Starting phenix.real_space_refine
on Wed Jul 30 10:05:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g6s_29781/07_2025/8g6s_29781.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g6s_29781/07_2025/8g6s_29781.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.47
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g6s_29781/07_2025/8g6s_29781.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g6s_29781/07_2025/8g6s_29781.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g6s_29781/07_2025/8g6s_29781.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g6s_29781/07_2025/8g6s_29781.cif"
  }
  resolution = 3.47
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.011
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     288      5.49       5
     S      13      5.16       5
     C    6944      2.51       5
     N    2330      2.21       5
     O    2905      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12480
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 795
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "D"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 801
          Classifications: {'peptide': 97}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 619
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "G"
      Number of atoms: 809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 809
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 726
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "I"
      Number of atoms: 2952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2952
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2987
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "K"
      Number of atoms: 582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 582
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   LEU K  73 " occ=0.80
      ... (6 atoms not shown)
      pdb=" CD2 LEU K  73 " occ=0.80
  Time building chain proxies: 7.18, per 1000 atoms: 0.58
  Number of scatterers: 12480
  At special positions: 0
  Unit cell: (125.13, 81.48, 132.89, 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      13     16.00
     P     288     15.00
     O    2905      8.00
     N    2330      7.00
     C    6944      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: 2.83
  Conformation dependent library (CDL) restraints added in 891.6 milliseconds
  

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1544

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 11 sheets defined
      69.5% alpha, 4.6% beta
      142 base pairs and 254 stacking pairs defined.
    Time for finding SS restraints: 5.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 64 through 79
      removed outlier: 3.996A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LYS A  79 " --> pdb=" O   ALA A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
      removed outlier: 3.621A  pdb=" N   GLY B  41 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.035A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LYS B  59 " --> pdb=" O   ARG B  55 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   THR B  71 " --> pdb=" O   ARG B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.549A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 22
      removed outlier: 3.583A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 37
    Processing helix  chain 'C' and resid 46 through 73
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.578A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 100 through 121
      removed outlier: 3.597A  pdb=" N   ALA D 121 " --> pdb=" O   LYS D 117 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 45 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.591A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LYS E  79 " --> pdb=" O   ALA E  75 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.538A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.774A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
      removed outlier: 3.606A  pdb=" N   GLY F  41 " --> pdb=" O   LEU F  37 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 77
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.686A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
      removed outlier: 3.677A  pdb=" N   ARG G  20 " --> pdb=" O   THR G  16 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ALA G  21 " --> pdb=" O   ARG G  17 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 26 through 37
      removed outlier: 3.765A  pdb=" N   VAL G  30 " --> pdb=" O   PRO G  26 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.599A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
      removed outlier: 3.658A  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 'H' and resid 34 through 46
      removed outlier: 3.644A  pdb=" N   VAL H  38 " --> pdb=" O   TYR H  34 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 121
      removed outlier: 3.754A  pdb=" N   ALA H 121 " --> pdb=" O   LYS H 117 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 22 through 35
    Processing helix  chain 'K' and resid 37 through 39
      No H-bonds generated for 'chain 'K' and resid 37 through 39'
    Processing helix  chain 'K' and resid 55 through 60
      removed outlier: 3.547A  pdb=" N   TYR K  59 " --> pdb=" O   LEU K  56 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.980A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.891A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.307A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.980A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.760A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.307A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 12 through 16
      removed outlier: 8.767A  pdb=" N   LEU K  67 " --> pdb=" O   GLN K   2 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   PHE K   4 " --> pdb=" O   LEU K  67 " (cutoff:3.500A)
      removed outlier: 7.672A  pdb=" N   LEU K  69 " --> pdb=" O   PHE K   4 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   LYS K   6 " --> pdb=" O   LEU K  69 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   LEU K  71 " --> pdb=" O   LYS K   6 " (cutoff:3.500A)

    412 hydrogen bonds defined for protein.
