Starting phenix.real_space_refine
on Wed May 14 20:57:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g6s_29781/05_2025/8g6s_29781.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g6s_29781/05_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_29781/05_2025/8g6s_29781.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g6s_29781/05_2025/8g6s_29781.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g6s_29781/05_2025/8g6s_29781.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g6s_29781/05_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-5687/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: 7.31, per 1000 atoms: 0.59
  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: 3.02
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 6.02
  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: 4.84

  Time building geometry restraints manager: 3.57 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:             1.090
  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:          0.500
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     33.480
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.040
  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:2.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.200
-------------------------------------------------------------------------------
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  : 1.014 
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: 0.3110
  time to fit residues: 54.6689
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  : 0.869 
-------------------------------------------------------------------------------
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 = 0.096653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.063954 restraints weight = 33545.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.2933 rms_B_bonded: 2.34
r_work: 0.2757 rms_B_bonded: 4.09 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:          0.1028

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  11.665  19192  Z= 0.352
  Chirality :  0.035   0.136   2193
  Planarity :  0.004   0.035   1426
  Dihedral  : 29.660 173.572   4087
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 6.98
  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   0.006   0.000   ARG K  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06604 (  775)
  hydrogen bonds       : angle       3.41188 ( 1944)
  covalent geometry    : bond        0.00478 (13288)
  covalent geometry    : angle       0.59474 (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  : 0.870 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8782 (tp30) cc_final: 0.8531 (tp30)
REVERT: C   64 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8397 (tt0)
REVERT: D   48 ASP cc_start: 0.9036 (p0) cc_final: 0.8362 (p0)
REVERT: E   73 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8697 (tm-30)
REVERT: F   27 GLN cc_start: 0.8863 (tp40) cc_final: 0.8135 (tm-30)
REVERT: F   47 SER cc_start: 0.8783 (OUTLIER) cc_final: 0.8581 (t)
REVERT: G   95 LYS cc_start: 0.8778 (tptp) cc_final: 0.8388 (ttmm)
REVERT: G   99 ARG cc_start: 0.8260 (mmt-90) cc_final: 0.7611 (mtp85)
REVERT: G  102 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8561 (mt)
REVERT: H  117 LYS cc_start: 0.9092 (tptm) cc_final: 0.8678 (ttpt)
REVERT: K   67 LEU cc_start: 0.9290 (tt) cc_final: 0.8578 (mp)
  outliers start: 14
  outliers final: 6
  residues processed: 134
  average time/residue: 0.2678
  time to fit residues: 49.8996
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  : 1.082 
-------------------------------------------------------------------------------
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:    0.0570
   chunk 68 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 84 optimal weight:   10.0000
   chunk 81 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.7102

-------------------------------------------------------------------------------
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 = 0.3695 r_free = 0.3695 target = 0.099217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.067130 restraints weight = 33927.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.2998 rms_B_bonded: 2.38
r_work: 0.2827 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2829
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2829 r_free = 0.2829    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2829 r_free = 0.2829    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2829
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.1223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13288  Z= 0.152
  Angle     :  0.540   9.221  19192  Z= 0.324
  Chirality :  0.033   0.127   2193
  Planarity :  0.004   0.034   1426
  Dihedral  : 29.553 173.668   4085
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 25.00 %
    Favored  : 73.55 %
  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:  2.91 (0.30), residues: 806
  helix:  3.06 (0.22), residues: 541
  sheet:  1.46 (1.09), residues: 26
  loop : -0.84 (0.40), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS H  79 
 PHE   0.010   0.001   PHE K   4 
 TYR   0.020   0.001   TYR H  80 
 ARG   0.004   0.000   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05011 (  775)
  hydrogen bonds       : angle       3.03815 ( 1944)
  covalent geometry    : bond        0.00317 (13288)
  covalent geometry    : angle       0.53999 (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
  138 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 128
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8746 (tp30) cc_final: 0.8452 (tp30)
REVERT: B   93 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7512 (mt0)
REVERT: C   64 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8383 (tt0)
REVERT: C   91 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7555 (tm-30)
REVERT: C   92 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8418 (mm-30)
REVERT: E   73 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8636 (tm-30)
REVERT: F   47 SER cc_start: 0.8648 (t) cc_final: 0.8393 (t)
REVERT: G   95 LYS cc_start: 0.8643 (tptp) cc_final: 0.8290 (ttmm)
REVERT: G   99 ARG cc_start: 0.8240 (mmt-90) cc_final: 0.7602 (mtp85)
REVERT: K   67 LEU cc_start: 0.9286 (tt) cc_final: 0.8612 (mp)
  outliers start: 10
  outliers final: 7
  residues processed: 135
  average time/residue: 0.2716
  time to fit residues: 50.7241
Evaluate side-chains
  130 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 122
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 74 optimal weight:    7.9990
   chunk 57 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 42 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
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 = 0.3653 r_free = 0.3653 target = 0.096588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.063846 restraints weight = 33675.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.2930 rms_B_bonded: 2.33
r_work: 0.2757 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2758
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2758 r_free = 0.2758    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2758 r_free = 0.2758    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2758
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.1536

