Starting phenix.real_space_refine
on Sat Aug 23 13:05:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g6s_29781/08_2025/8g6s_29781.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g6s_29781/08_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_29781/08_2025/8g6s_29781.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g6s_29781/08_2025/8g6s_29781.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g6s_29781/08_2025/8g6s_29781.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g6s_29781/08_2025/8g6s_29781.cif"
  }
  resolution = 3.47
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.32, per 1000 atoms: 0.27
  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: 0.94
  Conformation dependent library (CDL) restraints added in 338.2 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  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: 2.25
  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: 2.61

  Time building geometry restraints manager: 1.32 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:             1.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     15.240
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.970
-------------------------------------------------------------------------------
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 : 8.57
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.29 (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
 ARG   0.003   0.000   ARG C  71 
 TYR   0.029   0.001   TYR H  80 
 PHE   0.009   0.001   PHE E  78 
 HIS   0.005   0.001   HIS F  75 

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

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

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 130
  time to evaluate  : 0.325 
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: 0.1538
  time to fit residues: 26.9793
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  : 0.347 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.0970
   chunk 97 optimal weight:    8.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3698 r_free = 0.3698 target = 0.099230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.067224 restraints weight = 34002.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 2.38
r_work: 0.2836 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2838
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2838 r_free = 0.2838    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2839 r_free = 0.2839    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2839
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.0951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13288  Z= 0.159
  Angle     :  0.557  10.544  19192  Z= 0.332
  Chirality :  0.033   0.134   2193
  Planarity :  0.004   0.035   1426
  Dihedral  : 29.600 173.304   4087
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 23.41 %
    Favored  : 75.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.72 (0.30), residues: 806
  helix:  2.87 (0.22), residues: 542
  sheet:  1.50 (1.06), residues: 26
  loop : -0.81 (0.39), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  96 
 TYR   0.024   0.001   TYR H  80 
 PHE   0.010   0.001   PHE K   4 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (13288)
  covalent geometry    : angle       0.55689 (19192)
  hydrogen bonds       : bond        0.05372 (  775)
  hydrogen bonds       : angle       3.14562 ( 1944)

*********************** 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
  142 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 133
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8748 (tp30) cc_final: 0.8474 (tp30)
REVERT: B   93 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7532 (mt0)
REVERT: C   64 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8373 (tt0)
REVERT: D   48 ASP cc_start: 0.9037 (p0) cc_final: 0.8483 (p0)
REVERT: E   73 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8697 (tm-30)
REVERT: F   27 GLN cc_start: 0.8796 (tp40) cc_final: 0.8207 (tm-30)
REVERT: G   95 LYS cc_start: 0.8615 (tptp) cc_final: 0.8227 (ttmm)
REVERT: G   99 ARG cc_start: 0.8238 (mmt-90) cc_final: 0.7602 (mtp85)
REVERT: G  102 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8468 (mt)
REVERT: H  117 LYS cc_start: 0.9039 (tptm) cc_final: 0.8601 (ttpt)
REVERT: K   48 LYS cc_start: 0.5864 (mmtt) cc_final: 0.5410 (mmtt)
  outliers start: 9
  outliers final: 4
  residues processed: 139
  average time/residue: 0.1331
  time to fit residues: 25.6490
Evaluate side-chains
  126 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 120
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
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 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 6 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   chunk 60 optimal weight:    0.0170
   chunk 89 optimal weight:    7.9990
   chunk 52 optimal weight:    0.0050
   chunk 98 optimal weight:   10.0000
   chunk 96 optimal weight:    7.9990
   chunk 33 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.4834