    1218 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      363 hydrogen bonds
      726 hydrogen bond angles
      0 basepair planarities
      142 basepair parallelities
      254 stacking parallelities
  Total time for adding SS restraints: 4.29

  Time building geometry restraints manager: 3.41 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2894
        1.34 -     1.46: 4157
        1.46 -     1.58: 5637
        1.58 -     1.70: 576
        1.70 -     1.82: 24
  Bond restraints: 13288
  Sorted by residual:
  bond pdb=" N   HIS E 113 "
       pdb=" CA  HIS E 113 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.21e-02 6.83e+03 6.56e+00
  bond pdb=" N   ALA E 114 "
       pdb=" CA  ALA E 114 "
    ideal  model  delta    sigma   weight residual
    1.455  1.484 -0.029 1.25e-02 6.40e+03 5.37e+00
  bond pdb=" N   LYS E 115 "
       pdb=" CA  LYS E 115 "
    ideal  model  delta    sigma   weight residual
    1.462  1.490 -0.028 1.50e-02 4.44e+03 3.61e+00
  bond pdb=" CA  ALA E 114 "
       pdb=" CB  ALA E 114 "
    ideal  model  delta    sigma   weight residual
    1.530  1.506  0.024 1.51e-02 4.39e+03 2.47e+00
  bond pdb=" CE1 HIS E 113 "
       pdb=" NE2 HIS E 113 "
    ideal  model  delta    sigma   weight residual
    1.321  1.336 -0.015 1.00e-02 1.00e+04 2.39e+00
  ... (remaining 13283 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 18759
        1.79 -     3.58: 397
        3.58 -     5.37: 27
        5.37 -     7.17: 6
        7.17 -     8.96: 3
  Bond angle restraints: 19192
  Sorted by residual:
  angle pdb=" CA  GLN F  27 "
        pdb=" CB  GLN F  27 "
        pdb=" CG  GLN F  27 "
      ideal   model   delta    sigma   weight residual
     114.10  120.72   -6.62 2.00e+00 2.50e-01 1.09e+01
  angle pdb=" N   GLY H 101 "
        pdb=" CA  GLY H 101 "
        pdb=" C   GLY H 101 "
      ideal   model   delta    sigma   weight residual
     113.18  120.59   -7.41 2.37e+00 1.78e-01 9.77e+00
  angle pdb=" CA  GLU D  68 "
        pdb=" CB  GLU D  68 "
        pdb=" CG  GLU D  68 "
      ideal   model   delta    sigma   weight residual
     114.10  119.86   -5.76 2.00e+00 2.50e-01 8.29e+00
  angle pdb=" CA  GLU C  64 "
        pdb=" CB  GLU C  64 "
        pdb=" CG  GLU C  64 "
      ideal   model   delta    sigma   weight residual
     114.10  119.73   -5.63 2.00e+00 2.50e-01 7.93e+00
  angle pdb=" CA  HIS E 113 "
        pdb=" C   HIS E 113 "
        pdb=" O   HIS E 113 "
      ideal   model   delta    sigma   weight residual
     120.55  117.63    2.92 1.06e+00 8.90e-01 7.58e+00
  ... (remaining 19187 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.50: 5817
       34.50 -    69.00: 1426
       69.00 -   103.50: 17
      103.50 -   138.00: 3
      138.00 -   172.50: 1
  Dihedral angle restraints: 7264
    sinusoidal: 4874
      harmonic: 2390
  Sorted by residual:
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   47.50  172.50     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DC J  34 "
           pdb=" C3'  DC J  34 "
           pdb=" O3'  DC J  34 "
           pdb=" P    DT J  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   86.15  133.85     1      3.50e+01 8.16e-04 1.33e+01
  dihedral pdb=" C4'  DA J -38 "
           pdb=" C3'  DA J -38 "
           pdb=" O3'  DA J -38 "
           pdb=" P    DG J -37 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   93.09  126.91     1      3.50e+01 8.16e-04 1.25e+01
  ... (remaining 7261 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1455
       0.027 -    0.053: 536
       0.053 -    0.080: 131
       0.080 -    0.107: 48
       0.107 -    0.133: 23
  Chirality restraints: 2193
  Sorted by residual:
  chirality pdb=" CB  ILE D  86 "
            pdb=" CA  ILE D  86 "
            pdb=" CG1 ILE D  86 "
            pdb=" CG2 ILE D  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.13 2.00e-01 2.50e+01 4.44e-01
  chirality pdb=" CA  ILE C 111 "
            pdb=" N   ILE C 111 "
            pdb=" C   ILE C 111 "
            pdb=" CB  ILE C 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.17e-01
  chirality pdb=" CA  ILE G 111 "
            pdb=" N   ILE G 111 "
            pdb=" C   ILE G 111 "
            pdb=" CB  ILE G 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.11e-01
  ... (remaining 2190 not shown)

  Planarity restraints: 1426
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE E 112 "   -0.014 2.00e-02 2.50e+03   2.86e-02 8.18e+00
        pdb=" C   ILE E 112 "    0.049 2.00e-02 2.50e+03
        pdb=" O   ILE E 112 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   HIS E 113 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR H  80 "    0.012 2.00e-02 2.50e+03   1.24e-02 3.08e+00
        pdb=" CG  TYR H  80 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TYR H  80 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 TYR H  80 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR H  80 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR H  80 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR H  80 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR H  80 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  26 "   -0.022 2.00e-02 2.50e+03   9.22e-03 2.55e+00
        pdb=" N9   DG I  26 "    0.021 2.00e-02 2.50e+03
        pdb=" C8   DG I  26 "    0.002 2.00e-02 2.50e+03