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= 0.198
  Angle     :  0.573   9.535  19192  Z= 0.342
  Chirality :  0.034   0.137   2193
  Planarity :  0.004   0.034   1426
  Dihedral  : 29.548 176.404   4085
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 25.14 %
    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:  2.71 (0.30), residues: 806
  helix:  2.97 (0.22), residues: 538
  sheet:  1.46 (1.10), residues: 26
  loop : -1.06 (0.39), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F  75 
 PHE   0.011   0.001   PHE H  62 
 TYR   0.028   0.002   TYR H  80 
 ARG   0.005   0.000   ARG K  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06203 (  775)
  hydrogen bonds       : angle       3.17467 ( 1944)
  covalent geometry    : bond        0.00444 (13288)
  covalent geometry    : angle       0.57326 (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
  136 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.886 
Fit side-chains
REVERT: A  105 GLU cc_start: 0.8724 (tp30) cc_final: 0.8427 (tp30)
REVERT: B   93 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7781 (mt0)
REVERT: C   64 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8456 (tt0)
REVERT: D   29 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8481 (p)
REVERT: D   39 TYR cc_start: 0.8499 (t80) cc_final: 0.8230 (t80)
REVERT: G   95 LYS cc_start: 0.8810 (tptp) cc_final: 0.8406 (ttmm)
REVERT: G   99 ARG cc_start: 0.8249 (mmt-90) cc_final: 0.7599 (mtp85)
  outliers start: 22
  outliers final: 11
  residues processed: 130
  average time/residue: 0.2580
  time to fit residues: 46.9337
Evaluate side-chains
  124 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
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 D residue   29 THR
Chi-restraints excluded: chain E residue   57 SER
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 H residue   68 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 86 optimal weight:   10.0000
   chunk 85 optimal weight:   10.0000
   chunk 41 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
H  92 GLN
K  31 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.099130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.067037 restraints weight = 33767.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.2996 rms_B_bonded: 2.36
r_work: 0.2827 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2824
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2824
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.1656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13288  Z= 0.152
  Angle     :  0.541   8.072  19192  Z= 0.323
  Chirality :  0.033   0.179   2193
  Planarity :  0.004   0.036   1426
  Dihedral  : 29.507 177.636   4085
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 25.58 %
    Favored  : 71.53 %
  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:  2.98 (0.31), residues: 806
  helix:  3.11 (0.22), residues: 545
  sheet:  1.31 (1.05), residues: 26
  loop : -0.88 (0.40), residues: 235

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   0.021   0.001   TYR H  80 
 ARG   0.008   0.000   ARG K  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04833 (  775)
  hydrogen bonds       : angle       2.90861 ( 1944)
  covalent geometry    : bond        0.00320 (13288)
  covalent geometry    : angle       0.54057 (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
  147 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8708 (tp30) cc_final: 0.8433 (tp30)
REVERT: B   93 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7506 (mt0)
REVERT: C   64 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8412 (tt0)
REVERT: C   91 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7577 (tm-30)
REVERT: C   92 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8530 (mm-30)
REVERT: D   39 TYR cc_start: 0.8387 (t80) cc_final: 0.8143 (t80)
REVERT: E   73 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8447 (tt0)
REVERT: F   47 SER cc_start: 0.8594 (t) cc_final: 0.8348 (t)
REVERT: G   95 LYS cc_start: 0.8679 (tptp) cc_final: 0.8307 (ttmm)
REVERT: G   99 ARG cc_start: 0.8284 (mmt-90) cc_final: 0.7632 (mtp85)
  outliers start: 20
  outliers final: 11
  residues processed: 141
  average time/residue: 0.2775
  time to fit residues: 54.2013
Evaluate side-chains
  130 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 118
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
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 E residue   57 SER
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
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:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 84 optimal weight:   10.0000
   chunk 55 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 58 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0030
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.7390

-------------------------------------------------------------------------------
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 ** 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 = 0.3703 r_free = 0.3703 target = 0.099795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.067641 restraints weight = 34157.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 2.39
r_work: 0.2843 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2843
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2843 r_free = 0.2843    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 = 0.2843 r_free = 0.2843    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2843
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.1868