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

Flipped N/Q/H residues before XYZ refinement:
F  25 ASN
** K  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.100867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.069593 restraints weight = 34468.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 2.40
r_work: 0.2882 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2884
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2884
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13288  Z= 0.145
  Angle     :  0.523   8.149  19192  Z= 0.315
  Chirality :  0.032   0.130   2193
  Planarity :  0.004   0.034   1426
  Dihedral  : 29.477 173.656   4085
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 24.13 %
    Favored  : 74.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.03 (0.30), residues: 806
  helix:  3.12 (0.22), residues: 542
  sheet:  1.46 (1.09), residues: 26
  loop : -0.72 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G  71 
 TYR   0.014   0.001   TYR H  80 
 PHE   0.009   0.001   PHE K   4 
 HIS   0.004   0.001   HIS H  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (13288)
  covalent geometry    : angle       0.52349 (19192)
  hydrogen bonds       : bond        0.04507 (  775)
  hydrogen bonds       : angle       2.92673 ( 1944)

*********************** 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
  137 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8677 (tp30) cc_final: 0.8442 (tp30)
REVERT: B   93 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7415 (mt0)
REVERT: C   64 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8408 (tt0)
REVERT: D   97 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8836 (mp)
REVERT: E   73 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8630 (tt0)
REVERT: F   25 ASN cc_start: 0.8075 (OUTLIER) cc_final: 0.7464 (m-40)
REVERT: F   47 SER cc_start: 0.8494 (OUTLIER) cc_final: 0.8229 (t)
REVERT: G   95 LYS cc_start: 0.8551 (tptp) cc_final: 0.8200 (ttmm)
REVERT: G   99 ARG cc_start: 0.8314 (mmt-90) cc_final: 0.7685 (mtp85)
REVERT: H  117 LYS cc_start: 0.9038 (tptm) cc_final: 0.8590 (ttpt)
  outliers start: 12
  outliers final: 6
  residues processed: 134
  average time/residue: 0.1348
  time to fit residues: 25.3634
Evaluate side-chains
  130 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
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 D residue   97 LEU
Chi-restraints excluded: chain F residue   25 ASN
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  107 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 31 optimal weight:    0.5980
   chunk 21 optimal weight:    0.3980
   chunk 53 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 90 optimal weight:    8.9990
   chunk 89 optimal weight:    6.9990
   chunk 24 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
K  31 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.100092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.068241 restraints weight = 34100.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3023 rms_B_bonded: 2.38
r_work: 0.2856 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2854
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2854 r_free = 0.2854    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2854 r_free = 0.2854    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2854
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.1475

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= 0.154
  Angle     :  0.534   7.603  19192  Z= 0.320
  Chirality :  0.032   0.129   2193
  Planarity :  0.004   0.034   1426
  Dihedral  : 29.446 175.761   4085
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 24.28 %
    Favored  : 73.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.12 (0.30), residues: 806
  helix:  3.20 (0.22), residues: 543
  sheet:  1.42 (1.09), residues: 26
  loop : -0.73 (0.40), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K  54 
 TYR   0.016   0.001   TYR H  80 
 PHE   0.007   0.001   PHE K   4 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (13288)
  covalent geometry    : angle       0.53394 (19192)
  hydrogen bonds       : bond        0.04791 (  775)
  hydrogen bonds       : angle       2.90892 ( 1944)

*********************** 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
  138 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8665 (tp30) cc_final: 0.8428 (tp30)
REVERT: C   64 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8383 (tt0)
REVERT: C   91 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7475 (tm-30)
REVERT: C   92 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8408 (mm-30)
REVERT: D   39 TYR cc_start: 0.8320 (t80) cc_final: 0.8042 (t80)
REVERT: D   97 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8817 (mp)
REVERT: G   95 LYS cc_start: 0.8602 (tptp) cc_final: 0.8253 (ttmm)
REVERT: G   99 ARG cc_start: 0.8268 (mmt-90) cc_final: 0.7608 (mtp85)
  outliers start: 16
  outliers final: 9
  residues processed: 134
  average time/residue: 0.1194
  time to fit residues: 22.5732
Evaluate side-chains
  128 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
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   97 LEU
Chi-restraints excluded: chain D residue   97 LEU
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  107 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   chunk 91 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 74 optimal weight:    7.9990
   chunk 103 optimal weight:   20.0000
   chunk 17 optimal weight:    4.9990
   chunk 89 optimal weight:    7.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
B  75 HIS
C  38 ASN
E  76 GLN
H  92 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.096986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.064265 restraints weight = 33957.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.2937 rms_B_bonded: 2.35
r_work: 0.2763 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2763
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2763 r_free = 0.2763    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2763 r_free = 0.2763    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2763
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start:          0.1696