        pdb=" N7   DG I  26 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DG I  26 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I  26 "   -0.003 2.00e-02 2.50e+03
        pdb=" O6   DG I  26 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1   DG I  26 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2   DG I  26 "   -0.000 2.00e-02 2.50e+03
        pdb=" N2   DG I  26 "    0.005 2.00e-02 2.50e+03
        pdb=" N3   DG I  26 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DG I  26 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1423 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 449
        2.70 -     3.25: 10994
        3.25 -     3.80: 22410
        3.80 -     4.35: 26841
        4.35 -     4.90: 39404
  Nonbonded interactions: 100098
  Sorted by model distance:
  nonbonded pdb=" N   GLU H 102 "
            pdb=" OE1 GLU H 102 "
     model   vdw
     2.149 3.120
  nonbonded pdb=" O   TYR C  39 "
            pdb=" OG  SER D  75 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" N   GLU G  41 "
            pdb=" OE1 GLU G  41 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" OG1 THR F  82 "
            pdb=" OD2 ASP F  85 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   TYR G  39 "
            pdb=" OG  SER H  75 "
     model   vdw
     2.258 3.040
  ... (remaining 100093 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 134)
  selection = (chain 'E' and resid 39 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 25 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 16 through 118)
}
ncs_group {
  reference = (chain 'D' and resid 29 through 121)
  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=0.80 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.840
  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:          0.470
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     32.090
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
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      :  0.004   0.040  13288  Z= 0.170
  Angle     :  0.593   8.958  19192  Z= 0.352
  Chirality :  0.033   0.133   2193
  Planarity :  0.004   0.034   1426
  Dihedral  : 27.639 172.505   5720
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 24.86 %
    Favored  : 74.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.29 (0.30), residues: 806
  helix:  2.56 (0.23), residues: 532
  sheet:  1.56 (1.03), residues: 26
  loop : -0.91 (0.39), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F  75 
 PHE   0.009   0.001   PHE E  78 
 TYR   0.029   0.001   TYR H  80 
 ARG   0.003   0.000   ARG C  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11320 (  775)
  hydrogen bonds       : angle       4.30020 ( 1944)
  covalent geometry    : bond        0.00358 (13288)
  covalent geometry    : angle       0.59309 (19192)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 130
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8514 (tp30) cc_final: 0.8208 (tp30)
REVERT: C   64 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8043 (tt0)
REVERT: C   99 ARG cc_start: 0.7998 (mmt180) cc_final: 0.7426 (mtp85)
REVERT: D   48 ASP cc_start: 0.9145 (p0) cc_final: 0.8562 (p0)
REVERT: E   42 ARG cc_start: 0.8779 (mmm-85) cc_final: 0.8303 (mtp85)
REVERT: G   95 LYS cc_start: 0.8517 (tptp) cc_final: 0.8116 (ttmm)
REVERT: G   99 ARG cc_start: 0.7820 (mmt-90) cc_final: 0.6968 (mtp85)
REVERT: K    1 MET cc_start: 0.7299 (ppp) cc_final: 0.6868 (ppp)
REVERT: K   48 LYS cc_start: 0.6017 (mmtt) cc_final: 0.5610 (mmtt)
  outliers start: 3
  outliers final: 2
  residues processed: 131
  average time/residue: 0.3109
  time to fit residues: 54.5050
Evaluate side-chains
  120 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 118
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   50 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    7.9990
   chunk 80 optimal weight:    7.9990
   chunk 44 optimal weight:    5.9990
   chunk 27 optimal weight:    0.0670
   chunk 54 optimal weight:    4.9990
   chunk 42 optimal weight:    0.8980
   chunk 83 optimal weight:    8.9990
   chunk 32 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 96 optimal weight:    8.9990
   overall best weight:    2.1922

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
C  38 ASN
E  68 GLN
G  73 ASN
** K  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.096575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.063844 restraints weight = 33544.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.2932 rms_B_bonded: 2.35
r_work: 0.2757 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2760
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2760 r_free = 0.2760    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2760 r_free = 0.2760    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2760
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.1032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  13288  Z= 0.213
  Angle     :  0.595  11.666  19192  Z= 0.353
  Chirality :  0.035   0.136   2193
  Planarity :  0.004   0.035   1426
  Dihedral  : 29.660 173.571   4087
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 23.27 %
    Favored  : 74.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.48 (0.30), residues: 806
  helix:  2.74 (0.22), residues: 540
  sheet:  1.45 (1.05), residues: 26