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= 0.150
  Angle     :  0.544  10.504  19192  Z= 0.324
  Chirality :  0.032   0.127   2193
  Planarity :  0.004   0.036   1426
  Dihedral  : 29.479 178.279   4085
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 25.43 %
    Favored  : 71.97 %
  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:  2.96 (0.30), residues: 806
  helix:  3.14 (0.22), residues: 543
  sheet:  1.15 (1.02), residues: 26
  loop : -0.93 (0.40), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS F  75 
 PHE   0.007   0.001   PHE K   4 
 TYR   0.020   0.001   TYR H  80 
 ARG   0.008   0.000   ARG K  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04652 (  775)
  hydrogen bonds       : angle       2.83103 ( 1944)
  covalent geometry    : bond        0.00316 (13288)
  covalent geometry    : angle       0.54363 (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
  142 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 124
  time to evaluate  : 1.008 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8656 (tp30) cc_final: 0.8426 (tp30)
REVERT: B   84 MET cc_start: 0.8454 (tpp) cc_final: 0.7687 (mmm)
REVERT: B   93 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7505 (mt0)
REVERT: C   64 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8428 (tt0)
REVERT: D   29 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8444 (p)
REVERT: D   39 TYR cc_start: 0.8376 (t80) cc_final: 0.8127 (t80)
REVERT: E   73 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8398 (tt0)
REVERT: G   95 LYS cc_start: 0.8612 (tptp) cc_final: 0.8249 (ttmm)
REVERT: G   99 ARG cc_start: 0.8305 (mmt-90) cc_final: 0.7652 (mtp85)
REVERT: G  113 SER cc_start: 0.9291 (m) cc_final: 0.9010 (p)
REVERT: H   79 HIS cc_start: 0.7328 (OUTLIER) cc_final: 0.6681 (t-90)
REVERT: K    1 MET cc_start: 0.6887 (ppp) cc_final: 0.6448 (ppp)
  outliers start: 18
  outliers final: 11
  residues processed: 138
  average time/residue: 0.2695
  time to fit residues: 51.7910
Evaluate side-chains
  133 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
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 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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 75 optimal weight:    8.9990
   chunk 97 optimal weight:    8.9990
   chunk 99 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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
E  76 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.098510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.066389 restraints weight = 34022.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 2.36
r_work: 0.2811 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2807
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2807 r_free = 0.2807    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2807 r_free = 0.2807    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2807
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.1951

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= 0.167
  Angle     :  0.552   7.526  19192  Z= 0.328
  Chirality :  0.033   0.129   2193
  Planarity :  0.004   0.038   1426
  Dihedral  : 29.460 177.761   4085
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 25.58 %
    Favored  : 71.82 %
  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:  2.88 (0.30), residues: 806
  helix:  3.09 (0.22), residues: 543
  sheet:  1.11 (1.04), residues: 26
  loop : -0.99 (0.40), 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   0.006   0.000   ARG K  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05181 (  775)
  hydrogen bonds       : angle       2.93621 ( 1944)
  covalent geometry    : bond        0.00364 (13288)
  covalent geometry    : angle       0.55151 (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
  131 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8699 (tp30) cc_final: 0.8447 (tp30)
REVERT: B   84 MET cc_start: 0.8538 (tpp) cc_final: 0.7734 (mmm)
REVERT: B   93 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7591 (mt0)
REVERT: C   42 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7827 (mtm180)
REVERT: C   64 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8447 (tt0)
REVERT: C   91 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7634 (tm-30)
REVERT: C   92 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8619 (mm-30)
REVERT: D   29 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8436 (p)
REVERT: D   39 TYR cc_start: 0.8429 (t80) cc_final: 0.8175 (t80)
REVERT: E   73 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8467 (tt0)
REVERT: G   95 LYS cc_start: 0.8643 (tptp) cc_final: 0.8215 (ttmm)
REVERT: G   99 ARG cc_start: 0.8302 (mmt-90) cc_final: 0.7637 (mtp85)
REVERT: G  113 SER cc_start: 0.9313 (m) cc_final: 0.9058 (p)
  outliers start: 18
  outliers final: 14
  residues processed: 126
  average time/residue: 0.2695
  time to fit residues: 47.1389
Evaluate side-chains
  128 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
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   95 LYS
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain E residue   57 SER
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   64 GLU
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  107 VAL
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:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 96 optimal weight:    7.9990
   chunk 50 optimal weight:    0.9980
   chunk 71 optimal weight:   10.0000
   chunk 60 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 100 optimal weight:   10.0000
   chunk 55 optimal weight:    0.7980
   overall best weight:    1.7584

