Starting phenix.real_space_refine
on Sat Oct 11 02:12:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8whb_37538/10_2025/8whb_37538.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8whb_37538/10_2025/8whb_37538.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8whb_37538/10_2025/8whb_37538.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8whb_37538/10_2025/8whb_37538.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8whb_37538/10_2025/8whb_37538.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8whb_37538/10_2025/8whb_37538.cif"
  }
  resolution = 3.17
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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     268      5.49       5
     S      12      5.16       5
     C    6211      2.51       5
     N    2067      2.21       5
     O    2618      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11176
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 733
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 733
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 2, 'TRANS': 88}
    Chain: "B"
      Number of atoms: 636
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 636
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "C"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 783
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "D"
      Number of atoms: 694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 694
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 3, 'TRANS': 85}
    Chain: "E"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 799
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 621
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 621
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 1, 'TRANS': 75}
    Chain: "G"
      Number of atoms: 700
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 700
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 4, 'TRANS': 88}
    Chain: "H"
      Number of atoms: 716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 716
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 3, 'TRANS': 88}
    Chain: "I"
      Number of atoms: 2729
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 134, 2729
          Classifications: {'DNA': 134}
          Link IDs: {'rna3p': 133}
    Chain: "J"
      Number of atoms: 2765
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 134, 2765
          Classifications: {'DNA': 134}
          Link IDs: {'rna3p': 133}
  Time building chain proxies: 2.56, per 1000 atoms: 0.23
  Number of scatterers: 11176
  At special positions: 0
  Unit cell: (118.845, 101.745, 127.395, 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      12     16.00
     P     268     15.00
     O    2618      8.00
     N    2067      7.00
     C    6211      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: 0.89
  Conformation dependent library (CDL) restraints added in 279.0 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1352

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 10 sheets defined
      74.4% alpha, 3.3% beta
      86 base pairs and 224 stacking pairs defined.
    Time for finding SS restraints: 1.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.668A  pdb=" N   LEU A  48 " --> pdb=" O   GLY A  44 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ARG A  49 " --> pdb=" O   THR A  45 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   GLN A  55 " --> pdb=" O   ILE A  51 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 74
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.639A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA A  90 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ASP A 106 " --> pdb=" O   GLY A 102 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   LEU A 109 " --> pdb=" O   GLU A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.747A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.697A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LYS B  59 " --> pdb=" O   ARG B  55 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ILE B  60 " --> pdb=" O   GLY B  56 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   PHE B  61 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.909A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 23
    Processing helix  chain 'C' and resid 27 through 37
    Processing helix  chain 'C' and resid 47 through 74
    Processing helix  chain 'C' and resid 80 through 91
    Processing helix  chain 'C' and resid 91 through 98
    Processing helix  chain 'C' and resid 113 through 117
      removed outlier: 3.966A  pdb=" N   LEU C 117 " --> pdb=" O   ASN C 114 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 74
    Processing helix  chain 'D' and resid 80 through 109
      removed outlier: 3.736A  pdb=" N   ASN D 109 " --> pdb=" O   LEU D 105 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 115 through 127
      removed outlier: 3.732A  pdb=" N   ILE D 119 " --> pdb=" O   THR D 115 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   GLN D 120 " --> pdb=" O   SER D 116 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 128 through 149
      removed outlier: 3.743A  pdb=" N   SER D 137 " --> pdb=" O   LYS D 133 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 45 through 55