  loop : -1.03 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS F  75 
 PHE   0.011   0.001   PHE H  62 
 TYR   0.031   0.002   TYR H  80 
 ARG   0.007   0.000   ARG K  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06606 (  775)
  hydrogen bonds       : angle       3.41179 ( 1944)
  covalent geometry    : bond        0.00478 (13288)
  covalent geometry    : angle       0.59531 (19192)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 123
  time to evaluate  : 0.982 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8781 (tp30) cc_final: 0.8529 (tp30)
REVERT: C   64 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8397 (tt0)
REVERT: D   48 ASP cc_start: 0.9037 (p0) cc_final: 0.8363 (p0)
REVERT: E   73 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8688 (tm-30)
REVERT: F   27 GLN cc_start: 0.8864 (tp40) cc_final: 0.8133 (tm-30)
REVERT: F   47 SER cc_start: 0.8784 (OUTLIER) cc_final: 0.8581 (t)
REVERT: G   95 LYS cc_start: 0.8779 (tptp) cc_final: 0.8388 (ttmm)
REVERT: G   99 ARG cc_start: 0.8263 (mmt-90) cc_final: 0.7612 (mtp85)
REVERT: G  102 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8560 (mt)
REVERT: H  117 LYS cc_start: 0.9090 (tptm) cc_final: 0.8675 (ttpt)
REVERT: K   67 LEU cc_start: 0.9294 (tt) cc_final: 0.8589 (mp)
  outliers start: 14
  outliers final: 6
  residues processed: 134
  average time/residue: 0.2708
  time to fit residues: 50.7453
Evaluate side-chains
  120 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   47 SER
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  107 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 87 optimal weight:    7.9990
   chunk 91 optimal weight:    6.9990
   chunk 102 optimal weight:    0.8980
   chunk 68 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 84 optimal weight:   10.0000
   chunk 81 optimal weight:    7.9990
   chunk 15 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  31 GLN ** 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 = 0.3673 r_free = 0.3673 target = 0.097825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.065270 restraints weight = 33925.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 2.37
r_work: 0.2791 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2791
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2791 r_free = 0.2791    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2791 r_free = 0.2791    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2791
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.1290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13288  Z= 0.170
  Angle     :  0.552   9.826  19192  Z= 0.331
  Chirality :  0.033   0.131   2193
  Planarity :  0.004   0.034   1426
  Dihedral  : 29.574 173.886   4085
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 24.86 %
    Favored  : 72.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.76 (0.30), residues: 806
  helix:  2.98 (0.22), residues: 540
  sheet:  1.49 (1.10), residues: 26
  loop : -0.97 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F  75 
 PHE   0.009   0.001   PHE K   4 
 TYR   0.026   0.001   TYR H  80 
 ARG   0.002   0.000   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05559 (  775)
  hydrogen bonds       : angle       3.12513 ( 1944)
  covalent geometry    : bond        0.00368 (13288)
  covalent geometry    : angle       0.55248 (19192)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 1.615 
Fit side-chains
REVERT: A  105 GLU cc_start: 0.8770 (tp30) cc_final: 0.8476 (tp30)
REVERT: B   93 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7635 (mt0)
REVERT: C   64 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8416 (tt0)
REVERT: C   91 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7589 (tm-30)
REVERT: C   92 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8471 (mm-30)
REVERT: D   39 TYR cc_start: 0.8417 (t80) cc_final: 0.8155 (t80)
REVERT: G   95 LYS cc_start: 0.8711 (tptp) cc_final: 0.8333 (ttmm)
REVERT: G   99 ARG cc_start: 0.8265 (mmt-90) cc_final: 0.7624 (mtp85)
  outliers start: 15
  outliers final: 7
  residues processed: 130
  average time/residue: 0.3220
  time to fit residues: 58.4288
Evaluate side-chains
  122 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 114
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue  107 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 39 optimal weight:    4.9990
   chunk 41 optimal weight:    0.6980
   chunk 74 optimal weight:    6.9990
   chunk 57 optimal weight:    7.9990
   chunk 51 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  92 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.096085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.063216 restraints weight = 33538.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.2915 rms_B_bonded: 2.33
r_work: 0.2742 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2740
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2740 r_free = 0.2740    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2740 r_free = 0.2740    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2740
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.1643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  13288  Z= 0.205
  Angle     :  0.579   9.800  19192  Z= 0.345
  Chirality :  0.034   0.134   2193
  Planarity :  0.004   0.036   1426
  Dihedral  : 29.578 176.909   4085
