through 1634
      removed outlier: 4.332A  pdb=" N   ARG O1633 " --> pdb=" O   ASP O1630 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1657 through 1662
    Processing helix  chain 'O' and resid 1672 through 1676
      removed outlier: 4.013A  pdb=" N   CYS O1676 " --> pdb=" O   GLY O1673 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1722 through 1734
      removed outlier: 4.159A  pdb=" N   LYS O1727 " --> pdb=" O   HIS O1723 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ALA O1728 " --> pdb=" O   LYS O1724 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   LYS O1731 " --> pdb=" O   LYS O1727 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ALA O1734 " --> pdb=" O   VAL O1730 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1735 through 1737
      No H-bonds generated for 'chain 'O' and resid 1735 through 1737'
    Processing helix  chain 'O' and resid 1759 through 1764
      removed outlier: 3.859A  pdb=" N   PHE O1763 " --> pdb=" O   CYS O1760 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 44 through 57
    Processing helix  chain 'a' and resid 63 through 77
      removed outlier: 3.975A  pdb=" N   ASP a  77 " --> pdb=" O   GLU a  73 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 85 through 113
    Processing helix  chain 'a' and resid 114 through 116
      No H-bonds generated for 'chain 'a' and resid 114 through 116'
    Processing helix  chain 'a' and resid 120 through 132
    Processing helix  chain 'b' and resid 24 through 29
      removed outlier: 4.050A  pdb=" N   GLN b  27 " --> pdb=" O   ASP b  24 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 30 through 41
    Processing helix  chain 'b' and resid 49 through 76
      removed outlier: 3.565A  pdb=" N   ASP b  68 " --> pdb=" O   ASN b  64 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 82 through 93
    Processing helix  chain 'c' and resid 16 through 22
    Processing helix  chain 'c' and resid 26 through 37
    Processing helix  chain 'c' and resid 45 through 73
      removed outlier: 4.152A  pdb=" N   VAL c  49 " --> pdb=" O   ALA c  45 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 79 through 90
      removed outlier: 3.554A  pdb=" N   ASN c  89 " --> pdb=" O   LEU c  85 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 90 through 97
    Processing helix  chain 'd' and resid 37 through 49
    Processing helix  chain 'd' and resid 55 through 85
    Processing helix  chain 'd' and resid 90 through 102
    Processing helix  chain 'd' and resid 103 through 123
      removed outlier: 4.034A  pdb=" N   LYS d 108 " --> pdb=" O   GLY d 104 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 25 through 29
    Processing helix  chain 'f' and resid 30 through 41
    Processing helix  chain 'f' and resid 49 through 76
      removed outlier: 3.555A  pdb=" N   GLU f  53 " --> pdb=" O   LEU f  49 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ASP f  68 " --> pdb=" O   ASN f  64 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 82 through 93
    Processing helix  chain 'g' and resid 16 through 22
    Processing helix  chain 'g' and resid 26 through 37
    Processing helix  chain 'g' and resid 45 through 73
      removed outlier: 4.275A  pdb=" N   VAL g  49 " --> pdb=" O   ALA g  45 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 79 through 90
      removed outlier: 3.533A  pdb=" N   LEU g  83 " --> pdb=" O   ILE g  79 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASP g  90 " --> pdb=" O   ALA g  86 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 90 through 97
    Processing helix  chain 'g' and resid 112 through 116
    Processing helix  chain 'h' and resid 37 through 49
      removed outlier: 3.903A  pdb=" N   GLN h  47 " --> pdb=" O   LYS h  43 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   VAL h  48 " --> pdb=" O   VAL h  44 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 55 through 84
    Processing helix  chain 'h' and resid 90 through 102
    Processing helix  chain 'h' and resid 103 through 122
    Processing helix  chain 'k' and resid 939 through 944
    Processing helix  chain 'e' and resid 44 through 57
    Processing helix  chain 'e' and resid 63 through 76
    Processing helix  chain 'e' and resid 85 through 114
    Processing helix  chain 'e' and resid 120 through 132
    Processing sheet with id=AA1, first strand: chain 'O' and resid 1617 through 1618
      removed outlier: 7.522A  pdb=" N   VAL O1617 " --> pdb=" O   VAL O1720 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'O' and resid 1664 through 1665
      removed outlier: 7.206A  pdb=" N   VAL O1785 " --> pdb=" O   GLU O1715 " (cutoff:3.500A)
      removed outlier: 4.695A  pdb=" N   GLU O1715 " --> pdb=" O   VAL O1785 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   PHE O1787 " --> pdb=" O   VAL O1713 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'O' and resid 1689 through 1695
      removed outlier: 4.259A  pdb=" N   THR O1694 " --> pdb=" O   GLY O1698 " (cutoff:3.500A)
      removed outlier: 7.466A  pdb=" N   GLY O1698 " --> pdb=" O   THR O1694 " (cutoff:3.500A)
      removed outlier: 13.439A  pdb=" N   TRP O1699 " --> pdb=" O   PHE O1801 " (cutoff:3.500A)
      removed outlier: 10.494A  pdb=" N   PHE O1801 " --> pdb=" O   TRP O1699 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   LEU O1701 " --> pdb=" O   LEU O1799 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   ASN O1765 " --> pdb=" O   PHE O1801 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'a' and resid 83 through 84
      removed outlier: 7.391A  pdb=" N   ARG a  83 " --> pdb=" O   VAL b  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'a' and resid 118 through 119
    Processing sheet with id=AA6, first strand: chain 'b' and resid 96 through 98
      removed outlier: 6.540A  pdb=" N   THR b  96 " --> pdb=" O   THR g 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'c' and resid 42 through 43
      removed outlier: 7.127A  pdb=" N   ARG c  42 " --> pdb=" O   ILE d  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'c' and resid 77 through 78
    Processing sheet with id=AA9, first strand: chain 'c' and resid 101 through 102
      removed outlier: 6.553A  pdb=" N   THR c 101 " --> pdb=" O   TYR f  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'f' and resid 45 through 46
      removed outlier: 7.199A  pdb=" N   ARG f  45 " --> pdb=" O   ILE e 119 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'f' and resid 80 through 81
    Processing sheet with id=AB3, first strand: chain 'g' and resid 42 through 43
      removed outlier: 7.753A  pdb=" N   ARG g  42 " --> pdb=" O   ILE h  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'g' and resid 77 through 78

    440 hydrogen bonds defined for protein.
    1281 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      326 hydrogen bonds
      652 hydrogen bond angles
      0 basepair planarities
      126 basepair parallelities
      220 stacking parallelities
  Total time for adding SS restraints: 2.81

