Starting phenix.real_space_refine
on Fri Jul  3 09:45:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rzc_54399/07_2026/9rzc_54399.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rzc_54399/07_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rzc_54399/07_2026/9rzc_54399.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rzc_54399/07_2026/9rzc_54399.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rzc_54399/07_2026/9rzc_54399.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rzc_54399/07_2026/9rzc_54399.map"
  }
  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-dev-6108/lib/python3.11/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: 2.23, per 1000 atoms: 0.17
  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: 0.70
  Conformation dependent library (CDL) restraints added in 273.7 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: 1.25
  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: 2.49

  Time building geometry restraints manager: 1.00 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=" C3'  DA T  71 "
       pdb=" C2'  DA T  71 "
    ideal  model  delta    sigma   weight residual
    1.516  1.559 -0.043 8.00e-03 1.56e+04 2.91e+01
  bond pdb=" C3'  DC N  74 "
       pdb=" C2'  DC N  74 "
    ideal  model  delta    sigma   weight residual
    1.516  1.557 -0.041 8.00e-03 1.56e+04 2.69e+01
  bond pdb=" C3'  DT N  27 "
       pdb=" C2'  DT N  27 "
    ideal  model  delta    sigma   weight residual
    1.516  1.557 -0.041 8.00e-03 1.56e+04 2.58e+01
  bond pdb=" C1'  DT N  41 "
       pdb=" N1   DT N  41 "
    ideal  model  delta    sigma   weight residual
    1.468  1.534 -0.066 1.40e-02 5.10e+03 2.20e+01
  bond pdb=" C1'  DT T 109 "
       pdb=" N1   DT T 109 "
    ideal  model  delta    sigma   weight residual
    1.468  1.533 -0.065 1.40e-02 5.10e+03 2.17e+01
  ... (remaining 13987 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 17819
        2.01 -     4.01: 1781
        4.01 -     6.02: 312
        6.02 -     8.03: 53
        8.03 -    10.03: 7
  Bond angle restraints: 19972
  Sorted by residual:
  angle pdb=" O4'  DC N 103 "
        pdb=" C1'  DC N 103 "
        pdb=" N1   DC N 103 "
      ideal   model   delta    sigma   weight residual
     108.00  115.46   -7.46 7.00e-01 2.04e+00 1.13e+02
  angle pdb=" O5'  DT N 104 "
        pdb=" C5'  DT N 104 "
        pdb=" C4'  DT N 104 "
      ideal   model   delta    sigma   weight residual
     109.40  117.66   -8.26 8.00e-01 1.56e+00 1.07e+02
  angle pdb=" O4'  DA N  90 "
        pdb=" C1'  DA N  90 "
        pdb=" N9   DA N  90 "
      ideal   model   delta    sigma   weight residual
     108.00  101.52    6.48 7.00e-01 2.04e+00 8.57e+01
  angle pdb=" O4'  DG T 150 "
        pdb=" C1'  DG T 150 "
        pdb=" N9   DG T 150 "
      ideal   model   delta    sigma   weight residual
     108.00  113.91   -5.91 7.00e-01 2.04e+00 7.12e+01
  angle pdb=" O4'  DA N 120 "
        pdb=" C1'  DA N 120 "
        pdb=" N9   DA N 120 "
      ideal   model   delta    sigma   weight residual
     108.00  102.38    5.62 7.00e-01 2.04e+00 6.45e+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 -    0.067: 1493
       0.067 -    0.134: 549
       0.134 -    0.200: 168
       0.200 -    0.267: 25
       0.267 -    0.334: 2
  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     -2.73   -2.40   -0.33 2.00e-01 2.50e+01 2.79e+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     -2.73   -2.42   -0.32 2.00e-01 2.50e+01 2.49e+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
  ... (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:             1.690
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     11.080
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.098  13992  Z= 0.672
  Angle     :  1.293  10.034  19972  Z= 0.950
  Chirality :  0.075   0.334   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/Z
  covalent geometry    : bond        0.00825 /  0.67 (13992)
  covalent geometry    : angle       1.29318 /  0.95 (19972)
  hydrogen bonds       : bond        0.11601 / 13.41 (  766)
  hydrogen bonds       : angle       4.65857 /  6.31 ( 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  : 0.363 
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: 0.1287
  time to fit residues: 60.2837
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  : 0.299 
-------------------------------------------------------------------------------
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:   10.0000
   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...