      removed outlier: 3.606A  pdb=" N   ARG E  49 " --> pdb=" O   THR E  45 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 76
      removed outlier: 3.586A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.791A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ALA E  90 " --> pdb=" O   SER E  86 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ALA E  98 " --> pdb=" O   GLU E  94 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   TYR E  99 " --> pdb=" O   ALA E  95 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLY E 102 " --> pdb=" O   ALA E  98 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ASP E 106 " --> pdb=" O   GLY E 102 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   LEU E 109 " --> pdb=" O   GLU E 105 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ILE E 112 " --> pdb=" O   ASN E 108 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 130
      removed outlier: 3.804A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.871A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   ARG F  55 " --> pdb=" O   TYR F  51 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   GLY F  56 " --> pdb=" O   GLU F  52 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   LYS F  59 " --> pdb=" O   ARG F  55 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ARG F  67 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   THR F  73 " --> pdb=" O   ALA F  69 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 3.689A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 27 through 38
    Processing helix  chain 'G' and resid 46 through 74
      removed outlier: 4.452A  pdb=" N   VAL G  50 " --> pdb=" O   ALA G  46 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LEU G  59 " --> pdb=" O   VAL G  55 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LEU G  66 " --> pdb=" O   GLU G  62 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ASN G  74 " --> pdb=" O   ALA G  70 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 80 through 91
      removed outlier: 3.602A  pdb=" N   ASP G  91 " --> pdb=" O   ALA G  87 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 98
    Processing helix  chain 'H' and resid 62 through 74
    Processing helix  chain 'H' and resid 80 through 109
      removed outlier: 3.786A  pdb=" N   ASN H 109 " --> pdb=" O   LEU H 105 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 116 through 127
      removed outlier: 3.879A  pdb=" N   THR H 121 " --> pdb=" O   ARG H 117 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 128 through 148
      removed outlier: 3.667A  pdb=" N   ALA H 132 " --> pdb=" O   PRO H 128 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   HIS H 134 " --> pdb=" O   GLU H 130 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   SER H 137 " --> pdb=" O   LYS H 133 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.960A  pdb=" N   ARG A  83 " --> pdb=" O   VAL F  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
    Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 46
      removed outlier: 7.545A  pdb=" N   ARG B  45 " --> pdb=" O   ILE E 119 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 81
    Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 98
      removed outlier: 7.000A  pdb=" N   THR B  96 " --> pdb=" O   THR C 102 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 43 through 44
      removed outlier: 7.449A  pdb=" N   ARG C  43 " --> pdb=" O   ILE D 114 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'C' and resid 78 through 79
    Processing sheet with id=AA8, first strand: chain 'F' and resid 96 through 98
      removed outlier: 6.609A  pdb=" N   THR F  96 " --> pdb=" O   THR G 102 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44
      removed outlier: 7.158A  pdb=" N   ARG G  43 " --> pdb=" O   ILE H 114 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79

    359 hydrogen bonds defined for protein.
    1056 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      216 hydrogen bonds
      432 hydrogen bond angles
      0 basepair planarities
      86 basepair parallelities
      224 stacking parallelities
  Total time for adding SS restraints: 2.05

  Time building geometry restraints manager: 1.17 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1313
        1.32 -     1.44: 4203
        1.44 -     1.56: 5846
        1.56 -     1.68: 537
        1.68 -     1.80: 22
  Bond restraints: 11921
  Sorted by residual:
  bond pdb=" N   GLU F  52 "
       pdb=" CA  GLU F  52 "
    ideal  model  delta    sigma   weight residual
    1.455  1.504 -0.049 1.29e-02 6.01e+03 1.44e+01
  bond pdb=" NE  ARG C  89 "
       pdb=" CZ  ARG C  89 "
    ideal  model  delta    sigma   weight residual
    1.326  1.365 -0.039 1.10e-02 8.26e+03 1.27e+01
  bond pdb=" N   ILE F  26 "
       pdb=" CA  ILE F  26 "
    ideal  model  delta    sigma   weight residual
    1.459  1.503 -0.044 1.25e-02 6.40e+03 1.23e+01
  bond pdb=" N   GLN F  27 "
       pdb=" CA  GLN F  27 "
    ideal  model  delta    sigma   weight residual
    1.457  1.500 -0.043 1.35e-02 5.49e+03 1.02e+01
  bond pdb=" N   LYS F  59 "
       pdb=" CA  LYS F  59 "
    ideal  model  delta    sigma   weight residual
    1.459  1.499 -0.041 1.28e-02 6.10e+03 1.01e+01
  ... (remaining 11916 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.80: 16857
        2.80 -     5.59: 352