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 24.71 %
    Favored  : 71.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.59 (0.30), residues: 806
  helix:  2.88 (0.22), residues: 539
  sheet:  1.36 (1.06), residues: 26
  loop : -1.12 (0.39), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.011   0.001   PHE H  62 
 TYR   0.032   0.002   TYR H  80 
 ARG   0.005   0.000   ARG K  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06400 (  775)
  hydrogen bonds       : angle       3.21884 ( 1944)
  covalent geometry    : bond        0.00462 (13288)
  covalent geometry    : angle       0.57908 (19192)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 1.016 
Fit side-chains
REVERT: A  105 GLU cc_start: 0.8738 (tp30) cc_final: 0.8435 (tp30)
REVERT: B   93 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7804 (mt0)
REVERT: C   64 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8418 (tt0)
REVERT: D   29 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8494 (p)
REVERT: D   39 TYR cc_start: 0.8493 (t80) cc_final: 0.8225 (t80)
REVERT: G   95 LYS cc_start: 0.8791 (tptp) cc_final: 0.8409 (ttmm)
REVERT: G   99 ARG cc_start: 0.8255 (mmt-90) cc_final: 0.7589 (mtp85)
  outliers start: 24
  outliers final: 12
  residues processed: 131
  average time/residue: 0.3448
  time to fit residues: 62.4497
Evaluate side-chains
  128 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 1.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain E residue   90 MET
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain K residue    4 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 86 optimal weight:   10.0000
   chunk 85 optimal weight:   10.0000
   chunk 41 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0970
   chunk 25 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 HIS
H  92 GLN
K  31 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.099226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.067298 restraints weight = 33705.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.2999 rms_B_bonded: 2.36
r_work: 0.2831 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2831
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2831 r_free = 0.2831    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2831 r_free = 0.2831    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2831
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.1735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  13288  Z= 0.151
  Angle     :  0.546   9.584  19192  Z= 0.325
  Chirality :  0.033   0.178   2193
  Planarity :  0.004   0.038   1426
  Dihedral  : 29.512 178.414   4085
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 26.30 %
    Favored  : 71.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.97 (0.31), residues: 806
  helix:  3.13 (0.22), residues: 545
  sheet:  1.25 (1.04), residues: 26
  loop : -0.92 (0.40), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS F  75 
 PHE   0.008   0.001   PHE E  78 
 TYR   0.017   0.001   TYR H  80 
 ARG   0.005   0.000   ARG K  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04674 (  775)
  hydrogen bonds       : angle       2.89049 ( 1944)
  covalent geometry    : bond        0.00316 (13288)
  covalent geometry    : angle       0.54630 (19192)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8686 (tp30) cc_final: 0.8413 (tp30)
REVERT: B   93 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7414 (mt0)
REVERT: C   64 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8402 (tt0)
REVERT: C   91 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7578 (tm-30)
REVERT: C   92 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8550 (mm-30)
REVERT: D   39 TYR cc_start: 0.8370 (t80) cc_final: 0.8131 (t80)
REVERT: E   73 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8443 (tt0)
REVERT: F   47 SER cc_start: 0.8590 (t) cc_final: 0.8327 (t)
REVERT: G   95 LYS cc_start: 0.8669 (tptp) cc_final: 0.8289 (ttmm)
REVERT: G   99 ARG cc_start: 0.8264 (mmt-90) cc_final: 0.7627 (mtp85)
REVERT: K   67 LEU cc_start: 0.9262 (tt) cc_final: 0.8696 (mp)
  outliers start: 16
  outliers final: 8
  residues processed: 141
  average time/residue: 0.3650
  time to fit residues: 71.7459
Evaluate side-chains
  128 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 119
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue  107 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 97 optimal weight:    8.9990
   chunk 14 optimal weight:    4.9990
   chunk 54 optimal weight:    5.9990
   chunk 84 optimal weight:   10.0000
   chunk 55 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 62 optimal weight:    6.9990
   chunk 40 optimal weight:    4.9990
   overall best weight:    1.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 ASN
H  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.096912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.064279 restraints weight = 34313.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.2931 rms_B_bonded: 2.37
r_work: 0.2760 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2759
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2759 r_free = 0.2759    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2759 r_free = 0.2759    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2759
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.1895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13288  Z= 0.195