O1740 HIS
** O1780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O1782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a 113 HIS
** b  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
d  47 GLN
** d  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
d 109 HIS
e  68 GLN
e  93 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.075371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.054045 restraints weight = 49218.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.055461 restraints weight = 24086.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.056326 restraints weight = 16060.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.056804 restraints weight = 12955.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.056982 restraints weight = 11654.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  13992  Z= 0.181
  Angle     :  0.830   9.683  19972  Z= 0.469
  Chirality :  0.054   0.252   2237
  Planarity :  0.006   0.054   1664
  Dihedral  : 29.644 173.525   3901
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 10.14 %
    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:  0.34 (0.25), residues: 983
  helix:  1.26 (0.21), residues: 569
  sheet: -0.18 (0.78), residues: 28
  loop : -1.34 (0.27), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG g  35 
 TYR   0.028   0.003   TYR O1716 
 PHE   0.026   0.002   PHE c  25 
 TRP   0.034   0.006   TRP O1699 
 HIS   0.011   0.002   HIS a  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.18 (13992)
  covalent geometry    : angle       0.82967 /  0.47 (19972)
  hydrogen bonds       : bond        0.05515 /  6.26 (  766)
  hydrogen bonds       : angle       3.70967 /  4.99 ( 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
  230 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 210
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1623 LYS cc_start: 0.5096 (pttm) cc_final: 0.4674 (tptm)
REVERT: O 1739 ILE cc_start: 0.5533 (pt) cc_final: 0.4741 (mt)
REVERT: O 1764 MET cc_start: 0.7392 (tpp) cc_final: 0.7183 (tpp)
REVERT: a  106 ASP cc_start: 0.8112 (m-30) cc_final: 0.7780 (m-30)
REVERT: a  123 ASP cc_start: 0.8727 (m-30) cc_final: 0.8169 (m-30)
REVERT: b   53 GLU cc_start: 0.7903 (tp30) cc_final: 0.7673 (tp30)
REVERT: b   59 LYS cc_start: 0.8381 (ttpp) cc_final: 0.8166 (tttp)
REVERT: b   63 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7473 (mt-10)
REVERT: b   77 LYS cc_start: 0.8924 (mmtt) cc_final: 0.8648 (mmtp)
REVERT: c   41 GLU cc_start: 0.7569 (tp30) cc_final: 0.7350 (tp30)
REVERT: d  116 LYS cc_start: 0.8936 (ttpt) cc_final: 0.8719 (ptpt)
REVERT: f   96 THR cc_start: 0.8876 (m) cc_final: 0.8600 (t)
REVERT: g   73 ASN cc_start: 0.8697 (m-40) cc_final: 0.8303 (m110)
REVERT: g   76 THR cc_start: 0.8525 (p) cc_final: 0.8252 (t)
REVERT: g  101 THR cc_start: 0.8992 (m) cc_final: 0.8469 (p)
REVERT: g  111 ILE cc_start: 0.8100 (mt) cc_final: 0.7810 (tt)
REVERT: g  114 VAL cc_start: 0.9128 (m) cc_final: 0.8871 (p)
REVERT: h   71 GLU cc_start: 0.8077 (tp30) cc_final: 0.7527 (tp30)
REVERT: e   56 LYS cc_start: 0.8491 (ttpp) cc_final: 0.8147 (tttm)
  outliers start: 20
  outliers final: 10
  residues processed: 225
  average time/residue: 0.1012
  time to fit residues: 32.7115
Evaluate side-chains
  195 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 185
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   46 VAL
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 f residue   66 ILE
Chi-restraints excluded: chain h residue   68 ASP
Chi-restraints excluded: chain k residue  936 GLU
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:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 19 optimal weight:    7.9990
   chunk 70 optimal weight:    0.9990
   chunk 55 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   chunk 93 optimal weight:    1.9990
   chunk 34 optimal weight:    6.9990
   chunk 90 optimal weight:    0.7980
   chunk 105 optimal weight:    2.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** O1682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O1780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O1782 GLN
** O1813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
b  93 GLN
** d  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
e  93 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.074078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.052644 restraints weight = 49437.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.054045 restraints weight = 24515.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.054904 restraints weight = 16329.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.055375 restraints weight = 13190.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.055539 restraints weight = 11872.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.3068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  13992  Z= 0.191
  Angle     :  0.740   9.280  19972  Z= 0.422
  Chirality :  0.049   0.352   2237
  Planarity :  0.005   0.045   1664
  Dihedral  : 30.022 170.294   3901
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 10.97 %
    Favored  : 86.44 %
  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:  0.71 (0.26), residues: 983
  helix:  1.63 (0.21), residues: 569
  sheet: -1.36 (0.69), residues: 43