-------------------------------------------------------------------------------
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 = 0.3659 r_free = 0.3659 target = 0.097062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.064540 restraints weight = 34093.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 2.36
r_work: 0.2766 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2769
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2769 r_free = 0.2769    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2769 r_free = 0.2769    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2769
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13288  Z= 0.188
  Angle     :  0.579  10.660  19192  Z= 0.342
  Chirality :  0.033   0.125   2193
  Planarity :  0.004   0.049   1426
  Dihedral  : 29.482 177.259   4085
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 24.86 %
    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:  2.81 (0.30), residues: 806
  helix:  3.02 (0.22), residues: 542
  sheet:  1.06 (1.05), residues: 26
  loop : -0.95 (0.40), residues: 238

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   0.028   0.001   TYR H  80 
 ARG   0.006   0.000   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05828 (  775)
  hydrogen bonds       : angle       3.04901 ( 1944)
  covalent geometry    : bond        0.00417 (13288)
  covalent geometry    : angle       0.57910 (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
  137 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 0.910 
Fit side-chains
REVERT: A  105 GLU cc_start: 0.8711 (tp30) cc_final: 0.8432 (tp30)
REVERT: B   93 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7722 (mt0)
REVERT: C   42 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7824 (mtm180)
REVERT: C   64 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8478 (tt0)
REVERT: C   77 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8172 (mtm-85)
REVERT: C   92 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8546 (mm-30)
REVERT: D   29 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8507 (p)
REVERT: D   39 TYR cc_start: 0.8497 (t80) cc_final: 0.8237 (t80)
REVERT: E   73 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8448 (tt0)
REVERT: G   95 LYS cc_start: 0.8693 (tptp) cc_final: 0.8283 (ttmm)
REVERT: G   99 ARG cc_start: 0.8314 (mmt-90) cc_final: 0.7637 (mtp85)
REVERT: G  113 SER cc_start: 0.9192 (m) cc_final: 0.8925 (p)
REVERT: H   79 HIS cc_start: 0.7412 (OUTLIER) cc_final: 0.6774 (t-90)
REVERT: K    1 MET cc_start: 0.7074 (ppp) cc_final: 0.6629 (ppp)
  outliers start: 22
  outliers final: 15
  residues processed: 131
  average time/residue: 0.3108
  time to fit residues: 56.2836
Evaluate side-chains
  132 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 1.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
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 C residue   95 LYS
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain E residue   57 SER
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   64 GLU
Chi-restraints excluded: chain G residue  102 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:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 72 optimal weight:   10.0000
   chunk 33 optimal weight:    2.9990
   chunk 92 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9980
   chunk 95 optimal weight:    7.9990
   chunk 71 optimal weight:   10.0000
   chunk 102 optimal weight:    0.0770
   chunk 10 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   overall best weight:    1.1942

-------------------------------------------------------------------------------
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 = 0.3682 r_free = 0.3682 target = 0.098435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.066219 restraints weight = 33875.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 2.35
r_work: 0.2809 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2806
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2806 r_free = 0.2806    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2806 r_free = 0.2806    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2806
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.2156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  13288  Z= 0.163
  Angle     :  0.554   7.859  19192  Z= 0.329
  Chirality :  0.032   0.126   2193
  Planarity :  0.004   0.039   1426
  Dihedral  : 29.448 178.030   4085
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 25.14 %
    Favored  : 72.25 %
  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:  0.98 (1.04), residues: 26
  loop : -0.89 (0.41), 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   0.018   0.001   TYR H  80 
 ARG   0.002   0.000   ARG K  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05034 (  775)
  hydrogen bonds       : angle       2.91183 ( 1944)
  covalent geometry    : bond        0.00353 (13288)
  covalent geometry    : angle       0.55416 (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
  134 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8687 (tp30) cc_final: 0.8436 (tp30)
REVERT: B   93 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7553 (mt0)
REVERT: C   42 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7828 (mtm180)
REVERT: C   64 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8443 (tt0)
REVERT: C   77 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8228 (mtm-85)
REVERT: D   29 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8507 (p)
REVERT: D   39 TYR cc_start: 0.8454 (t80) cc_final: 0.8213 (t80)
REVERT: E   73 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8437 (tt0)
REVERT: G   95 LYS cc_start: 0.8635 (tptp) cc_final: 0.8195 (ttmm)
REVERT: G   99 ARG cc_start: 0.8308 (mmt-90) cc_final: 0.7640 (mtp85)
REVERT: G  113 SER cc_start: 0.9120 (m) cc_final: 0.8851 (p)
REVERT: H   79 HIS cc_start: 0.7334 (OUTLIER) cc_final: 0.6665 (t-90)
REVERT: K    1 MET cc_start: 0.7115 (ppp) cc_final: 0.6648 (ppp)
  outliers start: 18
  outliers final: 13
  residues processed: 130
  average time/residue: 0.3034
  time to fit residues: 54.2364
Evaluate side-chains
  130 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 1.397 
-------------------------------------------------------------------------------
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 E residue   57 SER
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   64 GLU
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain H residue   79 HIS
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:    0.9990
   chunk 53 optimal weight:    0.1980
   chunk 88 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9990
   chunk 80 optimal weight:    8.9990
   chunk 13 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9990
   chunk 60 optimal weight:    4.9990
   chunk 105 optimal weight:    7.9990
   overall best weight:    0.7784