  Angle     :  0.572   8.444  19192  Z= 0.340
  Chirality :  0.034   0.133   2193
  Planarity :  0.004   0.037   1426
  Dihedral  : 29.536 178.252   4085
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 25.14 %
    Favored  : 71.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.73 (0.30), residues: 806
  helix:  2.98 (0.22), residues: 543
  sheet:  1.09 (1.04), residues: 26
  loop : -1.06 (0.40), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS F  75 
 PHE   0.010   0.001   PHE H  62 
 TYR   0.035   0.002   TYR F  88 
 ARG   0.009   0.000   ARG K  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05892 (  775)
  hydrogen bonds       : angle       3.07105 ( 1944)
  covalent geometry    : bond        0.00436 (13288)
  covalent geometry    : angle       0.57157 (19192)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 1.311 
Fit side-chains
REVERT: A  105 GLU cc_start: 0.8717 (tp30) cc_final: 0.8447 (tp30)
REVERT: B   84 MET cc_start: 0.8615 (tpp) cc_final: 0.7910 (mmm)
REVERT: B   93 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7765 (mt0)
REVERT: C   42 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7907 (mtm180)
REVERT: C   64 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8459 (tt0)
REVERT: C   77 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8167 (mtm-85)
REVERT: D   29 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8487 (p)
REVERT: D   39 TYR cc_start: 0.8496 (t80) cc_final: 0.8225 (t80)
REVERT: E   73 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8462 (tt0)
REVERT: G   95 LYS cc_start: 0.8779 (tptp) cc_final: 0.8383 (ttmm)
REVERT: G   99 ARG cc_start: 0.8249 (mmt-90) cc_final: 0.7604 (mtp85)
REVERT: G  113 SER cc_start: 0.9343 (m) cc_final: 0.9088 (p)
REVERT: K    1 MET cc_start: 0.7261 (ppp) cc_final: 0.6825 (ppp)
  outliers start: 21
  outliers final: 13
  residues processed: 133
  average time/residue: 0.4256
  time to fit residues: 79.3632
Evaluate side-chains
  131 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 1.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  107 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 97 optimal weight:    8.9990
   chunk 99 optimal weight:    0.6980
   chunk 4 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 19 optimal weight:    0.1980
   chunk 11 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  92 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.099021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.067010 restraints weight = 33927.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 2.37
r_work: 0.2817 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2819
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2819 r_free = 0.2819    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2819 r_free = 0.2819    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2819
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.1965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  13288  Z= 0.152
  Angle     :  0.547   8.229  19192  Z= 0.326
  Chirality :  0.032   0.128   2193
  Planarity :  0.004   0.041   1426
  Dihedral  : 29.481 178.666   4085
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 25.29 %
    Favored  : 71.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.94 (0.31), residues: 806
  helix:  3.14 (0.22), residues: 543
  sheet:  1.00 (1.05), residues: 26
  loop : -0.96 (0.40), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS F  75 
 PHE   0.009   0.001   PHE K   4 
 TYR   0.022   0.001   TYR F  88 
 ARG   0.005   0.000   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04801 (  775)
  hydrogen bonds       : angle       2.87527 ( 1944)
  covalent geometry    : bond        0.00319 (13288)
  covalent geometry    : angle       0.54669 (19192)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 1.435 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8687 (tp30) cc_final: 0.8432 (tp30)
REVERT: B   93 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7502 (mt0)
REVERT: C   42 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7893 (mtm180)
REVERT: C   64 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8421 (tt0)
REVERT: C   91 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7615 (tm-30)
REVERT: C   92 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8598 (mm-30)
REVERT: D   29 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8464 (p)
REVERT: D   39 TYR cc_start: 0.8420 (t80) cc_final: 0.8179 (t80)
REVERT: E   73 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8334 (tt0)
REVERT: G   95 LYS cc_start: 0.8687 (tptp) cc_final: 0.8260 (ttmm)
REVERT: G   99 ARG cc_start: 0.8266 (mmt-90) cc_final: 0.7617 (mtp85)
REVERT: G  113 SER cc_start: 0.9258 (m) cc_final: 0.8985 (p)
REVERT: H   79 HIS cc_start: 0.7244 (OUTLIER) cc_final: 0.6587 (t-90)
  outliers start: 21
  outliers final: 13
  residues processed: 137
  average time/residue: 0.2726
  time to fit residues: 52.1958
Evaluate side-chains
  135 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue   79 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 85 optimal weight:   10.0000
   chunk 17 optimal weight:    5.9990
   chunk 47 optimal weight:    0.8980
   chunk 96 optimal weight:    7.9990
   chunk 50 optimal weight:    0.9980
   chunk 71 optimal weight:   10.0000