  loop : -1.14 (0.29), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG O1683 
 TYR   0.020   0.002   TYR g  39 
 PHE   0.015   0.002   PHE c  25 
 TRP   0.037   0.005   TRP O1699 
 HIS   0.008   0.002   HIS f  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00364 /  0.19 (13992)
  covalent geometry    : angle       0.74034 /  0.42 (19972)
  hydrogen bonds       : bond        0.04990 /  5.65 (  766)
  hydrogen bonds       : angle       3.52020 /  4.78 ( 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: 22
    poor density    : 191
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1623 LYS cc_start: 0.5197 (pttm) cc_final: 0.4840 (tptm)
REVERT: O 1634 MET cc_start: 0.5402 (ppp) cc_final: 0.5174 (ptp)
REVERT: O 1764 MET cc_start: 0.7489 (tpp) cc_final: 0.7287 (tpp)
REVERT: b   59 LYS cc_start: 0.8349 (ttpp) cc_final: 0.7924 (tttm)
REVERT: b   63 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7513 (mt-10)
REVERT: c   41 GLU cc_start: 0.7723 (tp30) cc_final: 0.7457 (tp30)
REVERT: d   83 TYR cc_start: 0.7689 (m-10) cc_final: 0.7289 (m-10)
REVERT: d  101 LEU cc_start: 0.9006 (tp) cc_final: 0.8554 (tt)
REVERT: d  113 GLU cc_start: 0.7979 (tp30) cc_final: 0.7628 (tp30)
REVERT: d  116 LYS cc_start: 0.8964 (ttpt) cc_final: 0.8677 (ptpt)
REVERT: g   39 TYR cc_start: 0.8267 (m-80) cc_final: 0.8058 (m-80)
REVERT: g   73 ASN cc_start: 0.8746 (m-40) cc_final: 0.8311 (m110)
REVERT: g   76 THR cc_start: 0.8585 (p) cc_final: 0.8283 (t)
REVERT: g  101 THR cc_start: 0.9006 (m) cc_final: 0.8484 (p)
REVERT: g  111 ILE cc_start: 0.8362 (mt) cc_final: 0.8047 (tt)
REVERT: g  114 VAL cc_start: 0.9140 (m) cc_final: 0.8854 (p)
REVERT: h   46 LYS cc_start: 0.8726 (mmmt) cc_final: 0.8400 (mmmt)
REVERT: h   71 GLU cc_start: 0.8211 (tp30) cc_final: 0.7650 (tp30)
REVERT: e   56 LYS cc_start: 0.8537 (ttpp) cc_final: 0.8168 (tttm)
REVERT: e  120 MET cc_start: 0.8313 (mtm) cc_final: 0.7988 (mtm)
  outliers start: 22
  outliers final: 17
  residues processed: 207
  average time/residue: 0.0969
  time to fit residues: 29.1156
Evaluate side-chains
  194 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 177
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 O residue 1825 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   54 THR
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   58 LEU
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 k residue  936 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:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 113 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9980
   chunk 36 optimal weight:   30.0000
   chunk 2 optimal weight:    9.9990
   chunk 39 optimal weight:    8.9990
   chunk 88 optimal weight:    0.9990
   chunk 115 optimal weight:    0.8980
   chunk 95 optimal weight:    0.6980
   overall best weight:    1.1184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
O1686 HIS
O1780 ASN
** O1813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
d  84 ASN
f  93 GLN
h  63 ASN
k 949 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.074135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.052892 restraints weight = 49152.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.054273 restraints weight = 24166.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.055094 restraints weight = 16121.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.055543 restraints weight = 13118.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.055636 restraints weight = 11816.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.3391

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= 0.161
  Angle     :  0.682  10.945  19972  Z= 0.392
  Chirality :  0.047   0.261   2237
  Planarity :  0.005   0.054   1664
  Dihedral  : 30.091 169.736   3901
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 12.26 %
    Favored  : 84.20 %
  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:  1.00 (0.26), residues: 983
  helix:  1.89 (0.21), residues: 571
  sheet: -1.33 (0.70), residues: 43
  loop : -1.08 (0.30), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG a 131 
 TYR   0.020   0.002   TYR O1825 
 PHE   0.010   0.001   PHE k 948 
 TRP   0.039   0.004   TRP O1699 
 HIS   0.006   0.001   HIS b  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.16 (13992)
  covalent geometry    : angle       0.68244 /  0.39 (19972)
  hydrogen bonds       : bond        0.04322 /  4.91 (  766)
  hydrogen bonds       : angle       3.33093 /  4.51 ( 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
  222 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 192
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1623 LYS cc_start: 0.5026 (pttm) cc_final: 0.4664 (tptm)
REVERT: O 1634 MET cc_start: 0.5278 (ppp) cc_final: 0.4855 (ptt)
REVERT: O 1808 TYR cc_start: 0.6504 (t80) cc_final: 0.6189 (t80)
REVERT: a   82 LEU cc_start: 0.8589 (tp) cc_final: 0.8372 (tp)
REVERT: a   97 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6987 (mt-10)
REVERT: b   59 LYS cc_start: 0.8304 (ttpp) cc_final: 0.8095 (tttm)
REVERT: b   68 ASP cc_start: 0.8171 (m-30) cc_final: 0.7967 (m-30)
REVERT: b   84 MET cc_start: 0.8136 (tpp) cc_final: 0.7830 (tpp)
REVERT: c   41 GLU cc_start: 0.7745 (tp30) cc_final: 0.7464 (tp30)
REVERT: d   83 TYR cc_start: 0.7617 (m-10) cc_final: 0.7065 (m-10)