  Time building geometry restraints manager: 1.64 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2803
        1.33 -     1.45: 4098
        1.45 -     1.57: 6532
        1.57 -     1.69: 511
        1.69 -     1.82: 48
  Bond restraints: 13992
  Sorted by residual:
  bond pdb=" CB  GLU h  76 "
       pdb=" CG  GLU h  76 "
    ideal  model  delta    sigma   weight residual
    1.520  1.422  0.098 3.00e-02 1.11e+03 1.07e+01
  bond pdb=" CG  GLN b  93 "
       pdb=" CD  GLN b  93 "
    ideal  model  delta    sigma   weight residual
    1.516  1.446  0.070 2.50e-02 1.60e+03 7.87e+00
  bond pdb=" N   GLY a  33 "
       pdb=" CA  GLY a  33 "
    ideal  model  delta    sigma   weight residual
    1.451  1.496 -0.045 1.60e-02 3.91e+03 7.82e+00
  bond pdb=" N   ILE e  74 "
       pdb=" CA  ILE e  74 "
    ideal  model  delta    sigma   weight residual
    1.460  1.491 -0.031 1.19e-02 7.06e+03 6.65e+00
  bond pdb=" CG  ARG f  92 "
       pdb=" CD  ARG f  92 "
    ideal  model  delta    sigma   weight residual
    1.520  1.453  0.067 3.00e-02 1.11e+03 4.98e+00
  ... (remaining 13987 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 17837
        2.01 -     4.01: 1865
        4.01 -     6.02: 244
        6.02 -     8.03: 20
        8.03 -    10.03: 6
  Bond angle restraints: 19972
  Sorted by residual:
  angle pdb=" N   PHE e  78 "
        pdb=" CA  PHE e  78 "
        pdb=" C   PHE e  78 "
      ideal   model   delta    sigma   weight residual
     114.04  106.68    7.36 1.24e+00 6.50e-01 3.53e+01
  angle pdb=" CB  GLU h  76 "
        pdb=" CG  GLU h  76 "
        pdb=" CD  GLU h  76 "
      ideal   model   delta    sigma   weight residual
     112.60  103.60    9.00 1.70e+00 3.46e-01 2.80e+01
  angle pdb=" C   ASN O1625 "
        pdb=" N   LYS O1626 "
        pdb=" CA  LYS O1626 "
      ideal   model   delta    sigma   weight residual
     120.58  128.84   -8.26 1.71e+00 3.42e-01 2.33e+01
  angle pdb=" O4'  DC N 103 "
        pdb=" C1'  DC N 103 "
        pdb=" N1   DC N 103 "
      ideal   model   delta    sigma   weight residual
     108.40  115.46   -7.06 1.50e+00 4.44e-01 2.21e+01
  angle pdb=" N   SER O1627 "
        pdb=" CA  SER O1627 "
        pdb=" C   SER O1627 "
      ideal   model   delta    sigma   weight residual
     111.37  119.09   -7.72 1.65e+00 3.67e-01 2.19e+01
  ... (remaining 19967 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.18: 6639
       34.18 -    68.36: 1099
       68.36 -   102.54: 27
      102.54 -   136.72: 0
      136.72 -   170.89: 2
  Dihedral angle restraints: 7767
    sinusoidal: 4866
      harmonic: 2901
  Sorted by residual:
  dihedral pdb=" C4'  DG N  93 "
           pdb=" C3'  DG N  93 "
           pdb=" O3'  DG N  93 "
           pdb=" P    DG N  94 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   49.11  170.89     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DG N  81 "
           pdb=" C3'  DG N  81 "
           pdb=" O3'  DG N  81 "
           pdb=" P    DT N  82 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   56.61  163.39     1      3.50e+01 8.16e-04 1.53e+01
  dihedral pdb=" CG  ARG O1784 "
           pdb=" CD  ARG O1784 "
           pdb=" NE  ARG O1784 "
           pdb=" CZ  ARG O1784 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -135.03  -44.97     2      1.50e+01 4.44e-03 1.07e+01
  ... (remaining 7764 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1329
       0.053 -    0.105: 676
       0.105 -    0.158: 193
       0.158 -    0.211: 34
       0.211 -    0.264: 5
  Chirality restraints: 2237
  Sorted by residual:
  chirality pdb=" C3'  DG N  81 "
            pdb=" C4'  DG N  81 "
            pdb=" O3'  DG N  81 "
            pdb=" C2'  DG N  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.40   -0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" CA  ILE e  74 "
            pdb=" N   ILE e  74 "
            pdb=" C   ILE e  74 "
            pdb=" CB  ILE e  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" C3'  DG N  93 "
            pdb=" C4'  DG N  93 "
            pdb=" O3'  DG N  93 "
            pdb=" C2'  DG N  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.42   -0.25 2.00e-01 2.50e+01 1.50e+00
  ... (remaining 2234 not shown)

  Planarity restraints: 1664
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC N  47 "    0.063 2.00e-02 2.50e+03   4.43e-02 4.41e+01
        pdb=" N1   DC N  47 "   -0.107 2.00e-02 2.50e+03
        pdb=" C2   DC N  47 "    0.041 2.00e-02 2.50e+03
        pdb=" O2   DC N  47 "   -0.017 2.00e-02 2.50e+03
        pdb=" N3   DC N  47 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DC N  47 "    0.007 2.00e-02 2.50e+03
        pdb=" N4   DC N  47 "    0.010 2.00e-02 2.50e+03
        pdb=" C5   DC N  47 "    0.006 2.00e-02 2.50e+03
        pdb=" C6   DC N  47 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC N  92 "   -0.047 2.00e-02 2.50e+03   3.73e-02 3.13e+01
        pdb=" N1   DC N  92 "    0.092 2.00e-02 2.50e+03
        pdb=" C2   DC N  92 "   -0.039 2.00e-02 2.50e+03
        pdb=" O2   DC N  92 "    0.012 2.00e-02 2.50e+03
        pdb=" N3   DC N  92 "    0.005 2.00e-02 2.50e+03
        pdb=" C4   DC N  92 "   -0.006 2.00e-02 2.50e+03
        pdb=" N4   DC N  92 "   -0.004 2.00e-02 2.50e+03
        pdb=" C5   DC N  92 "   -0.009 2.00e-02 2.50e+03
        pdb=" C6   DC N  92 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT N  27 "   -0.058 2.00e-02 2.50e+03   3.49e-02 3.04e+01
        pdb=" N1   DT N  27 "    0.088 2.00e-02 2.50e+03
        pdb=" C2   DT N  27 "   -0.025 2.00e-02 2.50e+03
        pdb=" O2   DT N  27 "    0.011 2.00e-02 2.50e+03
        pdb=" N3   DT N  27 "    0.000 2.00e-02 2.50e+03
        pdb=" C4   DT N  27 "   -0.008 2.00e-02 2.50e+03
        pdb=" O4   DT N  27 "   -0.012 2.00e-02 2.50e+03
        pdb=" C5   DT N  27 "    0.006 2.00e-02 2.50e+03
        pdb=" C7   DT N  27 "   -0.007 2.00e-02 2.50e+03
        pdb=" C6   DT N  27 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1661 not shown)

  Histogram of nonbonded interaction distances:
        2.40 -     2.90: 4366
        2.90 -     3.40: 12556
        3.40 -     3.90: 25366
        3.90 -     4.40: 29405
        4.40 -     4.90: 40975
  Nonbonded interactions: 112668
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG a 116 "
            pdb=" O   THR a 118 "
     model   vdw
     2.396 3.120
  nonbonded pdb=" CZ  ARG f  92 "
            pdb=" OE1 GLU h  76 "
     model   vdw
     2.526 3.270
  nonbonded pdb=" NH1 ARG f  92 "
            pdb=" OE1 GLU h  76 "
     model   vdw
     2.532 3.120
  nonbonded pdb=" N   ASP e  77 "
            pdb=" OD1 ASP e  77 "
     model   vdw
     2.555 3.120
  nonbonded pdb=" O   ARG e  72 "
            pdb=" CG  GLN e  76 "
     model   vdw
     2.565 3.440
  ... (remaining 112663 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'a' and resid 39 through 133)
  selection = chain 'e'
}
ncs_group {
  reference = chain 'b'
  selection = chain 'f'
}
ncs_group {
  reference = (chain 'c' and resid 15 through 117)
  selection = chain 'g'
}
ncs_group {
  reference = (chain 'd' and resid 35 through 123)
  selection = chain 'h'
}