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= 0.198
  Angle     :  0.578   9.177  19192  Z= 0.343
  Chirality :  0.034   0.161   2193
  Planarity :  0.004   0.035   1426
  Dihedral  : 29.503 178.701   4085
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 24.13 %
    Favored  : 72.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.75 (0.30), residues: 806
  helix:  2.92 (0.22), residues: 544
  sheet:  1.41 (1.04), residues: 26
  loop : -0.92 (0.40), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG G  29 
 TYR   0.027   0.002   TYR H  80 
 PHE   0.011   0.001   PHE H  62 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 (13288)
  covalent geometry    : angle       0.57756 (19192)
  hydrogen bonds       : bond        0.06244 (  775)
  hydrogen bonds       : angle       3.11628 ( 1944)

*********************** 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
  140 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 117
  time to evaluate  : 0.427 
Fit side-chains
REVERT: A  105 GLU cc_start: 0.8706 (tp30) cc_final: 0.8446 (tp30)
REVERT: C   64 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8510 (tt0)
REVERT: D   29 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8486 (p)
REVERT: D   39 TYR cc_start: 0.8526 (t80) cc_final: 0.8259 (t80)
REVERT: D   97 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8882 (mp)
REVERT: F   25 ASN cc_start: 0.8281 (m-40) cc_final: 0.7965 (m-40)
REVERT: G   95 LYS cc_start: 0.8782 (tptp) cc_final: 0.8389 (ttmm)
REVERT: G   99 ARG cc_start: 0.8325 (mmt-90) cc_final: 0.7672 (mtp85)
REVERT: K    1 MET cc_start: 0.7053 (ppp) cc_final: 0.6561 (ppp)
  outliers start: 23
  outliers final: 12
  residues processed: 134
  average time/residue: 0.1405
  time to fit residues: 26.0377
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  : 0.352 
-------------------------------------------------------------------------------
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   97 LEU
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue   90 MET
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   64 GLU
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 56 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9990
   chunk 87 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 3 optimal weight:    0.7980
   chunk 4 optimal weight:    5.9990
   chunk 64 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.9584

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.098613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.066293 restraints weight = 33732.841|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 2.36
r_work: 0.2804 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2807
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2807 r_free = 0.2807    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2807 r_free = 0.2807    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2807
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.1781

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= 0.157
  Angle     :  0.546   8.409  19192  Z= 0.326
  Chirality :  0.032   0.128   2193
  Planarity :  0.004   0.035   1426
  Dihedral  : 29.485 179.761   4085
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 24.57 %
    Favored  : 72.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.94 (0.30), residues: 806
  helix:  3.08 (0.22), residues: 543
  sheet:  1.32 (1.04), residues: 26
  loop : -0.84 (0.40), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K  54 
 TYR   0.017   0.001   TYR H  80 
 PHE   0.009   0.001   PHE K   4 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (13288)
  covalent geometry    : angle       0.54572 (19192)
  hydrogen bonds       : bond        0.05200 (  775)
  hydrogen bonds       : angle       2.92936 ( 1944)