-------------------------------------------------------------------------------
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 = 0.3696 r_free = 0.3696 target = 0.099213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.067258 restraints weight = 33890.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.2999 rms_B_bonded: 2.34
r_work: 0.2832 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2832
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2832 r_free = 0.2832    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 = 0.2832 r_free = 0.2832    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2832
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.2236

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= 0.152
  Angle     :  0.552   8.258  19192  Z= 0.327
  Chirality :  0.032   0.125   2193
  Planarity :  0.004   0.038   1426
  Dihedral  : 29.431 177.818   4085
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 25.72 %
    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:  3.01 (0.31), residues: 806
  helix:  3.16 (0.22), residues: 543
  sheet:  0.92 (1.01), residues: 26
  loop : -0.82 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS F  75 
 PHE   0.010   0.001   PHE K   4 
 TYR   0.022   0.001   TYR H  80 
 ARG   0.006   0.000   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04696 (  775)
  hydrogen bonds       : angle       2.84158 ( 1944)
  covalent geometry    : bond        0.00323 (13288)
  covalent geometry    : angle       0.55188 (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
  131 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8653 (tp30) cc_final: 0.8418 (tp30)
REVERT: C   64 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8428 (tt0)
REVERT: D   29 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8511 (p)
REVERT: D   39 TYR cc_start: 0.8424 (t80) cc_final: 0.8204 (t80)
REVERT: E   73 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8536 (tt0)
REVERT: G   95 LYS cc_start: 0.8629 (tptp) cc_final: 0.8214 (ttmm)
REVERT: G   99 ARG cc_start: 0.8289 (mmt-90) cc_final: 0.7618 (mtp85)
REVERT: G  113 SER cc_start: 0.9053 (m) cc_final: 0.8784 (p)
REVERT: H   79 HIS cc_start: 0.7229 (OUTLIER) cc_final: 0.6621 (t-90)
REVERT: K    1 MET cc_start: 0.6798 (ppp) cc_final: 0.6276 (ppp)
  outliers start: 15
  outliers final: 12
  residues processed: 128
  average time/residue: 0.2653
  time to fit residues: 47.5594
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  : 0.853 
-------------------------------------------------------------------------------
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 D residue   29 THR
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain E residue   57 SER
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 99 optimal weight:    7.9990
   chunk 105 optimal weight:    7.9990
   chunk 40 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 88 optimal weight:    6.9990
   chunk 70 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 43 optimal weight:    0.8980
   chunk 10 optimal weight:    0.3980
   chunk 74 optimal weight:    7.9990
   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 = 0.3706 r_free = 0.3706 target = 0.100015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.068291 restraints weight = 34216.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3021 rms_B_bonded: 2.37
r_work: 0.2855 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2853
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    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 = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2853
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.2348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13288  Z= 0.149
  Angle     :  0.548   9.749  19192  Z= 0.325
  Chirality :  0.032   0.124   2193
  Planarity :  0.004   0.037   1426
  Dihedral  : 29.396 177.575   4085
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 26.01 %
    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:  3.07 (0.31), residues: 806
  helix:  3.19 (0.22), residues: 545
  sheet:  0.89 (1.00), residues: 26
  loop : -0.77 (0.41), residues: 235

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   0.015   0.001   TYR H  80 
 ARG   0.002   0.000   ARG K  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04474 (  775)
  hydrogen bonds       : angle       2.80543 ( 1944)
  covalent geometry    : bond        0.00317 (13288)
  covalent geometry    : angle       0.54843 (19192)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 5527.62 seconds
wall clock time: 96 minutes 15.88 seconds (5775.88 seconds total)