REVERT: d  101 LEU cc_start: 0.8963 (tp) cc_final: 0.8600 (tt)
REVERT: d  116 LYS cc_start: 0.8950 (ttpt) cc_final: 0.8682 (ptpt)
REVERT: g   39 TYR cc_start: 0.8261 (m-80) cc_final: 0.8017 (m-80)
REVERT: g   73 ASN cc_start: 0.8782 (m-40) cc_final: 0.8320 (m110)
REVERT: g   76 THR cc_start: 0.8574 (p) cc_final: 0.8282 (t)
REVERT: g  101 THR cc_start: 0.8970 (m) cc_final: 0.8445 (p)
REVERT: g  111 ILE cc_start: 0.8392 (mt) cc_final: 0.8091 (tt)
REVERT: g  114 VAL cc_start: 0.9138 (m) cc_final: 0.8855 (p)
REVERT: h   71 GLU cc_start: 0.8218 (tp30) cc_final: 0.7710 (tp30)
REVERT: e   56 LYS cc_start: 0.8525 (ttpp) cc_final: 0.8198 (tttm)
REVERT: e   73 GLU cc_start: 0.8002 (pt0) cc_final: 0.7707 (pt0)
  outliers start: 30
  outliers final: 21
  residues processed: 209
  average time/residue: 0.0971
  time to fit residues: 29.5719
Evaluate side-chains
  197 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 176
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue 1691 VAL
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 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   54 THR
Chi-restraints excluded: chain c residue  104 GLN
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 f residue   66 ILE
Chi-restraints excluded: chain g residue   23 LEU
Chi-restraints excluded: chain h residue   64 SER
Chi-restraints excluded: chain h residue   68 ASP
Chi-restraints excluded: chain k residue  936 GLU
Chi-restraints excluded: chain e residue  117 VAL
Chi-restraints excluded: chain e residue  124 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 40 optimal weight:   10.0000
   chunk 33 optimal weight:    9.9990
   chunk 102 optimal weight:    0.9990
   chunk 55 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 9 optimal weight:   10.0000
   chunk 80 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
O1682 GLN
** O1813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  39 HIS
** f  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
h  47 GLN
h  63 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.073347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.051888 restraints weight = 49676.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.053209 restraints weight = 25387.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.054030 restraints weight = 17318.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.054433 restraints weight = 14149.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.054680 restraints weight = 12863.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.3576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  13992  Z= 0.207
  Angle     :  0.706   7.854  19972  Z= 0.398
  Chirality :  0.047   0.273   2237
  Planarity :  0.005   0.055   1664
  Dihedral  : 30.203 168.805   3901
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 14.27 %
    Favored  : 82.31 %
  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:  0.97 (0.26), residues: 983
  helix:  1.87 (0.21), residues: 570
  sheet: -1.05 (0.69), residues: 38
  loop : -1.12 (0.30), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG b  40 
 TYR   0.022   0.002   TYR O1803 
 PHE   0.017   0.002   PHE c  25 
 TRP   0.020   0.003   TRP O1699 
 HIS   0.006   0.002   HIS O1686 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00411 /  0.21 (13992)
  covalent geometry    : angle       0.70622 /  0.40 (19972)
  hydrogen bonds       : bond        0.04777 /  5.41 (  766)
  hydrogen bonds       : angle       3.43922 /  4.69 ( 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
  202 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 173
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1623 LYS cc_start: 0.5189 (pttm) cc_final: 0.4859 (tptm)
REVERT: O 1634 MET cc_start: 0.5161 (ppp) cc_final: 0.4747 (ptt)
REVERT: O 1764 MET cc_start: 0.6982 (tpp) cc_final: 0.6641 (tpp)
REVERT: O 1808 TYR cc_start: 0.6564 (t80) cc_final: 0.6268 (t80)
REVERT: b   59 LYS cc_start: 0.8411 (ttpp) cc_final: 0.7888 (tttm)
REVERT: c   41 GLU cc_start: 0.7673 (tp30) cc_final: 0.7389 (tp30)
REVERT: d   83 TYR cc_start: 0.7654 (m-10) cc_final: 0.7259 (m-10)
REVERT: d  101 LEU cc_start: 0.9016 (tp) cc_final: 0.8660 (tt)
REVERT: g   39 TYR cc_start: 0.8231 (m-80) cc_final: 0.7982 (m-80)
REVERT: g   73 ASN cc_start: 0.8773 (m-40) cc_final: 0.8334 (m110)
REVERT: g   76 THR cc_start: 0.8575 (p) cc_final: 0.8263 (t)
REVERT: g  101 THR cc_start: 0.8965 (m) cc_final: 0.8444 (p)
REVERT: g  111 ILE cc_start: 0.8529 (mt) cc_final: 0.8268 (tt)
REVERT: g  114 VAL cc_start: 0.9141 (m) cc_final: 0.8822 (p)
REVERT: h   71 GLU cc_start: 0.8182 (tp30) cc_final: 0.7693 (tp30)
REVERT: e   56 LYS cc_start: 0.8620 (ttpp) cc_final: 0.8239 (tttm)
  outliers start: 29
  outliers final: 27
  residues processed: 193
  average time/residue: 0.0926
  time to fit residues: 26.5688
Evaluate side-chains
  190 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 163
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue 1691 VAL
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 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   54 THR
Chi-restraints excluded: chain c residue  104 GLN
Chi-restraints excluded: chain d residue   90 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 g residue   40 SER
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   80 LEU