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 group one per residue
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:             1.710
  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:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.720
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
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      :  0.007   0.098  13992  Z= 0.329
  Angle     :  1.242  10.034  19972  Z= 0.779
  Chirality :  0.066   0.264   2237
  Planarity :  0.015   0.132   1664
  Dihedral  : 24.859 170.895   5899
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.24 %
    Favored  : 99.65 %
  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 are not related in a simple way.
  whole: -1.49 (0.23), residues: 983
  helix: -0.52 (0.19), residues: 562
  sheet: -1.21 (0.66), residues: 43
  loop : -1.52 (0.26), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.053   0.004   ARG f  92 
 TYR   0.027   0.007   TYR a  41 
 PHE   0.054   0.004   PHE c  25 
 TRP   0.019   0.005   TRP O1597 
 HIS   0.029   0.004   HIS f  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00682 (13992)
  covalent geometry    : angle       1.24156 (19972)
  hydrogen bonds       : bond        0.11601 (  766)
  hydrogen bonds       : angle       4.65857 ( 1933)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  351 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 350
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1623 LYS cc_start: 0.5221 (pttm) cc_final: 0.4759 (tptm)
REVERT: O 1634 MET cc_start: 0.6304 (ptm) cc_final: 0.5905 (ptp)
REVERT: O 1742 TYR cc_start: 0.4780 (m-80) cc_final: 0.4467 (m-10)
REVERT: b   53 GLU cc_start: 0.7442 (tp30) cc_final: 0.6954 (tp30)
REVERT: b   59 LYS cc_start: 0.8436 (ttpp) cc_final: 0.7647 (tttp)
REVERT: b   64 ASN cc_start: 0.8074 (m-40) cc_final: 0.7728 (m110)
REVERT: b   68 ASP cc_start: 0.7957 (m-30) cc_final: 0.7738 (m-30)
REVERT: b   85 ASP cc_start: 0.8128 (m-30) cc_final: 0.7928 (m-30)
REVERT: c   56 GLU cc_start: 0.8302 (tt0) cc_final: 0.8024 (tt0)
REVERT: c   95 LYS cc_start: 0.8647 (tttt) cc_final: 0.8303 (tptp)
REVERT: c  104 GLN cc_start: 0.7612 (mm-40) cc_final: 0.7376 (mm-40)
REVERT: d   79 ARG cc_start: 0.8186 (ttm110) cc_final: 0.7939 (mtm180)
REVERT: d  100 LEU cc_start: 0.9147 (mt) cc_final: 0.8744 (mt)
REVERT: f   96 THR cc_start: 0.8933 (m) cc_final: 0.8592 (t)
REVERT: g   17 ARG cc_start: 0.8324 (mtm180) cc_final: 0.7980 (mtm-85)
REVERT: g   39 TYR cc_start: 0.8434 (m-80) cc_final: 0.7811 (m-80)
REVERT: g   64 GLU cc_start: 0.8082 (tp30) cc_final: 0.7863 (tm-30)
REVERT: g   73 ASN cc_start: 0.8404 (m-40) cc_final: 0.8114 (m110)
REVERT: g   76 THR cc_start: 0.8434 (p) cc_final: 0.8134 (t)
REVERT: g  101 THR cc_start: 0.9064 (m) cc_final: 0.8571 (p)
REVERT: g  111 ILE cc_start: 0.8183 (mt) cc_final: 0.7777 (tt)
REVERT: g  114 VAL cc_start: 0.9122 (m) cc_final: 0.8847 (p)
REVERT: h   59 MET cc_start: 0.8452 (tpp) cc_final: 0.8214 (tpp)
REVERT: e   56 LYS cc_start: 0.8442 (ttpp) cc_final: 0.8045 (tttp)
  outliers start: 1
  outliers final: 0
  residues processed: 351
  average time/residue: 0.1659
  time to fit residues: 76.6360
Evaluate side-chains
  193 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.3980
   chunk 65 optimal weight:    0.0770
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 117 optimal weight:    0.9990
   overall best weight:    0.6540