*********************** 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
  137 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8682 (tp30) cc_final: 0.8431 (tp30)
REVERT: B   84 MET cc_start: 0.8475 (tpp) cc_final: 0.7787 (mmm)
REVERT: C   64 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8451 (tt0)
REVERT: C   91 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7567 (tm-30)
REVERT: C   92 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8517 (mm-30)
REVERT: D   39 TYR cc_start: 0.8424 (t80) cc_final: 0.8186 (t80)
REVERT: D   97 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8817 (mp)
REVERT: F   25 ASN cc_start: 0.8211 (m-40) cc_final: 0.7914 (m-40)
REVERT: G   95 LYS cc_start: 0.8691 (tptp) cc_final: 0.8315 (ttmm)
REVERT: G   99 ARG cc_start: 0.8290 (mmt-90) cc_final: 0.7640 (mtp85)
  outliers start: 17
  outliers final: 13
  residues processed: 133
  average time/residue: 0.1345
  time to fit residues: 24.8106
Evaluate side-chains
  130 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain D residue   97 LEU
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 G residue  114 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 102 optimal weight:    0.5980
   chunk 72 optimal weight:   10.0000
   chunk 43 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    6.9990
   chunk 64 optimal weight:    5.9990
   chunk 71 optimal weight:   10.0000
   chunk 19 optimal weight:    6.9990
   chunk 69 optimal weight:    0.7980
   chunk 28 optimal weight:    0.1980
   chunk 13 optimal weight:    0.9980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
H  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.098676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.066543 restraints weight = 34174.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.2977 rms_B_bonded: 2.38
r_work: 0.2807 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2811
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2811 r_free = 0.2811    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2811 r_free = 0.2811    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2811
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.1900

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= 0.160
  Angle     :  0.551   7.837  19192  Z= 0.328
  Chirality :  0.033   0.130   2193
  Planarity :  0.004   0.037   1426
  Dihedral  : 29.468 178.080   4085
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 24.57 %
    Favored  : 72.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.95 (0.30), residues: 806
  helix:  3.10 (0.22), residues: 543
  sheet:  1.18 (1.03), residues: 26
  loop : -0.84 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG K  54 
 TYR   0.015   0.001   TYR H  80 
 PHE   0.010   0.001   PHE K   4 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (13288)
  covalent geometry    : angle       0.55121 (19192)
  hydrogen bonds       : bond        0.05085 (  775)
  hydrogen bonds       : angle       2.89690 ( 1944)

*********************** 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
  138 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 0.331 
Fit side-chains
REVERT: A  105 GLU cc_start: 0.8673 (tp30) cc_final: 0.8427 (tp30)
REVERT: B   84 MET cc_start: 0.8554 (tpp) cc_final: 0.7815 (mmm)
REVERT: C   64 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8452 (tt0)
REVERT: D   29 THR cc_start: 0.8830 (OUTLIER) cc_final: 0.8465 (p)
REVERT: D   39 TYR cc_start: 0.8451 (t80) cc_final: 0.8211 (t80)
REVERT: D   97 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8826 (mp)
REVERT: F   25 ASN cc_start: 0.8219 (m-40) cc_final: 0.7976 (m110)
REVERT: G   95 LYS cc_start: 0.8668 (tptp) cc_final: 0.8238 (ttmm)
REVERT: G   99 ARG cc_start: 0.8305 (mmt-90) cc_final: 0.7666 (mtp85)
REVERT: H   79 HIS cc_start: 0.7337 (OUTLIER) cc_final: 0.6640 (t-90)
REVERT: K    1 MET cc_start: 0.6929 (ppp) cc_final: 0.6459 (ppp)
  outliers start: 21
  outliers final: 15
  residues processed: 133
  average time/residue: 0.1316
  time to fit residues: 24.4252
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  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain D residue   97 LEU
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 G residue  114 VAL
Chi-restraints excluded: chain H residue   79 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 102 optimal weight:    0.0270
   chunk 78 optimal weight:    6.9990
   chunk 67 optimal weight:    0.0770
   chunk 11 optimal weight:    3.9990
   chunk 97 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.8000

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

Flipped N/Q/H residues before XYZ refinement:
H  92 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.099584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.067713 restraints weight = 34168.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 2.38
r_work: 0.2838 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2836
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2836 r_free = 0.2836    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 = 0.2836 r_free = 0.2836    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2836
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.2028