        5.59 -     8.39: 31
        8.39 -    11.19: 2
       11.19 -    13.98: 5
  Bond angle restraints: 17247
  Sorted by residual:
  angle pdb=" O3'  DT J   9 "
        pdb=" C3'  DT J   9 "
        pdb=" C2'  DT J   9 "
      ideal   model   delta    sigma   weight residual
     111.50  125.48  -13.98 1.50e+00 4.44e-01 8.69e+01
  angle pdb=" N   THR E 107 "
        pdb=" CA  THR E 107 "
        pdb=" C   THR E 107 "
      ideal   model   delta    sigma   weight residual
     113.18  102.29   10.89 1.21e+00 6.83e-01 8.10e+01
  angle pdb=" O3'  DA I 106 "
        pdb=" C3'  DA I 106 "
        pdb=" C2'  DA I 106 "
      ideal   model   delta    sigma   weight residual
     111.50  124.99  -13.49 1.50e+00 4.44e-01 8.09e+01
  angle pdb=" O3'  DG I 126 "
        pdb=" C3'  DG I 126 "
        pdb=" C2'  DG I 126 "
      ideal   model   delta    sigma   weight residual
     111.50  124.43  -12.93 1.50e+00 4.44e-01 7.43e+01
  angle pdb=" O3'  DT J  24 "
        pdb=" C3'  DT J  24 "
        pdb=" C2'  DT J  24 "
      ideal   model   delta    sigma   weight residual
     111.50  124.43  -12.93 1.50e+00 4.44e-01 7.43e+01
  ... (remaining 17242 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.91: 5232
       34.91 -    69.82: 1200
       69.82 -   104.74: 34
      104.74 -   139.65: 2
      139.65 -   174.56: 4
  Dihedral angle restraints: 6472
    sinusoidal: 4381
      harmonic: 2091
  Sorted by residual:
  dihedral pdb=" CA  GLU H 118 "
           pdb=" C   GLU H 118 "
           pdb=" N   ILE H 119 "
           pdb=" CA  ILE H 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.95   27.05     0      5.00e+00 4.00e-02 2.93e+01
  dihedral pdb=" CA  LEU E  60 "
           pdb=" C   LEU E  60 "
           pdb=" N   LEU E  61 "
           pdb=" CA  LEU E  61 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.21  -22.79     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" CA  GLU E 133 "
           pdb=" C   GLU E 133 "
           pdb=" N   ARG E 134 "
           pdb=" CA  ARG E 134 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.16   20.84     0      5.00e+00 4.00e-02 1.74e+01
  ... (remaining 6469 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.164: 1955
       0.164 -    0.329: 12
       0.329 -    0.493: 0
       0.493 -    0.657: 2
       0.657 -    0.821: 3
  Chirality restraints: 1972
  Sorted by residual:
  chirality pdb=" C3'  DG I 126 "
            pdb=" C4'  DG I 126 "
            pdb=" O3'  DG I 126 "
            pdb=" C2'  DG I 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -1.84   -0.82 2.00e-01 2.50e+01 1.69e+01
  chirality pdb=" C3'  DA I 106 "
            pdb=" C4'  DA I 106 "
            pdb=" O3'  DA I 106 "
            pdb=" C2'  DA I 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -1.94   -0.72 2.00e-01 2.50e+01 1.31e+01
  chirality pdb=" C3'  DT J  24 "
            pdb=" C4'  DT J  24 "
            pdb=" O3'  DT J  24 "
            pdb=" C2'  DT J  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -1.98   -0.68 2.00e-01 2.50e+01 1.15e+01
  ... (remaining 1969 not shown)

  Planarity restraints: 1249
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J  27 "    0.045 2.00e-02 2.50e+03   2.09e-02 9.82e+00
        pdb=" N1   DC J  27 "   -0.015 2.00e-02 2.50e+03
        pdb=" C2   DC J  27 "   -0.016 2.00e-02 2.50e+03
        pdb=" O2   DC J  27 "   -0.010 2.00e-02 2.50e+03
        pdb=" N3   DC J  27 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4   DC J  27 "    0.007 2.00e-02 2.50e+03
        pdb=" N4   DC J  27 "    0.025 2.00e-02 2.50e+03
        pdb=" C5   DC J  27 "   -0.010 2.00e-02 2.50e+03
        pdb=" C6   DC J  27 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP E 106 "   -0.015 2.00e-02 2.50e+03   3.02e-02 9.12e+00
        pdb=" C   ASP E 106 "    0.052 2.00e-02 2.50e+03
        pdb=" O   ASP E 106 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   THR E 107 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR F  51 "   -0.015 2.00e-02 2.50e+03   3.00e-02 9.01e+00
        pdb=" C   TYR F  51 "    0.052 2.00e-02 2.50e+03
        pdb=" O   TYR F  51 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   GLU F  52 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1246 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 2427
        2.80 -     3.32: 9588
        3.32 -     3.85: 20983
        3.85 -     4.37: 25240
        4.37 -     4.90: 35944
  Nonbonded interactions: 94182
  Sorted by model distance:
  nonbonded pdb=" O   ASP C  91 "
            pdb=" OG  SER C  95 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OH  TYR G  58 "
            pdb=" OE2 GLU G  62 "
     model   vdw
     2.335 3.040
  nonbonded pdb=" NE  ARG E 131 "
            pdb=" OE2 GLU E 133 "
     model   vdw
     2.342 3.120
  nonbonded pdb=" OH  TYR C  40 "
            pdb=" OE1 GLU D  96 "
     model   vdw
     2.415 3.040
  nonbonded pdb=" NH2 ARG E 131 "
            pdb=" OE2 GLU E 133 "
     model   vdw
     2.420 3.120
  ... (remaining 94177 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'
  selection = (chain 'E' and resid 43 through 133)
}
ncs_group {
  reference = (chain 'B' and resid 24 through 100)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 18 through 110)
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'H' and resid 61 through 149)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.040