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

Flipped N/Q/H residues before XYZ refinement:
O1682 GLN
O1740 HIS
O1780 ASN
O1782 GLN
** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
b  93 GLN
d  47 GLN
** d  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
d 109 HIS
f  93 GLN
e  68 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.075496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.054261 restraints weight = 48890.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.055674 restraints weight = 23812.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.056515 restraints weight = 15786.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.056988 restraints weight = 12783.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.057206 restraints weight = 11496.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.3050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  13992  Z= 0.177
  Angle     :  0.660   7.319  19972  Z= 0.387
  Chirality :  0.039   0.166   2237
  Planarity :  0.005   0.040   1664
  Dihedral  : 29.642 165.930   3901
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  :  9.91 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.26), residues: 983
  helix:  1.64 (0.21), residues: 570
  sheet: -1.44 (0.63), residues: 43
  loop : -1.09 (0.29), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG g  35 
 TYR   0.026   0.002   TYR O1716 
 PHE   0.017   0.002   PHE c  25 
 TRP   0.018   0.004   TRP O1699 
 HIS   0.006   0.002   HIS a  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 (13992)
  covalent geometry    : angle       0.66005 (19972)
  hydrogen bonds       : bond        0.04345 (  766)
  hydrogen bonds       : angle       3.37808 ( 1933)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 217
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1623 LYS cc_start: 0.5267 (pttm) cc_final: 0.4967 (tptm)
REVERT: O 1635 GLN cc_start: 0.7820 (pm20) cc_final: 0.7587 (pm20)
REVERT: O 1739 ILE cc_start: 0.5582 (pt) cc_final: 0.4936 (mt)
REVERT: a  123 ASP cc_start: 0.8856 (m-30) cc_final: 0.8402 (m-30)
REVERT: c   41 GLU cc_start: 0.7708 (tp30) cc_final: 0.7466 (tp30)
REVERT: c   56 GLU cc_start: 0.8222 (tt0) cc_final: 0.7737 (tt0)
REVERT: c   95 LYS cc_start: 0.8600 (tttt) cc_final: 0.8258 (tptp)
REVERT: f   85 ASP cc_start: 0.8523 (m-30) cc_final: 0.8195 (m-30)
REVERT: f   96 THR cc_start: 0.8876 (m) cc_final: 0.8610 (t)
REVERT: g   39 TYR cc_start: 0.8115 (m-80) cc_final: 0.7907 (m-80)
REVERT: g   73 ASN cc_start: 0.8697 (m-40) cc_final: 0.8292 (m110)
REVERT: g   76 THR cc_start: 0.8581 (p) cc_final: 0.8305 (t)
REVERT: g  101 THR cc_start: 0.9022 (m) cc_final: 0.8508 (p)
REVERT: g  111 ILE cc_start: 0.8162 (mt) cc_final: 0.7884 (tt)
REVERT: g  114 VAL cc_start: 0.9096 (m) cc_final: 0.8880 (p)
REVERT: h   71 GLU cc_start: 0.8293 (tp30) cc_final: 0.7699 (tp30)
REVERT: h   85 LYS cc_start: 0.8944 (mtmm) cc_final: 0.8713 (mtmm)
REVERT: e   56 LYS cc_start: 0.8602 (ttpp) cc_final: 0.8260 (tttm)
  outliers start: 22
  outliers final: 11
  residues processed: 233
  average time/residue: 0.1037
  time to fit residues: 35.0495
Evaluate side-chains
  190 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 179
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue 1702 ARG
Chi-restraints excluded: chain O residue 1774 THR
Chi-restraints excluded: chain O residue 1789 THR
Chi-restraints excluded: chain a residue   46 VAL
Chi-restraints excluded: chain a residue  107 THR
Chi-restraints excluded: chain d residue  118 VAL
Chi-restraints excluded: chain f residue   58 LEU
Chi-restraints excluded: chain f residue   66 ILE
Chi-restraints excluded: chain h residue   64 SER
Chi-restraints excluded: chain e residue  117 VAL
Chi-restraints excluded: chain e residue  124 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 71 optimal weight:    0.8980
   chunk 59 optimal weight:    0.6980
   chunk 16 optimal weight:    9.9990
   chunk 19 optimal weight:    4.9990
   chunk 70 optimal weight:    0.7980
   chunk 55 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   chunk 105 optimal weight:    2.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** O1782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O1813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
b  93 GLN
d  84 ASN
g  31 HIS
h  47 GLN
** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.074670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.053285 restraints weight = 49131.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.054674 restraints weight = 24495.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.055525 restraints weight = 16345.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.055972 restraints weight = 13199.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.056181 restraints weight = 11891.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.3543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  13992  Z= 0.179
  Angle     :  0.622  10.221  19972  Z= 0.361
  Chirality :  0.038   0.142   2237
  Planarity :  0.004   0.045   1664
  Dihedral  : 29.436 165.286   3901
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 12.62 %
    Favored  : 84.91 %
  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 are not related in a simple way.
  whole:  1.20 (0.26), residues: 983
  helix:  2.07 (0.21), residues: 571
  sheet: -1.16 (0.65), residues: 38
  loop : -1.05 (0.29), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG O1683 
 TYR   0.017   0.002   TYR O1825 
 PHE   0.015   0.002   PHE c  25 
 TRP   0.025   0.003   TRP O1699 
 HIS   0.008   0.001   HIS f  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (13992)
  covalent geometry    : angle       0.62160 (19972)
  hydrogen bonds       : bond        0.03774 (  766)
  hydrogen bonds       : angle       3.28418 ( 1933)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 192
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1623 LYS cc_start: 0.5136 (pttm) cc_final: 0.4835 (tptm)
REVERT: O 1702 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7501 (ttm-80)
REVERT: O 1764 MET cc_start: 0.6897 (tpp) cc_final: 0.6569 (tpp)
REVERT: O 1775 GLN cc_start: 0.7770 (mt0) cc_final: 0.7417 (mt0)
REVERT: O 1808 TYR cc_start: 0.6508 (t80) cc_final: 0.6203 (t80)
REVERT: a   97 GLU cc_start: 0.7491 (mt-10) cc_final: 0.6881 (mt-10)
REVERT: b   68 ASP cc_start: 0.8213 (m-30) cc_final: 0.7997 (m-30)
REVERT: b   84 MET cc_start: 0.8107 (tpp) cc_final: 0.7780 (tpp)
REVERT: c   41 GLU cc_start: 0.7718 (tp30) cc_final: 0.7413 (tp30)
REVERT: c   56 GLU cc_start: 0.8133 (tt0) cc_final: 0.7852 (tt0)
REVERT: d  100 LEU cc_start: 0.9413 (mt) cc_final: 0.9035 (mt)
REVERT: d  101 LEU cc_start: 0.8999 (tp) cc_final: 0.8658 (tt)
REVERT: d  116 LYS cc_start: 0.8942 (ptpt) cc_final: 0.8736 (ptpt)
REVERT: g   39 TYR cc_start: 0.8240 (m-80) cc_final: 0.7935 (m-80)
REVERT: g   73 ASN cc_start: 0.8754 (m-40) cc_final: 0.8304 (m110)
REVERT: g   76 THR cc_start: 0.8588 (p) cc_final: 0.8317 (t)
REVERT: g  101 THR cc_start: 0.9014 (m) cc_final: 0.8495 (p)
REVERT: g  111 ILE cc_start: 0.8379 (mt) cc_final: 0.8088 (tt)
REVERT: g  114 VAL cc_start: 0.9118 (m) cc_final: 0.8890 (p)
REVERT: h   71 GLU cc_start: 0.8198 (tp30) cc_final: 0.7714 (tp30)
REVERT: h   85 LYS cc_start: 0.8918 (mtmm) cc_final: 0.8645 (mtmm)
REVERT: e   56 LYS cc_start: 0.8642 (ttpp) cc_final: 0.8280 (tttm)
  outliers start: 21
  outliers final: 15
  residues processed: 204
  average time/residue: 0.1114
  time to fit residues: 33.6521
Evaluate side-chains
  195 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 179
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue 1702 ARG
Chi-restraints excluded: chain O residue 1740 HIS
Chi-restraints excluded: chain O residue 1772 CYS
Chi-restraints excluded: chain O residue 1774 THR
Chi-restraints excluded: chain O residue 1789 THR
Chi-restraints excluded: chain a residue   46 VAL
Chi-restraints excluded: chain a residue   81 ASP
Chi-restraints excluded: chain a residue  107 THR
Chi-restraints excluded: chain b residue   54 THR
Chi-restraints excluded: chain d residue  118 VAL
Chi-restraints excluded: chain f residue   45 ARG
Chi-restraints excluded: chain f residue   58 LEU
Chi-restraints excluded: chain g residue   23 LEU
Chi-restraints excluded: chain h residue   68 ASP
Chi-restraints excluded: chain e residue   73 GLU
Chi-restraints excluded: chain e residue  124 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 114 optimal weight:    4.9990
   chunk 105 optimal weight:    2.9990
   chunk 79 optimal weight:    0.8980
   chunk 113 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   chunk 36 optimal weight:    9.9990
   chunk 2 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 88 optimal weight:    0.6980
   chunk 115 optimal weight:    0.9980
   chunk 95 optimal weight:    0.6980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** O1813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  39 HIS
d  82 HIS
h  47 GLN
e  68 GLN
** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.075162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.054061 restraints weight = 49288.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.055455 restraints weight = 24859.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.056266 restraints weight = 16717.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.056731 restraints weight = 13625.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.056900 restraints weight = 12283.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.3949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  13992  Z= 0.161
  Angle     :  0.585   8.289  19972  Z= 0.341
  Chirality :  0.036   0.171   2237
  Planarity :  0.004   0.046   1664
  Dihedral  : 29.194 162.901   3901
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 13.68 %
    Favored  : 83.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.45 (0.26), residues: 983
  helix:  2.27 (0.21), residues: 572
  sheet: -1.04 (0.64), residues: 38
  loop : -0.93 (0.30), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG O1679 
 TYR   0.022   0.002   TYR d  83 
 PHE   0.014   0.001   PHE c  25 
 TRP   0.013   0.002   TRP O1699 
 HIS   0.006   0.001   HIS f  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (13992)
  covalent geometry    : angle       0.58476 (19972)
  hydrogen bonds       : bond        0.03532 (  766)
  hydrogen bonds       : angle       3.09904 ( 1933)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 187
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1623 LYS cc_start: 0.5345 (pttm) cc_final: 0.5052 (tptm)
REVERT: O 1702 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7568 (ttm-80)
REVERT: O 1744 MET cc_start: 0.5419 (tpp) cc_final: 0.4637 (tpp)
REVERT: O 1764 MET cc_start: 0.7144 (tpp) cc_final: 0.6845 (tpp)
REVERT: O 1808 TYR cc_start: 0.6492 (t80) cc_final: 0.6161 (t80)
REVERT: a  106 ASP cc_start: 0.8096 (m-30) cc_final: 0.7655 (m-30)
REVERT: b   40 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8600 (ttm110)
REVERT: c   41 GLU cc_start: 0.7603 (tp30) cc_final: 0.7244 (tp30)
REVERT: d  100 LEU cc_start: 0.9429 (mt) cc_final: 0.9101 (mt)
REVERT: d  101 LEU cc_start: 0.8997 (tp) cc_final: 0.8681 (tt)
REVERT: g   39 TYR cc_start: 0.8216 (m-80) cc_final: 0.7934 (m-80)
REVERT: g   73 ASN cc_start: 0.8739 (m-40) cc_final: 0.8284 (m110)
REVERT: g   76 THR cc_start: 0.8511 (p) cc_final: 0.8232 (t)
REVERT: g  101 THR cc_start: 0.9013 (m) cc_final: 0.8509 (p)
REVERT: g  111 ILE cc_start: 0.8399 (mt) cc_final: 0.8152 (tt)
REVERT: g  114 VAL cc_start: 0.9109 (m) cc_final: 0.8816 (p)
REVERT: h   71 GLU cc_start: 0.8227 (tp30) cc_final: 0.7735 (tp30)
REVERT: h   85 LYS cc_start: 0.8818 (mtmm) cc_final: 0.8578 (mtmm)
REVERT: e   56 LYS cc_start: 0.8620 (ttpp) cc_final: 0.8284 (tttm)
  outliers start: 27
  outliers final: 20
  residues processed: 201
  average time/residue: 0.1149
  time to fit residues: 34.1471
Evaluate side-chains
  198 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 176
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue 1691 VAL
Chi-restraints excluded: chain O residue 1702 ARG
Chi-restraints excluded: chain O residue 1740 HIS
Chi-restraints excluded: chain O residue 1774 THR
Chi-restraints excluded: chain O residue 1789 THR
Chi-restraints excluded: chain a residue   39 HIS
Chi-restraints excluded: chain a residue   41 TYR
Chi-restraints excluded: chain a residue   46 VAL
Chi-restraints excluded: chain a residue   81 ASP
Chi-restraints excluded: chain a residue  107 THR
Chi-restraints excluded: chain b residue   40 ARG
Chi-restraints excluded: chain b residue   54 THR
Chi-restraints excluded: chain b residue   62 LEU
Chi-restraints excluded: chain d residue   93 GLU
Chi-restraints excluded: chain d residue  118 VAL
Chi-restraints excluded: chain f residue   45 ARG
Chi-restraints excluded: chain f residue   66 ILE
Chi-restraints excluded: chain g residue   23 LEU
Chi-restraints excluded: chain g residue   49 VAL
Chi-restraints excluded: chain h residue   64 SER
Chi-restraints excluded: chain h residue  113 GLU
Chi-restraints excluded: chain e residue   73 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 102 optimal weight:    0.0370
   chunk 55 optimal weight:    0.8980
   chunk 65 optimal weight:    5.9990
   chunk 73 optimal weight:    2.9990
   chunk 13 optimal weight:    0.2980
   chunk 9 optimal weight:    4.9990
   chunk 80 optimal weight:    3.9990
   chunk 89 optimal weight:    0.9980
   chunk 74 optimal weight:    0.0060
   overall best weight:    0.4274