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     :  0.544   7.242  19192  Z= 0.324
  Chirality :  0.032   0.128   2193
  Planarity :  0.004   0.036   1426
  Dihedral  : 29.433 178.128   4085
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 25.00 %
    Favored  : 72.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.06 (0.31), residues: 806
  helix:  3.18 (0.22), residues: 545
  sheet:  1.12 (1.03), residues: 26
  loop : -0.80 (0.41), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K  54 
 TYR   0.010   0.001   TYR H  80 
 PHE   0.009   0.001   PHE K   4 
 HIS   0.007   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (13288)
  covalent geometry    : angle       0.54397 (19192)
  hydrogen bonds       : bond        0.04671 (  775)
  hydrogen bonds       : angle       2.82294 ( 1944)

*********************** 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
  140 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 121
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A  105 GLU cc_start: 0.8629 (tp30) cc_final: 0.8415 (tp30)
REVERT: C   64 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8442 (tt0)
REVERT: D   29 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8470 (p)
REVERT: D   39 TYR cc_start: 0.8417 (t80) cc_final: 0.8185 (t80)
REVERT: D   97 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8810 (mp)
REVERT: F   25 ASN cc_start: 0.8230 (m-40) cc_final: 0.8006 (m110)
REVERT: G   95 LYS cc_start: 0.8622 (tptp) cc_final: 0.8220 (ttmm)
REVERT: G   99 ARG cc_start: 0.8279 (mmt-90) cc_final: 0.7657 (mtp85)
REVERT: K    1 MET cc_start: 0.6765 (ppp) cc_final: 0.6207 (ppp)
  outliers start: 19
  outliers final: 15
  residues processed: 134
  average time/residue: 0.1312
  time to fit residues: 24.7258
Evaluate side-chains
  135 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   43 VAL
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 96 optimal weight:    8.9990
   chunk 34 optimal weight:    0.4980
   chunk 43 optimal weight:    2.9990
   chunk 91 optimal weight:    6.9990
   chunk 24 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 83 optimal weight:   10.0000
   chunk 30 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
H  92 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.099262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.067255 restraints weight = 34071.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 2.36
r_work: 0.2829 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2826
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2826 r_free = 0.2826    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2826 r_free = 0.2826    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2826
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.2121

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= 0.160
  Angle     :  0.565  11.576  19192  Z= 0.333
  Chirality :  0.032   0.128   2193
  Planarity :  0.004   0.035   1426
  Dihedral  : 29.422 177.471   4085
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.01 (0.30), residues: 806
  helix:  3.15 (0.22), residues: 543
  sheet:  1.20 (1.03), residues: 26
  loop : -0.83 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  83 
 TYR   0.015   0.001   TYR H  80 
 PHE   0.009   0.001   PHE K   4 
 HIS   0.007   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (13288)
  covalent geometry    : angle       0.56477 (19192)
  hydrogen bonds       : bond        0.04893 (  775)
  hydrogen bonds       : angle       2.83892 ( 1944)

*********************** 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  : 0.220 
Fit side-chains
REVERT: A  105 GLU cc_start: 0.8658 (tp30) cc_final: 0.8417 (tp30)
REVERT: C   64 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8473 (tt0)
REVERT: D   29 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8481 (p)
REVERT: D   39 TYR cc_start: 0.8446 (t80) cc_final: 0.8209 (t80)
REVERT: D   97 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8827 (mp)
REVERT: F   25 ASN cc_start: 0.8270 (m-40) cc_final: 0.8048 (m110)
REVERT: G   95 LYS cc_start: 0.8620 (tptp) cc_final: 0.8221 (ttmm)
REVERT: G   99 ARG cc_start: 0.8285 (mmt-90) cc_final: 0.7631 (mtp85)
REVERT: H   79 HIS cc_start: 0.7237 (OUTLIER) cc_final: 0.6611 (t-90)
  outliers start: 18
  outliers final: 15
  residues processed: 129
  average time/residue: 0.1275
  time to fit residues: 23.0164
Evaluate side-chains
  133 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain D residue   97 LEU
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 G residue  114 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 19 optimal weight:    7.9990
   chunk 83 optimal weight:   10.0000
   chunk 60 optimal weight:    5.9990
   chunk 101 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 69 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 90 optimal weight:    8.9990
   chunk 9 optimal weight:    0.0470
   overall best weight:    0.7480