  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:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.010
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059  11921  Z= 0.356
  Angle     :  1.006  13.981  17247  Z= 0.640
  Chirality :  0.060   0.821   1972
  Planarity :  0.006   0.055   1249
  Dihedral  : 27.902 174.559   5120
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.53 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  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: -2.07 (0.29), residues: 707
  helix: -0.87 (0.22), residues: 510
  sheet:  None (None), residues: 0
  loop : -2.40 (0.37), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG G  89 
 TYR   0.013   0.003   TYR H  65 
 PHE   0.049   0.003   PHE C  26 
 HIS   0.006   0.001   HIS G  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00740 (11921)
  covalent geometry    : angle       1.00567 (17247)
  hydrogen bonds       : bond        0.20894 (  575)
  hydrogen bonds       : angle       7.77230 ( 1488)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.291 
Fit side-chains
REVERT: C  105 ASN cc_start: 0.8857 (t0) cc_final: 0.8656 (t0)
REVERT: C  111 ASN cc_start: 0.8084 (t0) cc_final: 0.7741 (p0)
REVERT: D  111 LYS cc_start: 0.8478 (mmtm) cc_final: 0.8191 (mtpt)
  outliers start: 0
  outliers final: 0
  residues processed: 202
  average time/residue: 0.1913
  time to fit residues: 47.4666
Evaluate side-chains
  152 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.0670
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    5.9990
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
C  85 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.126973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.090258 restraints weight = 21157.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 1.65
r_work: 0.3022 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.2744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  11921  Z= 0.172
  Angle     :  0.618   8.591  17247  Z= 0.366
  Chirality :  0.037   0.249   1972
  Planarity :  0.005   0.045   1249
  Dihedral  : 30.936 176.363   3713
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 10.40 %
    Favored  : 87.75 %
  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:  0.12 (0.31), residues: 707
  helix:  0.83 (0.23), residues: 522
  sheet:  None (None), residues: 0
  loop : -2.03 (0.39), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H 107 
 TYR   0.007   0.001   TYR A  54 
 PHE   0.011   0.001   PHE C  26 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (11921)
  covalent geometry    : angle       0.61843 (17247)
  hydrogen bonds       : bond        0.05139 (  575)
  hydrogen bonds       : angle       3.13871 ( 1488)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 164
  time to evaluate  : 0.192 
Fit side-chains
REVERT: B   84 MET cc_start: 0.8369 (mmm) cc_final: 0.7961 (mmt)
REVERT: C   18 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.7756 (mpp80)
REVERT: C   65 GLU cc_start: 0.8542 (tt0) cc_final: 0.8320 (tt0)
REVERT: C   74 ASN cc_start: 0.7070 (m-40) cc_final: 0.6480 (t0)
REVERT: C  105 ASN cc_start: 0.9022 (t0) cc_final: 0.8240 (t0)
REVERT: C  109 MET cc_start: 0.8272 (ptt) cc_final: 0.8049 (mtm)
REVERT: C  111 ASN cc_start: 0.8408 (t0) cc_final: 0.7740 (p0)
REVERT: D  111 LYS cc_start: 0.8437 (mmtm) cc_final: 0.8038 (mtpt)
REVERT: D  141 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8471 (ttpp)
REVERT: E   58 THR cc_start: 0.9492 (p) cc_final: 0.9288 (p)
REVERT: F   79 LYS cc_start: 0.9058 (mtpt) cc_final: 0.8731 (mtmt)
REVERT: F   96 THR cc_start: 0.9137 (m) cc_final: 0.8831 (p)
REVERT: H  104 LYS cc_start: 0.8374 (ttmt) cc_final: 0.7862 (ttmm)
REVERT: H  108 TYR cc_start: 0.7621 (m-10) cc_final: 0.7356 (m-10)
  outliers start: 11
  outliers final: 2
  residues processed: 168
  average time/residue: 0.1729
  time to fit residues: 36.2675
Evaluate side-chains
  158 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 154
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   18 ARG
Chi-restraints excluded: chain D residue  141 LYS
Chi-restraints excluded: chain G residue  101 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 51 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 14 optimal weight:    0.7980
   chunk 72 optimal weight:    5.9990
   chunk 2 optimal weight:    0.1980
   chunk 36 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 70 optimal weight:    7.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
H  74 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.125386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.090324 restraints weight = 21086.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 1.52
r_work: 0.3060 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.3916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11921  Z= 0.158
  Angle     :  0.559   6.924  17247  Z= 0.333
  Chirality :  0.035   0.145   1972
  Planarity :  0.004   0.039   1249
  Dihedral  : 30.731 178.625   3713
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 12.92 %
    Favored  : 84.90 %
  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:  1.51 (0.33), residues: 707
  helix:  1.86 (0.24), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.57 (0.42), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H 107 