Chi-restraints excluded: chain k residue  936 GLU
Chi-restraints excluded: chain e residue   71 VAL
Chi-restraints excluded: chain e residue  112 ILE
Chi-restraints excluded: chain e residue  117 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   chunk 83 optimal weight:    0.6980
   chunk 71 optimal weight:    0.7980
   chunk 116 optimal weight:    0.9990
   chunk 37 optimal weight:   20.0000
   chunk 105 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** O1813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  39 HIS
f  25 ASN
h  63 ASN
e  85 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.074153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.052795 restraints weight = 49069.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.054151 restraints weight = 24842.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.054967 restraints weight = 16816.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.055357 restraints weight = 13735.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.055438 restraints weight = 12513.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.3722

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= 0.149
  Angle     :  0.656   9.519  19972  Z= 0.376
  Chirality :  0.045   0.263   2237
  Planarity :  0.004   0.052   1664
  Dihedral  : 30.077 168.608   3901
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.09 %
    Favored  : 81.60 %
  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:  1.20 (0.27), residues: 983
  helix:  2.07 (0.21), residues: 571
  sheet: -0.79 (0.73), residues: 38
  loop : -1.09 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG g  29 
 TYR   0.013   0.001   TYR c  57 
 PHE   0.012   0.001   PHE e  67 
 TRP   0.018   0.002   TRP O1699 
 HIS   0.015   0.002   HIS a  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.15 (13992)
  covalent geometry    : angle       0.65639 /  0.38 (19972)
  hydrogen bonds       : bond        0.04100 /  4.68 (  766)
  hydrogen bonds       : angle       3.25846 /  4.45 ( 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: 28
    poor density    : 176
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1623 LYS cc_start: 0.5228 (pttm) cc_final: 0.4947 (tptm)
REVERT: O 1634 MET cc_start: 0.5172 (ppp) cc_final: 0.4804 (ptp)
REVERT: O 1764 MET cc_start: 0.6953 (tpp) cc_final: 0.6618 (tpp)
REVERT: O 1808 TYR cc_start: 0.6557 (t80) cc_final: 0.6276 (t80)
REVERT: b   68 ASP cc_start: 0.8130 (m-30) cc_final: 0.7926 (m-30)
REVERT: c   41 GLU cc_start: 0.7661 (tp30) cc_final: 0.7361 (tp30)
REVERT: d   83 TYR cc_start: 0.7565 (m-10) cc_final: 0.7123 (m-10)
REVERT: d  101 LEU cc_start: 0.8978 (tp) cc_final: 0.8682 (tt)
REVERT: d  113 GLU cc_start: 0.8024 (tp30) cc_final: 0.7818 (tp30)
REVERT: g   73 ASN cc_start: 0.8763 (m-40) cc_final: 0.8295 (m110)
REVERT: g   76 THR cc_start: 0.8538 (p) cc_final: 0.8227 (t)
REVERT: g  101 THR cc_start: 0.8980 (m) cc_final: 0.8485 (p)
REVERT: g  111 ILE cc_start: 0.8472 (mt) cc_final: 0.8183 (tt)
REVERT: g  114 VAL cc_start: 0.9125 (m) cc_final: 0.8806 (p)
REVERT: h   46 LYS cc_start: 0.8674 (mmmt) cc_final: 0.8407 (mmmt)
REVERT: h   71 GLU cc_start: 0.8159 (tp30) cc_final: 0.7651 (tp30)
REVERT: e   56 LYS cc_start: 0.8571 (ttpp) cc_final: 0.8224 (tttm)
  outliers start: 28
  outliers final: 24
  residues processed: 191
  average time/residue: 0.0954
  time to fit residues: 27.0673
Evaluate side-chains
  188 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 164
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
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 1740 HIS
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   46 VAL
Chi-restraints excluded: chain a residue   70 LEU
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   93 GLU
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 g residue   40 SER
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  112 ILE
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:   10.0000
   chunk 55 optimal weight:    3.9990
   chunk 39 optimal weight:   10.0000
   chunk 102 optimal weight:    4.9990
   chunk 19 optimal weight:    6.9990
   chunk 13 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 117 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 112 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   overall best weight:    1.6984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** O1813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.073590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.052252 restraints weight = 49485.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.053575 restraints weight = 25239.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.054376 restraints weight = 17234.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.054814 restraints weight = 14132.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.055013 restraints weight = 12824.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.3854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  13992  Z= 0.190
  Angle     :  0.683   8.128  19972  Z= 0.387
  Chirality :  0.046   0.273   2237
  Planarity :  0.005   0.059   1664
  Dihedral  : 30.080 167.871   3901
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 14.86 %
    Favored  : 81.60 %