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

Flipped N/Q/H residues before XYZ refinement:
H  92 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.100236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.068267 restraints weight = 34175.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 2.39
r_work: 0.2859 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2858
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2858 r_free = 0.2858    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2858 r_free = 0.2858    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2858
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  13288  Z= 0.151
  Angle     :  0.555  12.342  19192  Z= 0.327
  Chirality :  0.032   0.125   2193
  Planarity :  0.004   0.037   1426
  Dihedral  : 29.383 177.780   4085
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 25.43 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.14 (0.31), residues: 806
  helix:  3.22 (0.22), residues: 545
  sheet:  1.18 (1.03), residues: 26
  loop : -0.71 (0.41), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K  54 
 TYR   0.012   0.001   TYR H  80 
 PHE   0.011   0.001   PHE K   4 
 HIS   0.007   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (13288)
  covalent geometry    : angle       0.55517 (19192)
  hydrogen bonds       : bond        0.04439 (  775)
  hydrogen bonds       : angle       2.78455 ( 1944)

********************** 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
  136 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A  105 GLU cc_start: 0.8630 (tp30) cc_final: 0.8401 (tp30)
REVERT: C   64 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8434 (tt0)
REVERT: D   29 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8459 (p)
REVERT: D   39 TYR cc_start: 0.8390 (t80) cc_final: 0.8176 (t80)
REVERT: D   97 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8797 (mp)
REVERT: G   95 LYS cc_start: 0.8513 (tptp) cc_final: 0.8106 (ttmm)
REVERT: G   99 ARG cc_start: 0.8277 (mmt-90) cc_final: 0.7623 (mtp85)
REVERT: H   79 HIS cc_start: 0.7107 (OUTLIER) cc_final: 0.6501 (t-90)
REVERT: H  117 LYS cc_start: 0.9080 (tptm) cc_final: 0.8609 (ttpt)
REVERT: K    1 MET cc_start: 0.6783 (ppp) cc_final: 0.6367 (ppp)
  outliers start: 16
  outliers final: 13
  residues processed: 131
  average time/residue: 0.1170
  time to fit residues: 21.5704
Evaluate side-chains
  135 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 119
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
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 D residue   97 LEU
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 G residue  114 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 89 optimal weight:    8.9990
   chunk 56 optimal weight:    0.6980
   chunk 59 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 72 optimal weight:   10.0000
   chunk 92 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 52 optimal weight:    0.4980
   chunk 81 optimal weight:    6.9990
   overall best weight:    1.8386

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

Flipped N/Q/H residues before XYZ refinement:
E  76 GLN
H  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.097680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.065204 restraints weight = 34018.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.2954 rms_B_bonded: 2.37
r_work: 0.2784 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2782
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2782 r_free = 0.2782    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2782 r_free = 0.2782    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2782
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8556
moved from start:          0.2257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  13288  Z= 0.191
  Angle     :  0.585  12.342  19192  Z= 0.344
  Chirality :  0.033   0.133   2193
  Planarity :  0.004   0.035   1426
  Dihedral  : 29.428 176.767   4085
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.95 (0.30), residues: 806
  helix:  3.11 (0.22), residues: 541
  sheet:  1.18 (1.01), residues: 26
  loop : -0.85 (0.40), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K  54 
 TYR   0.019   0.001   TYR H  80 
 PHE   0.010   0.001   PHE H  62 
 HIS   0.007   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 (13288)
  covalent geometry    : angle       0.58518 (19192)
  hydrogen bonds       : bond        0.05640 (  775)
  hydrogen bonds       : angle       2.99072 ( 1944)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2697.23 seconds
wall clock time: 46 minutes 56.80 seconds (2816.80 seconds total)