 TYR   0.006   0.001   TYR H  65 
 PHE   0.013   0.001   PHE C  26 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (11921)
  covalent geometry    : angle       0.55853 (17247)
  hydrogen bonds       : bond        0.04331 (  575)
  hydrogen bonds       : angle       2.67474 ( 1488)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 165
  time to evaluate  : 0.305 
Fit side-chains
REVERT: C   18 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8034 (mpp80)
REVERT: C   74 ASN cc_start: 0.6991 (m-40) cc_final: 0.6622 (t0)
REVERT: C  105 ASN cc_start: 0.8936 (t0) cc_final: 0.8131 (t0)
REVERT: C  111 ASN cc_start: 0.8403 (t0) cc_final: 0.7925 (p0)
REVERT: D  104 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7769 (mtmm)
REVERT: D  111 LYS cc_start: 0.8495 (mmtm) cc_final: 0.8097 (mtpt)
REVERT: F   79 LYS cc_start: 0.9039 (mtpt) cc_final: 0.8778 (mtmt)
  outliers start: 13
  outliers final: 4
  residues processed: 168
  average time/residue: 0.1799
  time to fit residues: 37.4712
Evaluate side-chains
  152 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 146
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue   18 ARG
Chi-restraints excluded: chain D residue  104 LYS
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue  102 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 58 optimal weight:   10.0000
   chunk 17 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 50 optimal weight:    0.0670
   chunk 11 optimal weight:    4.9990
   overall best weight:    0.7318

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
F  75 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.123572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.088407 restraints weight = 21123.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 1.51
r_work: 0.3017 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.2869 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8639
moved from start:          0.4449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11921  Z= 0.148
  Angle     :  0.540   7.057  17247  Z= 0.321
  Chirality :  0.034   0.136   1972
  Planarity :  0.004   0.043   1249
  Dihedral  : 30.538 178.071   3713
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 13.76 %
    Favored  : 84.06 %
  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:  2.04 (0.32), residues: 707
  helix:  2.24 (0.23), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.34 (0.41), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H 107 
 TYR   0.006   0.001   TYR H  65 
 PHE   0.010   0.001   PHE C  26 
 HIS   0.007   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (11921)
  covalent geometry    : angle       0.53969 (17247)
  hydrogen bonds       : bond        0.04105 (  575)
  hydrogen bonds       : angle       2.53449 ( 1488)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 155
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
REVERT: C   18 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8283 (mpp80)
REVERT: C   72 ARG cc_start: 0.8366 (ttp80) cc_final: 0.8140 (ttp-170)
REVERT: C   74 ASN cc_start: 0.7378 (m-40) cc_final: 0.6950 (t0)
REVERT: C  105 ASN cc_start: 0.9035 (t0) cc_final: 0.8530 (t0)
REVERT: C  111 ASN cc_start: 0.8542 (t0) cc_final: 0.7929 (p0)
REVERT: D  104 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7819 (mtmm)
REVERT: D  111 LYS cc_start: 0.8551 (mmtm) cc_final: 0.8088 (mtpt)
REVERT: F   79 LYS cc_start: 0.9174 (mtpt) cc_final: 0.8915 (mtmt)
REVERT: H   68 LYS cc_start: 0.9244 (ttmt) cc_final: 0.8983 (mtmt)
  outliers start: 13
  outliers final: 5
  residues processed: 160
  average time/residue: 0.1931
  time to fit residues: 38.4232
Evaluate side-chains
  157 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 150
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   18 ARG
Chi-restraints excluded: chain D residue  104 LYS
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue  102 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 82 optimal weight:   10.0000
   chunk 41 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 50 optimal weight:    0.6980
   chunk 84 optimal weight:    7.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
D  72 GLN
E 125 GLN
H 134 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.114540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.077618 restraints weight = 20669.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.2971 rms_B_bonded: 1.62
r_work: 0.2790 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.5237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11921  Z= 0.169
  Angle     :  0.559   7.115  17247  Z= 0.330
  Chirality :  0.035   0.145   1972
  Planarity :  0.004   0.034   1249
  Dihedral  : 30.488 179.842   3713
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 14.93 %
    Favored  : 83.05 %
  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:  2.07 (0.32), residues: 707
  helix:  2.22 (0.23), residues: 526
  sheet:  None (None), residues: 0
  loop : -1.28 (0.42), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 124 
 TYR   0.009   0.001   TYR B  51 
 PHE   0.019   0.001   PHE C  26 
 HIS   0.003   0.001   HIS D  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (11921)
  covalent geometry    : angle       0.55901 (17247)