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

Flipped N/Q/H residues before XYZ refinement:
** O1813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  39 HIS
d  82 HIS
** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.075805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.054895 restraints weight = 49200.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.056336 restraints weight = 24064.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.057177 restraints weight = 15936.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.057650 restraints weight = 12875.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.057871 restraints weight = 11549.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.4164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13992  Z= 0.143
  Angle     :  0.569   7.844  19972  Z= 0.332
  Chirality :  0.035   0.212   2237
  Planarity :  0.004   0.045   1664
  Dihedral  : 28.986 162.212   3901
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 15.45 %
    Favored  : 81.84 %
  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 are not related in a simple way.
  whole:  1.62 (0.27), residues: 983
  helix:  2.34 (0.21), residues: 573
  sheet: -0.73 (0.64), residues: 38
  loop : -0.78 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG f  95 
 TYR   0.029   0.002   TYR d  83 
 PHE   0.009   0.001   PHE e  67 
 TRP   0.025   0.003   TRP O1699 
 HIS   0.013   0.001   HIS a  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (13992)
  covalent geometry    : angle       0.56877 (19972)
  hydrogen bonds       : bond        0.03308 (  766)
  hydrogen bonds       : angle       3.02740 ( 1933)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 191
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1764 MET cc_start: 0.7055 (tpp) cc_final: 0.6790 (tpp)
REVERT: O 1808 TYR cc_start: 0.6440 (t80) cc_final: 0.6116 (t80)
REVERT: a  106 ASP cc_start: 0.7954 (m-30) cc_final: 0.7665 (m-30)
REVERT: b   40 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8618 (ttm110)
REVERT: c   41 GLU cc_start: 0.7659 (tp30) cc_final: 0.7247 (tp30)
REVERT: c   89 ASN cc_start: 0.8661 (m-40) cc_final: 0.8383 (m-40)
REVERT: d  101 LEU cc_start: 0.8939 (tp) cc_final: 0.8694 (tt)
REVERT: d  105 GLU cc_start: 0.6885 (tp30) cc_final: 0.6511 (tp30)
REVERT: d  108 LYS cc_start: 0.8357 (ttpt) cc_final: 0.8121 (ttpt)
REVERT: g   73 ASN cc_start: 0.8776 (m-40) cc_final: 0.8305 (m110)
REVERT: g   76 THR cc_start: 0.8507 (p) cc_final: 0.8235 (t)
REVERT: g  101 THR cc_start: 0.9003 (m) cc_final: 0.8508 (p)
REVERT: g  111 ILE cc_start: 0.8406 (mt) cc_final: 0.8109 (tt)
REVERT: g  114 VAL cc_start: 0.9098 (m) cc_final: 0.8810 (p)
REVERT: h  105 GLU cc_start: 0.6681 (tp30) cc_final: 0.6216 (tp30)
REVERT: h  108 LYS cc_start: 0.8505 (mttm) cc_final: 0.8287 (ttpt)
REVERT: e   56 LYS cc_start: 0.8621 (ttpp) cc_final: 0.8266 (tttm)
  outliers start: 23
  outliers final: 17
  residues processed: 207
  average time/residue: 0.1144
  time to fit residues: 35.0242
Evaluate side-chains
  193 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 175
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue 1691 VAL
Chi-restraints excluded: chain O residue 1702 ARG
Chi-restraints excluded: chain O residue 1740 HIS
Chi-restraints excluded: chain O residue 1774 THR
Chi-restraints excluded: chain O residue 1825 TYR
Chi-restraints excluded: chain a residue   41 TYR
Chi-restraints excluded: chain a residue   46 VAL
Chi-restraints excluded: chain a residue   81 ASP
Chi-restraints excluded: chain a residue  107 THR
Chi-restraints excluded: chain b residue   40 ARG
Chi-restraints excluded: chain b residue   62 LEU
Chi-restraints excluded: chain d residue  118 VAL
Chi-restraints excluded: chain f residue   45 ARG
Chi-restraints excluded: chain f residue   66 ILE
Chi-restraints excluded: chain g residue   49 VAL
Chi-restraints excluded: chain h residue   64 SER
Chi-restraints excluded: chain h residue  113 GLU
Chi-restraints excluded: chain e residue  124 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 33 optimal weight:   10.0000
   chunk 85 optimal weight:    5.9990
   chunk 76 optimal weight:    0.8980
   chunk 83 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 116 optimal weight:    0.6980
   chunk 37 optimal weight:    6.9990
   chunk 105 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   chunk 53 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0030
   overall best weight:    1.3194