   chunk 60 optimal weight:    6.9990
   chunk 10 optimal weight:    0.5980
   chunk 100 optimal weight:    9.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    1.4782

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  92 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.097708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.065285 restraints weight = 34047.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.2951 rms_B_bonded: 2.36
r_work: 0.2781 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2783
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2783 r_free = 0.2783    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2783 r_free = 0.2783    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2783
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13288  Z= 0.175
  Angle     :  0.565   9.799  19192  Z= 0.335
  Chirality :  0.033   0.128   2193
  Planarity :  0.004   0.037   1426
  Dihedral  : 29.482 177.368   4085
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 25.58 %
    Favored  : 71.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.85 (0.31), residues: 806
  helix:  3.05 (0.22), residues: 543
  sheet:  1.03 (1.06), residues: 26
  loop : -0.96 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS F  75 
 PHE   0.009   0.001   PHE H  62 
 TYR   0.027   0.001   TYR H  80 
 ARG   0.004   0.000   ARG A 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05494 (  775)
  hydrogen bonds       : angle       2.98691 ( 1944)
  covalent geometry    : bond        0.00383 (13288)
  covalent geometry    : angle       0.56489 (19192)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.963 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8696 (tp30) cc_final: 0.8424 (tp30)
REVERT: C   42 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7897 (mtm180)
REVERT: C   64 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8477 (tt0)
REVERT: C   77 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8190 (mtm-85)
REVERT: C   91 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7606 (tm-30)
REVERT: C   92 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8574 (mm-30)
REVERT: D   29 THR cc_start: 0.8868 (OUTLIER) cc_final: 0.8502 (p)
REVERT: D   39 TYR cc_start: 0.8474 (t80) cc_final: 0.8215 (t80)
REVERT: E   73 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8437 (tt0)
REVERT: G   95 LYS cc_start: 0.8671 (tptp) cc_final: 0.8268 (ttmm)
REVERT: G   99 ARG cc_start: 0.8286 (mmt-90) cc_final: 0.7625 (mtp85)
REVERT: G  113 SER cc_start: 0.9199 (m) cc_final: 0.8931 (p)
REVERT: H   79 HIS cc_start: 0.7368 (OUTLIER) cc_final: 0.6693 (t-90)
REVERT: K    1 MET cc_start: 0.7091 (ppp) cc_final: 0.6620 (ppp)
  outliers start: 17
  outliers final: 10
  residues processed: 132
  average time/residue: 0.2881
  time to fit residues: 52.1053
Evaluate side-chains
  130 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain H residue   79 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 72 optimal weight:   10.0000
   chunk 33 optimal weight:    0.8980
   chunk 92 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 95 optimal weight:    7.9990
   chunk 71 optimal weight:   10.0000
   chunk 102 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  92 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.099441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.067519 restraints weight = 34051.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 2.37
r_work: 0.2834 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2833
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2833 r_free = 0.2833    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2833 r_free = 0.2833    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2833
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13288  Z= 0.151
  Angle     :  0.543   7.332  19192  Z= 0.323
  Chirality :  0.032   0.128   2193
  Planarity :  0.004   0.040   1426
  Dihedral  : 29.434 178.148   4085
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 25.58 %
    Favored  : 72.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.02 (0.31), residues: 806
  helix:  3.17 (0.22), residues: 545
  sheet:  0.76 (1.03), residues: 26
  loop : -0.84 (0.41), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.001   HIS F  75 
 PHE   0.010   0.001   PHE K   4 
 TYR   0.018   0.001   TYR H  80 
 ARG   0.004   0.000   ARG A 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04623 (  775)
  hydrogen bonds       : angle       2.83039 ( 1944)
  covalent geometry    : bond        0.00320 (13288)
  covalent geometry    : angle       0.54296 (19192)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8651 (tp30) cc_final: 0.8398 (tp30)
REVERT: B   79 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8283 (mttp)
REVERT: C   42 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7885 (mtm180)
REVERT: C   64 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8426 (tt0)
REVERT: C   92 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8568 (mm-30)
REVERT: D   29 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8476 (p)
REVERT: D   39 TYR cc_start: 0.8415 (t80) cc_final: 0.8188 (t80)
REVERT: E   73 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8389 (tt0)
REVERT: G   95 LYS cc_start: 0.8635 (tptp) cc_final: 0.8216 (ttmm)
REVERT: G   99 ARG cc_start: 0.8275 (mmt-90) cc_final: 0.7624 (mtp85)