  hydrogen bonds       : bond        0.05089 (  575)
  hydrogen bonds       : angle       2.71189 ( 1488)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 163
  time to evaluate  : 0.294 
Fit side-chains
REVERT: C   18 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8299 (mpp80)
REVERT: C   73 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8246 (m-30)
REVERT: C   74 ASN cc_start: 0.8007 (m-40) cc_final: 0.7544 (t0)
REVERT: C  105 ASN cc_start: 0.9026 (t0) cc_final: 0.8205 (t0)
REVERT: C  111 ASN cc_start: 0.8512 (t0) cc_final: 0.8103 (p0)
REVERT: D  104 LYS cc_start: 0.8166 (mptt) cc_final: 0.7959 (mtmm)
REVERT: D  111 LYS cc_start: 0.8570 (mmtm) cc_final: 0.8053 (mtpt)
REVERT: F   79 LYS cc_start: 0.9112 (mtpt) cc_final: 0.8811 (mtmt)
REVERT: G   20 SER cc_start: 0.9182 (OUTLIER) cc_final: 0.8937 (m)
REVERT: H   68 LYS cc_start: 0.9238 (ttmt) cc_final: 0.8804 (mttt)
  outliers start: 12
  outliers final: 7
  residues processed: 169
  average time/residue: 0.1871
  time to fit residues: 39.4779
Evaluate side-chains
  167 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 157
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   18 ARG
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   20 SER
Chi-restraints excluded: chain G residue  102 THR
Chi-restraints excluded: chain H residue   64 ILE
Chi-restraints excluded: chain H residue  147 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 48 optimal weight:    5.9990
   chunk 91 optimal weight:    6.9990
   chunk 87 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 81 optimal weight:   10.0000
   chunk 12 optimal weight:    0.9990
   chunk 32 optimal weight:   20.0000
   chunk 79 optimal weight:    8.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
B  27 GLN
D  72 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.107855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.070816 restraints weight = 20686.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.2842 rms_B_bonded: 1.71
r_work: 0.2649 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8785
moved from start:          0.5697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.071  11921  Z= 0.307
  Angle     :  0.665   8.414  17247  Z= 0.387
  Chirality :  0.042   0.176   1972
  Planarity :  0.005   0.037   1249
  Dihedral  : 30.791 178.784   3713
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 14.93 %
    Favored  : 82.38 %
  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:  1.52 (0.32), residues: 707
  helix:  1.86 (0.23), residues: 523
  sheet:  None (None), residues: 0
  loop : -1.53 (0.42), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E  72 
 TYR   0.011   0.002   TYR B  51 
 PHE   0.020   0.002   PHE C  26 
 HIS   0.003   0.001   HIS D  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00720 (11921)
  covalent geometry    : angle       0.66512 (17247)
  hydrogen bonds       : bond        0.06704 (  575)
  hydrogen bonds       : angle       3.04080 ( 1488)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 157
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
REVERT: B   79 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8682 (ttmm)
REVERT: C   18 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8227 (mpp80)
REVERT: C   73 ASP cc_start: 0.8626 (m-30) cc_final: 0.8393 (m-30)
REVERT: C   74 ASN cc_start: 0.8453 (m-40) cc_final: 0.7945 (t0)
REVERT: C  105 ASN cc_start: 0.9079 (t0) cc_final: 0.8267 (t0)
REVERT: C  111 ASN cc_start: 0.8529 (t0) cc_final: 0.8292 (p0)
REVERT: D  104 LYS cc_start: 0.8349 (mptt) cc_final: 0.8130 (mtmm)
REVERT: D  111 LYS cc_start: 0.8928 (mmtm) cc_final: 0.8550 (mtpt)
REVERT: F   79 LYS cc_start: 0.9148 (mtpt) cc_final: 0.8852 (mtmt)
REVERT: H   63 LYS cc_start: 0.9038 (mptt) cc_final: 0.8648 (mmtm)
REVERT: H   68 LYS cc_start: 0.9263 (ttmt) cc_final: 0.8702 (mttt)
REVERT: H  101 GLU cc_start: 0.8567 (tp30) cc_final: 0.8316 (tp30)
  outliers start: 16
  outliers final: 10
  residues processed: 165
  average time/residue: 0.1828
  time to fit residues: 37.4807
Evaluate side-chains
  164 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 152
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain C residue   18 ARG
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue  102 THR
Chi-restraints excluded: chain H residue   64 ILE
Chi-restraints excluded: chain H residue  147 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 84 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 35 optimal weight:    0.1980
   chunk 38 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 68 optimal weight:   10.0000
   chunk 11 optimal weight:    0.6980
   chunk 63 optimal weight:    4.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  27 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.110534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.074055 restraints weight = 20599.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.2911 rms_B_bonded: 1.62
r_work: 0.2727 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8708
moved from start:          0.5829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11921  Z= 0.178
  Angle     :  0.584   7.291  17247  Z= 0.344
  Chirality :  0.035   0.155   1972
  Planarity :  0.004   0.035   1249
  Dihedral  : 30.538 179.119   3713
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 15.77 %