  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:  1.11 (0.27), residues: 983
  helix:  1.99 (0.21), residues: 571
  sheet: -0.83 (0.73), residues: 38
  loop : -1.12 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG O1679 
 TYR   0.023   0.002   TYR a  99 
 PHE   0.020   0.002   PHE O1681 
 TRP   0.040   0.004   TRP O1699 
 HIS   0.006   0.001   HIS b  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00376 /  0.19 (13992)
  covalent geometry    : angle       0.68307 /  0.39 (19972)
  hydrogen bonds       : bond        0.04424 /  5.02 (  766)
  hydrogen bonds       : angle       3.30502 /  4.52 ( 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
  196 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 166
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1623 LYS cc_start: 0.5126 (pttm) cc_final: 0.4888 (tptm)
REVERT: O 1634 MET cc_start: 0.5251 (ppp) cc_final: 0.4731 (ptp)
REVERT: O 1775 GLN cc_start: 0.7797 (mt0) cc_final: 0.7368 (mt0)
REVERT: O 1808 TYR cc_start: 0.6577 (t80) cc_final: 0.6301 (t80)
REVERT: c   41 GLU cc_start: 0.7729 (tp30) cc_final: 0.7398 (tp30)
REVERT: d   83 TYR cc_start: 0.7554 (m-10) cc_final: 0.7069 (m-10)
REVERT: d  101 LEU cc_start: 0.9006 (tp) cc_final: 0.8750 (tt)
REVERT: g   73 ASN cc_start: 0.8771 (m-40) cc_final: 0.8315 (m110)
REVERT: g   76 THR cc_start: 0.8579 (p) cc_final: 0.8257 (t)
REVERT: g  101 THR cc_start: 0.8971 (m) cc_final: 0.8435 (p)
REVERT: g  111 ILE cc_start: 0.8549 (mt) cc_final: 0.8312 (tt)
REVERT: g  114 VAL cc_start: 0.9126 (m) cc_final: 0.8800 (p)
REVERT: h   71 GLU cc_start: 0.8241 (tp30) cc_final: 0.7653 (tp30)
REVERT: e   56 LYS cc_start: 0.8624 (ttpp) cc_final: 0.8286 (tttm)
  outliers start: 30
  outliers final: 28
  residues processed: 184
  average time/residue: 0.0896
  time to fit residues: 24.3805
Evaluate side-chains
  188 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 160
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
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 1711 THR
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 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   70 LEU
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   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   58 LEU
Chi-restraints excluded: chain g residue   23 LEU
Chi-restraints excluded: chain g residue   40 SER
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   71 VAL
Chi-restraints excluded: chain e residue  112 ILE
Chi-restraints excluded: chain e residue  117 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 29 optimal weight:    0.3980
   chunk 85 optimal weight:    0.9980
   chunk 111 optimal weight:    0.7980
   chunk 8 optimal weight:    9.9990
   chunk 55 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 80 optimal weight:    0.3980
   chunk 76 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 10 optimal weight:    9.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** O1813 GLN ** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.074355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.053056 restraints weight = 48910.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.054400 restraints weight = 24819.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.055204 restraints weight = 16924.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.055629 restraints weight = 13869.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.055713 restraints weight = 12613.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.3982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  13992  Z= 0.150
  Angle     :  0.641   8.843  19972  Z= 0.369
  Chirality :  0.044   0.267   2237
  Planarity :  0.004   0.047   1664
  Dihedral  : 29.895 167.457   3901
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 15.57 %
    Favored  : 81.60 %
  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:  1.26 (0.27), residues: 983
  helix:  2.08 (0.22), residues: 572
  sheet: -0.70 (0.73), residues: 38
  loop : -1.01 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG g  29 
 TYR   0.017   0.001   TYR a  99 
 PHE   0.011   0.001   PHE a  67 
 TRP   0.026   0.002   TRP O1699 
 HIS   0.005   0.001   HIS a  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.15 (13992)
  covalent geometry    : angle       0.64137 /  0.37 (19972)
  hydrogen bonds       : bond        0.03891 /  4.46 (  766)
  hydrogen bonds       : angle       3.20735 /  4.41 ( 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
  195 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 171
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
REVERT: O 1634 MET cc_start: 0.5341 (ppp) cc_final: 0.5119 (ppp)
REVERT: O 1764 MET cc_start: 0.6581 (tpp) cc_final: 0.6359 (tpp)
REVERT: O 1775 GLN cc_start: 0.7857 (mt0) cc_final: 0.7439 (mt0)
REVERT: O 1808 TYR cc_start: 0.6565 (t80) cc_final: 0.6286 (t80)
REVERT: c   41 GLU cc_start: 0.7673 (tp30) cc_final: 0.7323 (tp30)
REVERT: d   86 ARG cc_start: 0.7524 (mmp80) cc_final: 0.6965 (mmp80)
REVERT: g   73 ASN cc_start: 0.8777 (m-40) cc_final: 0.8302 (m110)
REVERT: g   76 THR cc_start: 0.8548 (p) cc_final: 0.8234 (t)
REVERT: g  101 THR cc_start: 0.8963 (m) cc_final: 0.8470 (p)
REVERT: g  111 ILE cc_start: 0.8497 (mt) cc_final: 0.8239 (tt)
REVERT: g  114 VAL cc_start: 0.9106 (m) cc_final: 0.8775 (p)