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

Flipped N/Q/H residues before XYZ refinement:
** O1813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  39 HIS
b  64 ASN
b  93 GLN
d  82 HIS
h  47 GLN
** h  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.074533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.053335 restraints weight = 49374.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.054752 restraints weight = 24723.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.055595 restraints weight = 16528.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.056017 restraints weight = 13389.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.056296 restraints weight = 12119.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.4251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  13992  Z= 0.189
  Angle     :  0.601   8.043  19972  Z= 0.346
  Chirality :  0.037   0.174   2237
  Planarity :  0.004   0.046   1664
  Dihedral  : 29.184 161.485   3901
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 16.16 %
    Favored  : 80.07 %
  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 are not related in a simple way.
  whole:  1.46 (0.27), residues: 983
  helix:  2.13 (0.22), residues: 577
  sheet: -0.25 (0.76), residues: 29
  loop : -0.80 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG a  52 
 TYR   0.027   0.002   TYR d  83 
 PHE   0.013   0.001   PHE c  25 
 TRP   0.025   0.002   TRP O1699 
 HIS   0.008   0.001   HIS f  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 (13992)
  covalent geometry    : angle       0.60143 (19972)
  hydrogen bonds       : bond        0.03725 (  766)
  hydrogen bonds       : angle       3.18544 ( 1933)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 172
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1714 LEU cc_start: 0.7770 (tp) cc_final: 0.7264 (pp)
REVERT: O 1808 TYR cc_start: 0.6562 (t80) cc_final: 0.6254 (t80)
REVERT: a  106 ASP cc_start: 0.8078 (m-30) cc_final: 0.7690 (m-30)
REVERT: d   83 TYR cc_start: 0.7591 (m-80) cc_final: 0.7020 (m-80)
REVERT: d  101 LEU cc_start: 0.9031 (tp) cc_final: 0.8721 (tt)
REVERT: g   73 ASN cc_start: 0.8767 (m-40) cc_final: 0.8300 (m110)
REVERT: g   76 THR cc_start: 0.8525 (p) cc_final: 0.8224 (t)
REVERT: g  101 THR cc_start: 0.9000 (m) cc_final: 0.8487 (p)
REVERT: g  111 ILE cc_start: 0.8496 (mt) cc_final: 0.8199 (tt)
REVERT: g  114 VAL cc_start: 0.9099 (m) cc_final: 0.8780 (p)
REVERT: e   56 LYS cc_start: 0.8685 (ttpp) cc_final: 0.8320 (tttm)
  outliers start: 32
  outliers final: 28
  residues processed: 192
  average time/residue: 0.1078
  time to fit residues: 31.2919
Evaluate side-chains
  189 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 161
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue 1691 VAL
Chi-restraints excluded: chain O residue 1702 ARG
Chi-restraints excluded: chain O residue 1740 HIS
Chi-restraints excluded: chain O residue 1752 ILE
Chi-restraints excluded: chain O residue 1772 CYS
Chi-restraints excluded: chain O residue 1774 THR
Chi-restraints excluded: chain O residue 1825 TYR
Chi-restraints excluded: chain a residue   39 HIS
Chi-restraints excluded: chain a residue   41 TYR
Chi-restraints excluded: chain a residue   46 VAL
Chi-restraints excluded: chain a residue   51 ILE
Chi-restraints excluded: chain a residue   81 ASP
Chi-restraints excluded: chain a residue  107 THR
Chi-restraints excluded: chain b residue   50 ILE
Chi-restraints excluded: chain b residue   54 THR
Chi-restraints excluded: chain b residue   62 LEU
Chi-restraints excluded: chain c residue   91 GLU
Chi-restraints excluded: chain d residue   93 GLU
Chi-restraints excluded: chain d residue  118 VAL
Chi-restraints excluded: chain f residue   45 ARG
Chi-restraints excluded: chain f residue   66 ILE
Chi-restraints excluded: chain g residue   49 VAL
Chi-restraints excluded: chain h residue   64 SER
Chi-restraints excluded: chain h residue   68 ASP
Chi-restraints excluded: chain h residue  113 GLU
Chi-restraints excluded: chain e residue  100 LEU
Chi-restraints excluded: chain e residue  117 VAL
Chi-restraints excluded: chain e residue  124 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 102 optimal weight:    0.8980
   chunk 19 optimal weight:    5.9990
   chunk 13 optimal weight:    0.0020
   chunk 62 optimal weight:    2.9990
   chunk 117 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   chunk 112 optimal weight:    3.9990
   chunk 14 optimal weight:    7.9990
   overall best weight:    1.1392