    Favored  : 82.38 %
  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:  1.87 (0.32), residues: 707
  helix:  2.13 (0.23), residues: 523
  sheet:  None (None), residues: 0
  loop : -1.48 (0.43), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  72 
 TYR   0.009   0.001   TYR B  51 
 PHE   0.013   0.001   PHE C  26 
 HIS   0.003   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (11921)
  covalent geometry    : angle       0.58399 (17247)
  hydrogen bonds       : bond        0.05030 (  575)
  hydrogen bonds       : angle       2.72475 ( 1488)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 157
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: C   18 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8272 (mtp85)
REVERT: C   73 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8289 (m-30)
REVERT: C   74 ASN cc_start: 0.8267 (m-40) cc_final: 0.7807 (t0)
REVERT: C  105 ASN cc_start: 0.9028 (t0) cc_final: 0.8174 (t0)
REVERT: C  111 ASN cc_start: 0.8503 (t0) cc_final: 0.8264 (p0)
REVERT: D  104 LYS cc_start: 0.8183 (mptt) cc_final: 0.7956 (mtmm)
REVERT: D  111 LYS cc_start: 0.8769 (mmtm) cc_final: 0.8320 (mtpt)
REVERT: F   79 LYS cc_start: 0.9130 (mtpt) cc_final: 0.8829 (mtmt)
REVERT: H   68 LYS cc_start: 0.9252 (ttmt) cc_final: 0.8998 (mttt)
  outliers start: 11
  outliers final: 6
  residues processed: 159
  average time/residue: 0.1850
  time to fit residues: 36.7504
Evaluate side-chains
  164 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 156
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   18 ARG
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain H residue   64 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 85 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   chunk 91 optimal weight:    6.9990
   chunk 39 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
B  27 GLN
D  72 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.112466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.076544 restraints weight = 20768.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.2959 rms_B_bonded: 1.61
r_work: 0.2781 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.5962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11921  Z= 0.154
  Angle     :  0.548   7.169  17247  Z= 0.325
  Chirality :  0.034   0.141   1972
  Planarity :  0.004   0.035   1249
  Dihedral  : 30.347 179.546   3713
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 16.28 %
    Favored  : 82.05 %
  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:  2.30 (0.33), residues: 707
  helix:  2.43 (0.23), residues: 526
  sheet:  None (None), residues: 0
  loop : -1.33 (0.42), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  72 
 TYR   0.005   0.001   TYR H  62 
 PHE   0.010   0.001   PHE A  67 
 HIS   0.002   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (11921)
  covalent geometry    : angle       0.54836 (17247)
  hydrogen bonds       : bond        0.04187 (  575)
  hydrogen bonds       : angle       2.56348 ( 1488)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 154
  time to evaluate  : 0.310 
Fit side-chains
REVERT: C   73 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8124 (m-30)
REVERT: C   74 ASN cc_start: 0.7922 (m-40) cc_final: 0.7500 (t0)
REVERT: C  105 ASN cc_start: 0.9008 (t0) cc_final: 0.8120 (t0)
REVERT: D  111 LYS cc_start: 0.8668 (mmtm) cc_final: 0.8211 (mtpt)
REVERT: F   79 LYS cc_start: 0.9086 (mtpt) cc_final: 0.8811 (mtmt)
REVERT: H   63 LYS cc_start: 0.9013 (mptt) cc_final: 0.8602 (mmtm)
REVERT: H   68 LYS cc_start: 0.9199 (ttmt) cc_final: 0.8619 (mttt)
REVERT: H  130 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7625 (tm-30)
  outliers start: 10
  outliers final: 7
  residues processed: 159
  average time/residue: 0.1792
  time to fit residues: 35.6130
Evaluate side-chains
  150 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 142
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain G residue  102 THR
Chi-restraints excluded: chain H residue   64 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 80 optimal weight:   10.0000
   chunk 61 optimal weight:    6.9990
   chunk 89 optimal weight:    5.9990
   chunk 52 optimal weight:    9.9990
   chunk 36 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 91 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.109367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.073115 restraints weight = 20307.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.2896 rms_B_bonded: 1.47
r_work: 0.2719 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2567 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8867
moved from start:          0.6024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  11921  Z= 0.227
  Angle     :  0.592   7.577  17247  Z= 0.348
  Chirality :  0.037   0.164   1972
  Planarity :  0.004   0.035   1249
  Dihedral  : 30.418 178.640   3713
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 16.11 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.23 (0.32), residues: 707
  helix:  2.37 (0.23), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.23 (0.43), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  72 
 TYR   0.009   0.001   TYR B  51 
 PHE   0.018   0.002   PHE C  26 
 HIS   0.003   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00526 (11921)