REVERT: h   71 GLU cc_start: 0.8233 (tp30) cc_final: 0.7658 (tp30)
REVERT: e   56 LYS cc_start: 0.8586 (ttpp) cc_final: 0.8237 (tttm)
  outliers start: 24
  outliers final: 23
  residues processed: 188
  average time/residue: 0.0993
  time to fit residues: 27.3226
Evaluate side-chains
  185 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 162
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue 1691 VAL
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 1789 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   70 LEU
Chi-restraints excluded: chain a residue  107 THR
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   58 LEU
Chi-restraints excluded: chain g residue   23 LEU
Chi-restraints excluded: chain g residue   40 SER
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   71 VAL
Chi-restraints excluded: chain e residue  117 VAL
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:    4.9990
   chunk 93 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 9 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 4 optimal weight:    9.9990
   chunk 116 optimal weight:    0.8980
   chunk 89 optimal weight:    0.9990
   chunk 88 optimal weight:    1.9990
   chunk 7 optimal weight:   10.0000
   overall best weight:    1.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
O1782 GLN
** O1813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.074122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.052792 restraints weight = 49501.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.054165 restraints weight = 24612.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.054998 restraints weight = 16574.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.055394 restraints weight = 13464.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.055651 restraints weight = 12239.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.4105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  13992  Z= 0.162
  Angle     :  0.662   9.336  19972  Z= 0.375
  Chirality :  0.044   0.268   2237
  Planarity :  0.004   0.047   1664
  Dihedral  : 29.890 166.999   3901
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 15.68 %
    Favored  : 81.13 %
  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:  1.21 (0.27), residues: 983
  helix:  2.06 (0.22), residues: 572
  sheet: -0.78 (0.72), residues: 38
  loop : -1.05 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG e  42 
 TYR   0.016   0.002   TYR a  99 
 PHE   0.012   0.001   PHE e  67 
 TRP   0.030   0.003   TRP O1699 
 HIS   0.006   0.001   HIS b  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.16 (13992)
  covalent geometry    : angle       0.66220 /  0.38 (19972)
  hydrogen bonds       : bond        0.04060 /  4.61 (  766)
  hydrogen bonds       : angle       3.24649 /  4.47 ( 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
  191 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 164
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
REVERT: O 1714 LEU cc_start: 0.7864 (tp) cc_final: 0.7456 (pp)
REVERT: O 1764 MET cc_start: 0.6631 (tpp) cc_final: 0.6430 (tpp)
REVERT: O 1775 GLN cc_start: 0.7902 (mt0) cc_final: 0.7502 (mt0)
REVERT: O 1808 TYR cc_start: 0.6641 (t80) cc_final: 0.6371 (t80)
REVERT: c   41 GLU cc_start: 0.7759 (tp30) cc_final: 0.7403 (tp30)
REVERT: d   86 ARG cc_start: 0.7463 (mmp80) cc_final: 0.7024 (mmp80)
REVERT: d  105 GLU cc_start: 0.6684 (tp30) cc_final: 0.6457 (tp30)
REVERT: g   73 ASN cc_start: 0.8821 (m-40) cc_final: 0.8351 (m110)
REVERT: g   76 THR cc_start: 0.8572 (p) cc_final: 0.8259 (t)
REVERT: g  101 THR cc_start: 0.8977 (m) cc_final: 0.8443 (p)
REVERT: g  111 ILE cc_start: 0.8524 (mt) cc_final: 0.8256 (tt)
REVERT: g  114 VAL cc_start: 0.9113 (m) cc_final: 0.8781 (p)
REVERT: h   71 GLU cc_start: 0.8277 (tp30) cc_final: 0.7711 (tp30)
REVERT: e   56 LYS cc_start: 0.8722 (ttpp) cc_final: 0.8328 (tttm)
  outliers start: 27
  outliers final: 26
  residues processed: 183
  average time/residue: 0.0864
  time to fit residues: 23.9028
Evaluate side-chains
  186 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 160
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue 1631 ILE
Chi-restraints excluded: chain O residue 1651 ILE
Chi-restraints excluded: chain O residue 1691 VAL
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   70 LEU
Chi-restraints excluded: chain a residue  107 THR
Chi-restraints excluded: chain b residue   54 THR
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   58 LEU
Chi-restraints excluded: chain g residue   23 LEU
Chi-restraints excluded: chain g residue   40 SER
Chi-restraints excluded: chain g residue   49 VAL
Chi-restraints excluded: chain h residue   64 SER
Chi-restraints excluded: chain e residue   71 VAL
Chi-restraints excluded: chain e residue  124 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 99 optimal weight:    0.8980
   chunk 43 optimal weight:    9.9990
   chunk 17 optimal weight:    0.1980
   chunk 50 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 9 optimal weight:   10.0000
   chunk 101 optimal weight:    0.7980
   chunk 1 optimal weight:   10.0000