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

Flipped N/Q/H residues before XYZ refinement:
** O1813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  39 HIS
d  82 HIS
h  47 GLN
** h  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.074701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.053545 restraints weight = 49091.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.054960 restraints weight = 24575.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.055818 restraints weight = 16462.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.056249 restraints weight = 13299.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.056521 restraints weight = 12020.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.4382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  13992  Z= 0.176
  Angle     :  0.587   8.037  19972  Z= 0.339
  Chirality :  0.036   0.231   2237
  Planarity :  0.004   0.046   1664
  Dihedral  : 29.104 161.286   3901
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 15.92 %
    Favored  : 80.19 %
  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 are not related in a simple way.
  whole:  1.46 (0.27), residues: 983
  helix:  2.11 (0.21), residues: 579
  sheet: -0.25 (0.77), residues: 29
  loop : -0.78 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG a  40 
 TYR   0.029   0.002   TYR d  83 
 PHE   0.011   0.001   PHE c  25 
 TRP   0.023   0.002   TRP O1699 
 HIS   0.008   0.001   HIS a  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (13992)
  covalent geometry    : angle       0.58710 (19972)
  hydrogen bonds       : bond        0.03567 (  766)
  hydrogen bonds       : angle       3.15545 ( 1933)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 170
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1714 LEU cc_start: 0.7778 (tp) cc_final: 0.7291 (pp)
REVERT: O 1744 MET cc_start: 0.6093 (tpp) cc_final: 0.5860 (tpp)
REVERT: a  106 ASP cc_start: 0.8116 (m-30) cc_final: 0.7714 (m-30)
REVERT: b   40 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.7530 (ttm110)
REVERT: d   83 TYR cc_start: 0.7608 (m-80) cc_final: 0.7194 (m-80)
REVERT: d  101 LEU cc_start: 0.9021 (tp) cc_final: 0.8703 (tt)
REVERT: d  105 GLU cc_start: 0.6678 (tp30) cc_final: 0.6312 (tp30)
REVERT: d  108 LYS cc_start: 0.8434 (ttpt) cc_final: 0.8117 (ttpt)
REVERT: g   73 ASN cc_start: 0.8801 (m-40) cc_final: 0.8318 (m110)
REVERT: g   76 THR cc_start: 0.8544 (p) cc_final: 0.8249 (t)
REVERT: g  101 THR cc_start: 0.8982 (m) cc_final: 0.8495 (p)
REVERT: g  111 ILE cc_start: 0.8530 (mt) cc_final: 0.8236 (tt)
REVERT: g  114 VAL cc_start: 0.9092 (m) cc_final: 0.8776 (p)
REVERT: e   56 LYS cc_start: 0.8712 (ttpp) cc_final: 0.8341 (tttm)
  outliers start: 33
  outliers final: 29
  residues processed: 189
  average time/residue: 0.1184
  time to fit residues: 32.9952
Evaluate side-chains
  195 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 165
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue 1651 ILE
Chi-restraints excluded: chain O residue 1691 VAL
Chi-restraints excluded: chain O residue 1702 ARG
Chi-restraints excluded: chain O residue 1740 HIS
Chi-restraints excluded: chain O residue 1752 ILE
Chi-restraints excluded: chain O residue 1774 THR
Chi-restraints excluded: chain O residue 1825 TYR
Chi-restraints excluded: chain a residue   39 HIS
Chi-restraints excluded: chain a residue   41 TYR
Chi-restraints excluded: chain a residue   46 VAL
Chi-restraints excluded: chain a residue   81 ASP
Chi-restraints excluded: chain a residue  107 THR
Chi-restraints excluded: chain b residue   40 ARG
Chi-restraints excluded: chain b residue   50 ILE
Chi-restraints excluded: chain b residue   54 THR
Chi-restraints excluded: chain b residue   62 LEU
Chi-restraints excluded: chain b residue   81 VAL
Chi-restraints excluded: chain c residue   91 GLU
Chi-restraints excluded: chain d residue   90 THR
Chi-restraints excluded: chain d residue   93 GLU
Chi-restraints excluded: chain d residue  118 VAL
Chi-restraints excluded: chain f residue   45 ARG
Chi-restraints excluded: chain f residue   66 ILE
Chi-restraints excluded: chain g residue   49 VAL
Chi-restraints excluded: chain h residue   64 SER
Chi-restraints excluded: chain h residue   68 ASP
Chi-restraints excluded: chain h residue  113 GLU
Chi-restraints excluded: chain e residue  100 LEU
Chi-restraints excluded: chain e residue  112 ILE
Chi-restraints excluded: chain e residue  124 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 29 optimal weight:   20.0000
   chunk 85 optimal weight:    4.9990
   chunk 111 optimal weight:    0.9990
   chunk 8 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 22 optimal weight:    9.9990
   chunk 80 optimal weight:    0.9990
   chunk 76 optimal weight:    4.9990
   chunk 30 optimal weight:    8.9990
   chunk 10 optimal weight:    5.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** O1813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  39 HIS
d  82 HIS
** g  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** h  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.071938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.050674 restraints weight = 49437.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.051972 restraints weight = 25631.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.052770 restraints weight = 17619.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.053181 restraints weight = 14437.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.053435 restraints weight = 13105.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.4407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.110  13992  Z= 0.350
  Angle     :  0.748   9.766  19972  Z= 0.419
  Chirality :  0.044   0.302   2237
  Planarity :  0.006   0.051   1664
  Dihedral  : 30.027 162.238   3901
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 16.04 %
    Favored  : 79.60 %
  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 are not related in a simple way.
  whole:  0.64 (0.26), residues: 983
  helix:  1.46 (0.21), residues: 576
  sheet: -0.21 (0.80), residues: 28
  loop : -1.14 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG e 116 
 TYR   0.035   0.003   TYR a  99 
 PHE   0.018   0.003   PHE b  61 
 TRP   0.040   0.005   TRP O1699 
 HIS   0.011   0.002   HIS a  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00789 (13992)
  covalent geometry    : angle       0.74792 (19972)
  hydrogen bonds       : bond        0.05682 (  766)
  hydrogen bonds       : angle       3.67501 ( 1933)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 162
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1714 LEU cc_start: 0.7654 (tp) cc_final: 0.7189 (pp)
REVERT: O 1740 HIS cc_start: 0.0347 (OUTLIER) cc_final: -0.0130 (m-70)
REVERT: a  106 ASP cc_start: 0.7812 (m-30) cc_final: 0.7385 (m-30)
REVERT: b   84 MET cc_start: 0.8097 (tpp) cc_final: 0.7205 (tpp)
REVERT: d  101 LEU cc_start: 0.9031 (tp) cc_final: 0.8696 (tt)
REVERT: g   73 ASN cc_start: 0.8807 (m-40) cc_final: 0.8361 (m110)
REVERT: g   76 THR cc_start: 0.8586 (p) cc_final: 0.8226 (t)
REVERT: g  101 THR cc_start: 0.9047 (m) cc_final: 0.8515 (p)
REVERT: g  111 ILE cc_start: 0.8911 (mt) cc_final: 0.8566 (tt)
REVERT: g  114 VAL cc_start: 0.9094 (m) cc_final: 0.8669 (p)
REVERT: h   59 MET cc_start: 0.8449 (tpp) cc_final: 0.8105 (tpp)
REVERT: e   56 LYS cc_start: 0.8897 (ttpp) cc_final: 0.8501 (tttm)
  outliers start: 37
  outliers final: 31
  residues processed: 185
  average time/residue: 0.1116
  time to fit residues: 31.0500
Evaluate side-chains
  184 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 152
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue 1651 ILE
Chi-restraints excluded: chain O residue 1691 VAL
Chi-restraints excluded: chain O residue 1702 ARG
Chi-restraints excluded: chain O residue 1740 HIS
Chi-restraints excluded: chain O residue 1752 ILE
Chi-restraints excluded: chain O residue 1772 CYS
Chi-restraints excluded: chain O residue 1774 THR
Chi-restraints excluded: chain O residue 1789 THR
Chi-restraints excluded: chain O residue 1825 TYR
Chi-restraints excluded: chain a residue   39 HIS
Chi-restraints excluded: chain a residue   41 TYR
Chi-restraints excluded: chain a residue   46 VAL
Chi-restraints excluded: chain a residue   51 ILE
Chi-restraints excluded: chain a residue   81 ASP
Chi-restraints excluded: chain a residue  107 THR
Chi-restraints excluded: chain a residue  124 ILE
Chi-restraints excluded: chain b residue   50 ILE
Chi-restraints excluded: chain b residue   54 THR
Chi-restraints excluded: chain b residue   62 LEU
Chi-restraints excluded: chain b residue   81 VAL
Chi-restraints excluded: chain d residue   90 THR
Chi-restraints excluded: chain d residue   93 GLU
Chi-restraints excluded: chain d residue  118 VAL
Chi-restraints excluded: chain f residue   45 ARG
Chi-restraints excluded: chain f residue   54 THR
Chi-restraints excluded: chain g residue   49 VAL
Chi-restraints excluded: chain h residue   68 ASP
Chi-restraints excluded: chain h residue   71 GLU
Chi-restraints excluded: chain h residue  113 GLU
Chi-restraints excluded: chain e residue  100 LEU
Chi-restraints excluded: chain e residue  112 ILE
Chi-restraints excluded: chain e residue  124 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 85 optimal weight:    0.6980
   chunk 93 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 116 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
O1766 HIS
** O1813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  39 HIS
d  82 HIS
d 109 HIS
** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.074427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.053270 restraints weight = 49306.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.054669 restraints weight = 24580.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.055458 restraints weight = 16498.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.055962 restraints weight = 13474.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.056231 restraints weight = 12125.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.4583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  13992  Z= 0.165
  Angle     :  0.605   8.846  19972  Z= 0.348
  Chirality :  0.037   0.298   2237
  Planarity :  0.004   0.047   1664
  Dihedral  : 29.351 162.141   3901
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 17.33 %
    Favored  : 79.72 %
  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 are not related in a simple way.
  whole:  1.31 (0.27), residues: 983
  helix:  1.98 (0.21), residues: 579
  sheet: -0.14 (0.80), residues: 28
  loop : -0.84 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG a  40 
 TYR   0.025   0.002   TYR d  83 
 PHE   0.012   0.001   PHE O1805 
 TRP   0.030   0.003   TRP O1699 
 HIS   0.006   0.001   HIS d 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (13992)
  covalent geometry    : angle       0.60542 (19972)
  hydrogen bonds       : bond        0.03508 (  766)
  hydrogen bonds       : angle       3.23454 ( 1933)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 170
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1623 LYS cc_start: 0.5640 (tptm) cc_final: 0.5283 (mmmt)
REVERT: O 1714 LEU cc_start: 0.7713 (tp) cc_final: 0.7217 (pp)
REVERT: O 1775 GLN cc_start: 0.7916 (mt0) cc_final: 0.7671 (mt0)
REVERT: a  106 ASP cc_start: 0.8036 (m-30) cc_final: 0.7684 (m-30)
REVERT: b   84 MET cc_start: 0.8115 (tpp) cc_final: 0.7666 (tpp)
REVERT: d   83 TYR cc_start: 0.7613 (m-10) cc_final: 0.7350 (m-80)
REVERT: d  101 LEU cc_start: 0.8930 (tp) cc_final: 0.8684 (tt)
REVERT: d  105 GLU cc_start: 0.6428 (tp30) cc_final: 0.5843 (tp30)
REVERT: d  108 LYS cc_start: 0.8342 (ttpt) cc_final: 0.7789 (ttpt)
REVERT: g   73 ASN cc_start: 0.8791 (m-40) cc_final: 0.8327 (m110)
REVERT: g   76 THR cc_start: 0.8569 (p) cc_final: 0.8261 (t)
REVERT: g  101 THR cc_start: 0.9043 (m) cc_final: 0.8581 (p)
REVERT: g  114 VAL cc_start: 0.9099 (m) cc_final: 0.8770 (p)
REVERT: h   71 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7545 (tp30)
REVERT: h  105 GLU cc_start: 0.6719 (tp30) cc_final: 0.6450 (tp30)
REVERT: e   56 LYS cc_start: 0.8738 (ttpp) cc_final: 0.8419 (tttm)
  outliers start: 25
  outliers final: 17
  residues processed: 186
  average time/residue: 0.1093
  time to fit residues: 30.8073
Evaluate side-chains
  177 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 159
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue 1691 VAL
Chi-restraints excluded: chain O residue 1772 CYS
Chi-restraints excluded: chain O residue 1789 THR
Chi-restraints excluded: chain O residue 1825 TYR
Chi-restraints excluded: chain a residue   39 HIS
Chi-restraints excluded: chain a residue   41 TYR
Chi-restraints excluded: chain a residue  107 THR
Chi-restraints excluded: chain b residue   62 LEU
Chi-restraints excluded: chain b residue   81 VAL
Chi-restraints excluded: chain c residue   91 GLU
Chi-restraints excluded: chain d residue   90 THR
Chi-restraints excluded: chain d residue   93 GLU
Chi-restraints excluded: chain f residue   45 ARG
Chi-restraints excluded: chain g residue   49 VAL
Chi-restraints excluded: chain g residue  107 VAL
Chi-restraints excluded: chain h residue   71 GLU
Chi-restraints excluded: chain h residue  113 GLU
Chi-restraints excluded: chain e residue  100 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 80 optimal weight:    0.0030
   chunk 34 optimal weight:    0.0370
   chunk 99 optimal weight:    0.7980
   chunk 43 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   chunk 15 optimal weight:    0.3980
   chunk 9 optimal weight:    4.9990
   chunk 101 optimal weight:    0.6980
   chunk 1 optimal weight:    4.9990
   overall best weight:    0.3868