  covalent geometry    : angle       0.59154 (17247)
  hydrogen bonds       : bond        0.05570 (  575)
  hydrogen bonds       : angle       2.76894 ( 1488)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 148
  time to evaluate  : 0.363 
Fit side-chains
REVERT: B   79 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8805 (ttmm)
REVERT: C   73 ASP cc_start: 0.8591 (m-30) cc_final: 0.8369 (m-30)
REVERT: C   74 ASN cc_start: 0.8316 (m-40) cc_final: 0.7829 (t0)
REVERT: C  105 ASN cc_start: 0.9102 (t0) cc_final: 0.8251 (t0)
REVERT: D  100 SER cc_start: 0.9300 (m) cc_final: 0.9091 (p)
REVERT: F   79 LYS cc_start: 0.9187 (mtpt) cc_final: 0.8933 (mtmt)
REVERT: H   68 LYS cc_start: 0.9254 (ttmt) cc_final: 0.8898 (mttt)
REVERT: H  130 GLU cc_start: 0.8467 (mm-30) cc_final: 0.7927 (tm-30)
  outliers start: 8
  outliers final: 6
  residues processed: 151
  average time/residue: 0.1737
  time to fit residues: 33.0996
Evaluate side-chains
  152 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 145
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain C residue  111 ASN
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain G residue  102 THR
Chi-restraints excluded: chain H residue   64 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 73 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 83 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.110024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.073857 restraints weight = 20469.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.2912 rms_B_bonded: 1.47
r_work: 0.2735 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2583 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8852
moved from start:          0.6050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11921  Z= 0.176
  Angle     :  0.572   7.248  17247  Z= 0.338
  Chirality :  0.035   0.167   1972
  Planarity :  0.004   0.044   1249
  Dihedral  : 30.394 178.803   3713
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 16.61 %
    Favored  : 82.21 %
  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:  2.22 (0.32), residues: 707
  helix:  2.39 (0.23), residues: 524
  sheet:  None (None), residues: 0
  loop : -1.39 (0.42), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  72 
 TYR   0.012   0.001   TYR F  98 
 PHE   0.017   0.001   PHE C  26 
 HIS   0.002   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 (11921)
  covalent geometry    : angle       0.57229 (17247)
  hydrogen bonds       : bond        0.05159 (  575)
  hydrogen bonds       : angle       2.71463 ( 1488)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 146
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
REVERT: B   79 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8791 (ttmm)
REVERT: C   73 ASP cc_start: 0.8583 (m-30) cc_final: 0.8359 (m-30)
REVERT: C   74 ASN cc_start: 0.8240 (m-40) cc_final: 0.7769 (t0)
REVERT: C  105 ASN cc_start: 0.9096 (t0) cc_final: 0.8245 (t0)
REVERT: F   79 LYS cc_start: 0.9178 (mtpt) cc_final: 0.8926 (mtmt)
REVERT: H   63 LYS cc_start: 0.9038 (mptt) cc_final: 0.8679 (mmtm)
REVERT: H   68 LYS cc_start: 0.9249 (ttmt) cc_final: 0.8905 (mttt)
REVERT: H  130 GLU cc_start: 0.8444 (mm-30) cc_final: 0.7922 (tm-30)
  outliers start: 7
  outliers final: 5
  residues processed: 149
  average time/residue: 0.1793
  time to fit residues: 33.7345
Evaluate side-chains
  151 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 145
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain G residue  102 THR
Chi-restraints excluded: chain H residue   64 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0070
   chunk 22 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 81 optimal weight:   10.0000
   chunk 82 optimal weight:    8.9990
   chunk 93 optimal weight:   10.0000
   chunk 40 optimal weight:    2.9990
   chunk 80 optimal weight:   10.0000
   chunk 56 optimal weight:    3.9990
   overall best weight:    2.2004

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.111057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.076199 restraints weight = 20625.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.2983 rms_B_bonded: 1.51
r_work: 0.2800 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2649 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8876
moved from start:          0.6323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  11921  Z= 0.213
  Angle     :  0.578   7.154  17247  Z= 0.340
  Chirality :  0.036   0.166   1972
  Planarity :  0.004   0.036   1249
  Dihedral  : 30.388 179.182   3713
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 16.78 %
    Favored  : 82.05 %
  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:  2.21 (0.32), residues: 707
  helix:  2.37 (0.23), residues: 523
  sheet:  None (None), residues: 0
  loop : -1.30 (0.43), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  72 
 TYR   0.009   0.001   TYR B  51 
 PHE   0.017   0.002   PHE C  26 
 HIS   0.002   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 (11921)
  covalent geometry    : angle       0.57782 (17247)
  hydrogen bonds       : bond        0.05234 (  575)
  hydrogen bonds       : angle       2.73945 ( 1488)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3086.67 seconds
wall clock time: 53 minutes 17.33 seconds (3197.33 seconds total)