REVERT: G  113 SER cc_start: 0.9099 (m) cc_final: 0.8843 (p)
REVERT: H   79 HIS cc_start: 0.7160 (OUTLIER) cc_final: 0.6523 (t-90)
REVERT: K    1 MET cc_start: 0.6834 (ppp) cc_final: 0.6352 (ppp)
  outliers start: 16
  outliers final: 12
  residues processed: 132
  average time/residue: 0.2790
  time to fit residues: 52.0638
Evaluate side-chains
  136 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain H residue   79 HIS
Chi-restraints excluded: chain K residue   50 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 84 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9980
   chunk 53 optimal weight:    0.2980
   chunk 88 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9980
   chunk 80 optimal weight:    8.9990
   chunk 13 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   chunk 100 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 105 optimal weight:    8.9990
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  76 GLN
H  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.098515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.066277 restraints weight = 33911.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.2976 rms_B_bonded: 2.37
r_work: 0.2807 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2805
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2805 r_free = 0.2805    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2805 r_free = 0.2805    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2805
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13288  Z= 0.164
  Angle     :  0.556   8.734  19192  Z= 0.330
  Chirality :  0.033   0.129   2193
  Planarity :  0.004   0.037   1426
  Dihedral  : 29.438 177.174   4085
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 26.01 %
    Favored  : 71.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.93 (0.31), residues: 806
  helix:  3.11 (0.22), residues: 543
  sheet:  0.71 (1.02), residues: 26
  loop : -0.88 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS F  75 
 PHE   0.009   0.001   PHE K   4 
 TYR   0.023   0.001   TYR H  80 
 ARG   0.003   0.000   ARG A 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05083 (  775)
  hydrogen bonds       : angle       2.89648 ( 1944)
  covalent geometry    : bond        0.00358 (13288)
  covalent geometry    : angle       0.55609 (19192)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 1.651 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8696 (tp30) cc_final: 0.8437 (tp30)
REVERT: B   79 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8301 (mttp)
REVERT: C   42 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7878 (mtm180)
REVERT: C   64 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8459 (tt0)
REVERT: D   29 THR cc_start: 0.8867 (OUTLIER) cc_final: 0.8500 (p)
REVERT: D   39 TYR cc_start: 0.8444 (t80) cc_final: 0.8194 (t80)
REVERT: E   73 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8525 (tt0)
REVERT: G   95 LYS cc_start: 0.8617 (tptp) cc_final: 0.8196 (ttmm)
REVERT: G   99 ARG cc_start: 0.8305 (mmt-90) cc_final: 0.7638 (mtp85)
REVERT: G  113 SER cc_start: 0.9094 (m) cc_final: 0.8842 (p)
REVERT: H   79 HIS cc_start: 0.7259 (OUTLIER) cc_final: 0.6617 (t-90)
REVERT: K    1 MET cc_start: 0.6894 (ppp) cc_final: 0.6388 (ppp)
  outliers start: 16
  outliers final: 12
  residues processed: 128
  average time/residue: 0.2900
  time to fit residues: 51.4130
Evaluate side-chains
  131 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain H residue   79 HIS
Chi-restraints excluded: chain K residue   50 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 99 optimal weight:    0.5980
   chunk 105 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 88 optimal weight:    6.9990
   chunk 70 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 10 optimal weight:    0.3980
   chunk 74 optimal weight:    7.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  92 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.100103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.068356 restraints weight = 34223.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3023 rms_B_bonded: 2.38
r_work: 0.2856 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2855
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2855
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.2355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13288  Z= 0.148
  Angle     :  0.546   9.532  19192  Z= 0.324
  Chirality :  0.032   0.126   2193
  Planarity :  0.004   0.039   1426
  Dihedral  : 29.394 177.871   4085
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 25.87 %
    Favored  : 71.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.05 (0.31), residues: 806
  helix:  3.19 (0.22), residues: 545
  sheet:  0.70 (1.01), residues: 26
  loop : -0.80 (0.41), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS F  75 
 PHE   0.010   0.001   PHE K   4 
 TYR   0.045   0.001   TYR F  88 
 ARG   0.003   0.000   ARG A 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04386 (  775)
  hydrogen bonds       : angle       2.79456 ( 1944)
  covalent geometry    : bond        0.00314 (13288)
  covalent geometry    : angle       0.54570 (19192)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 6763.11 seconds
wall clock time: 122 minutes 56.47 seconds (7376.47 seconds total)