   overall best weight:    0.9782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** O1813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.074414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.053259 restraints weight = 49205.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.054613 restraints weight = 24894.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.055425 restraints weight = 16881.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.055811 restraints weight = 13775.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.056087 restraints weight = 12562.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.4207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13992  Z= 0.149
  Angle     :  0.646   9.431  19972  Z= 0.367
  Chirality :  0.043   0.266   2237
  Planarity :  0.004   0.047   1664
  Dihedral  : 29.796 166.460   3901
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 15.80 %
    Favored  : 81.49 %
  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:  1.25 (0.27), residues: 983
  helix:  2.08 (0.22), residues: 573
  sheet: -0.70 (0.71), residues: 39
  loop : -1.05 (0.31), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG e  42 
 TYR   0.013   0.001   TYR a  99 
 PHE   0.011   0.001   PHE e  67 
 TRP   0.029   0.003   TRP O1699 
 HIS   0.005   0.001   HIS f  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.15 (13992)
  covalent geometry    : angle       0.64642 /  0.37 (19972)
  hydrogen bonds       : bond        0.03807 /  4.34 (  766)
  hydrogen bonds       : angle       3.17768 /  4.40 ( 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
  191 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 168
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
REVERT: O 1634 MET cc_start: 0.5008 (ppp) cc_final: 0.3995 (ppp)
REVERT: O 1714 LEU cc_start: 0.7906 (tp) cc_final: 0.7454 (pp)
REVERT: O 1752 ILE cc_start: 0.5982 (OUTLIER) cc_final: 0.5641 (tp)
REVERT: O 1775 GLN cc_start: 0.7979 (mt0) cc_final: 0.7562 (mt0)
REVERT: O 1808 TYR cc_start: 0.6595 (t80) cc_final: 0.6328 (t80)
REVERT: c   41 GLU cc_start: 0.7675 (tp30) cc_final: 0.7312 (tp30)
REVERT: d   86 ARG cc_start: 0.7522 (mmp80) cc_final: 0.6948 (mmp80)
REVERT: d  105 GLU cc_start: 0.6746 (tp30) cc_final: 0.6101 (tp30)
REVERT: d  108 LYS cc_start: 0.8358 (ttpt) cc_final: 0.7886 (ttpp)
REVERT: g   76 THR cc_start: 0.8516 (p) cc_final: 0.8202 (t)
REVERT: g  101 THR cc_start: 0.8982 (m) cc_final: 0.8465 (p)
REVERT: g  111 ILE cc_start: 0.8517 (mt) cc_final: 0.8271 (tt)
REVERT: g  114 VAL cc_start: 0.9103 (m) cc_final: 0.8780 (p)
REVERT: h   59 MET cc_start: 0.8462 (tpp) cc_final: 0.8075 (tpp)
REVERT: e   56 LYS cc_start: 0.8664 (ttpp) cc_final: 0.8330 (tttm)
  outliers start: 23
  outliers final: 19
  residues processed: 183
  average time/residue: 0.0940
  time to fit residues: 25.7042
Evaluate side-chains
  181 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 161
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue 1691 VAL
Chi-restraints excluded: chain O residue 1752 ILE
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   70 LEU
Chi-restraints excluded: chain a residue  107 THR
Chi-restraints excluded: chain b residue   54 THR
Chi-restraints excluded: chain c residue   91 GLU
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 g residue   40 SER
Chi-restraints excluded: chain g residue   49 VAL
Chi-restraints excluded: chain h residue   64 SER
Chi-restraints excluded: chain e residue   71 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 8 optimal weight:   10.0000
   chunk 65 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 114 optimal weight:    0.6980
   chunk 85 optimal weight:    0.6980
   chunk 112 optimal weight:    0.9990
   chunk 2 optimal weight:    9.9990
   chunk 69 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
O1686 HIS
** O1813 GLN ** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.074693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.053295 restraints weight = 49035.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.054683 restraints weight = 24536.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.055502 restraints weight = 16538.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.055955 restraints weight = 13485.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.056154 restraints weight = 12210.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.4331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13992  Z= 0.142
  Angle     :  0.635   9.534  19972  Z= 0.362
  Chirality :  0.043   0.265   2237
  Planarity :  0.004   0.047   1664
  Dihedral  : 29.731 166.013   3901
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 16.27 %
    Favored  : 81.13 %
  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:  1.36 (0.27), residues: 983
  helix:  2.17 (0.21), residues: 573
  sheet: -0.67 (0.70), residues: 39
  loop : -0.99 (0.31), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG e  42 
 TYR   0.013   0.001   TYR a  99 
 PHE   0.011   0.001   PHE e  67 
 TRP   0.028   0.002   TRP O1699 
 HIS   0.005   0.001   HIS a  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.14 (13992)
  covalent geometry    : angle       0.63461 /  0.36 (19972)
  hydrogen bonds       : bond        0.03775 /  4.29 (  766)
  hydrogen bonds       : angle       3.15899 /  4.38 ( 1933)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1817.81 seconds
wall clock time: 32 minutes 6.30 seconds (1926.30 seconds total)