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

Flipped N/Q/H residues before XYZ refinement:
O1806 GLN
** O1813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
d  49 HIS
d  82 HIS
h  63 ASN
** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.075641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.054646 restraints weight = 49221.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.056070 restraints weight = 24542.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.056870 restraints weight = 16439.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.057419 restraints weight = 13378.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.057673 restraints weight = 11982.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.4836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13992  Z= 0.145
  Angle     :  0.589   9.348  19972  Z= 0.339
  Chirality :  0.036   0.263   2237
  Planarity :  0.004   0.047   1664
  Dihedral  : 28.974 161.030   3901
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 18.40 %
    Favored  : 79.72 %
  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 are not related in a simple way.
  whole:  1.53 (0.27), residues: 983
  helix:  2.22 (0.21), residues: 573
  sheet: -0.14 (0.69), residues: 31
  loop : -0.81 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.000   ARG a  40 
 TYR   0.023   0.002   TYR d  83 
 PHE   0.013   0.001   PHE O1816 
 TRP   0.026   0.002   TRP O1699 
 HIS   0.021   0.002   HIS a  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (13992)
  covalent geometry    : angle       0.58903 (19972)
  hydrogen bonds       : bond        0.03357 (  766)
  hydrogen bonds       : angle       3.18395 ( 1933)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 172
  time to evaluate  : 0.435 
Fit side-chains
REVERT: O 1623 LYS cc_start: 0.5602 (tptm) cc_final: 0.5299 (mmmt)
REVERT: O 1634 MET cc_start: 0.5424 (ppp) cc_final: 0.4742 (ppp)
REVERT: O 1699 TRP cc_start: 0.4490 (t-100) cc_final: 0.3921 (t-100)
REVERT: O 1714 LEU cc_start: 0.7718 (tp) cc_final: 0.7151 (pp)
REVERT: a   37 LYS cc_start: 0.7874 (pttm) cc_final: 0.7377 (ptmt)
REVERT: a  106 ASP cc_start: 0.8045 (m-30) cc_final: 0.7576 (m-30)
REVERT: c   89 ASN cc_start: 0.8589 (m-40) cc_final: 0.8226 (m-40)
REVERT: d   83 TYR cc_start: 0.7719 (m-10) cc_final: 0.7086 (m-80)
REVERT: d   86 ARG cc_start: 0.7477 (mmp80) cc_final: 0.6962 (mmp80)
REVERT: d  101 LEU cc_start: 0.8945 (tp) cc_final: 0.8681 (tt)
REVERT: d  105 GLU cc_start: 0.6268 (tp30) cc_final: 0.5928 (tp30)
REVERT: d  108 LYS cc_start: 0.8277 (ttpt) cc_final: 0.7928 (ttpp)
REVERT: g   73 ASN cc_start: 0.8763 (m-40) cc_final: 0.8284 (m110)
REVERT: g   76 THR cc_start: 0.8541 (p) cc_final: 0.8229 (t)
REVERT: g  101 THR cc_start: 0.8994 (m) cc_final: 0.8463 (p)
REVERT: g  114 VAL cc_start: 0.9097 (m) cc_final: 0.8785 (p)
REVERT: h   71 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7916 (tp30)
REVERT: e   56 LYS cc_start: 0.8662 (ttpp) cc_final: 0.8306 (tttm)
REVERT: e   82 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8534 (mt)
  outliers start: 16
  outliers final: 11
  residues processed: 180
  average time/residue: 0.1077
  time to fit residues: 29.1226
Evaluate side-chains
  176 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 163
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue 1691 VAL
Chi-restraints excluded: chain O residue 1825 TYR
Chi-restraints excluded: chain a residue  107 THR
Chi-restraints excluded: chain b residue   50 ILE
Chi-restraints excluded: chain b residue   62 LEU
Chi-restraints excluded: chain b residue   81 VAL
Chi-restraints excluded: chain c residue   91 GLU
Chi-restraints excluded: chain f residue   45 ARG
Chi-restraints excluded: chain g residue   49 VAL
Chi-restraints excluded: chain g residue  107 VAL
Chi-restraints excluded: chain h residue   71 GLU
Chi-restraints excluded: chain h residue  113 GLU
Chi-restraints excluded: chain e residue   82 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 65 optimal weight:    6.9990
   chunk 22 optimal weight:    0.0270
   chunk 114 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   chunk 112 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 88 optimal weight:    0.6980
   chunk 89 optimal weight:    0.6980
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
** O1813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  39 HIS
** c  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
d  49 HIS
** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.075837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.054823 restraints weight = 48966.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.056236 restraints weight = 24650.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.057108 restraints weight = 16514.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.057601 restraints weight = 13327.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.057807 restraints weight = 11964.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.4944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13992  Z= 0.150
  Angle     :  0.593   9.194  19972  Z= 0.338
  Chirality :  0.036   0.298   2237
  Planarity :  0.004   0.046   1664
  Dihedral  : 28.891 160.645   3901
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 19.58 %
    Favored  : 78.66 %
  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 are not related in a simple way.
  whole:  1.59 (0.27), residues: 983
  helix:  2.21 (0.21), residues: 580
  sheet: -0.17 (0.67), residues: 31
  loop : -0.72 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG g  81 
 TYR   0.024   0.002   TYR d  83 
 PHE   0.021   0.001   PHE h  65 
 TRP   0.026   0.002   TRP O1699 
 HIS   0.005   0.001   HIS O1766 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (13992)
  covalent geometry    : angle       0.59271 (19972)
  hydrogen bonds       : bond        0.03348 (  766)
  hydrogen bonds       : angle       3.19018 ( 1933)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2274.88 seconds
wall clock time: 40 minutes 9.69 seconds (2409.69 seconds total)