Starting phenix.real_space_refine
on Fri Feb  6 00:10:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mmk_48392/02_2026/9mmk_48392.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mmk_48392/02_2026/9mmk_48392.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mmk_48392/02_2026/9mmk_48392.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mmk_48392/02_2026/9mmk_48392.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mmk_48392/02_2026/9mmk_48392.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mmk_48392/02_2026/9mmk_48392.cif"
  }
  resolution = 3.2
  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=   0.012
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: 6
    Type Number    sf(0)   Gaussians
     P     285      5.49       5
     S      14      5.16       5
     C    6530      2.51       5
     N    2214      2.21       5
     O    2763      1.98       5
     H    9467      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 21273
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 1616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 1616
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 1283
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 1283
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "C"
      Number of atoms: 1715
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 1715
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 1471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 1471
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "E"
      Number of atoms: 1616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 1616
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 1315
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 1315
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 1715
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 1715
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 1471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 1471
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "I"
      Number of atoms: 4519
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 4519
          Classifications: {'DNA': 143}
          Modifications used: {'3*END': 1}
          Link IDs: {'rna3p': 142}
    Chain: "J"
      Number of atoms: 4552
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 4552
          Classifications: {'DNA': 143}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 142}
  Time building chain proxies: 4.03, per 1000 atoms: 0.19
  Number of scatterers: 21273
  At special positions: 0
  Unit cell: (77.77, 120.12, 120.89, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      14     16.00
     P     285     15.00
     O    2763      8.00
     N    2214      7.00
     C    6530      6.00
     H    9467      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.00
  Conformation dependent library (CDL) restraints added in 439.8 milliseconds
  

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1398

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 10 sheets defined
      72.2% alpha, 2.9% beta
      141 base pairs and 262 stacking pairs defined.
    Time for finding SS restraints: 3.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 56
    Processing helix  chain 'A' and resid 64 through 77
      removed outlier: 3.547A  pdb=" N   GLN A  77 " --> pdb=" O   ARG A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 114
      removed outlier: 3.863A  pdb=" N   VAL A  90 " --> pdb=" O   GLN A  86 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   MET A  91 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLY A 103 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LEU A 110 " --> pdb=" O   GLU A 106 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   CYS A 111 " --> pdb=" O   ASP A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 133
      removed outlier: 3.660A  pdb=" N   ILE A 125 " --> pdb=" O   MET A 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 30
    Processing helix  chain 'B' and resid 31 through 42
    Processing helix  chain 'B' and resid 50 through 77
      removed outlier: 3.711A  pdb=" N   GLU B  54 " --> pdb=" O   LEU B  50 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLY B  57 " --> pdb=" O   GLU B  53 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLU B  64 " --> pdb=" O   LYS B  60 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ASN B  65 " --> pdb=" O   VAL B  61 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   VAL B  66 " --> pdb=" O   PHE B  62 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ASP B  69 " --> pdb=" O   ASN B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 94
      removed outlier: 3.650A  pdb=" N   GLN B  94 " --> pdb=" O   ALA B  90 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 23
    Processing helix  chain 'C' and resid 27 through 38
    Processing helix  chain 'C' and resid 47 through 74
      removed outlier: 4.007A  pdb=" N   LEU C  66 " --> pdb=" O   GLU C  62 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 90
    Processing helix  chain 'C' and resid 93 through 98
    Processing helix  chain 'C' and resid 113 through 117
    Processing helix  chain 'D' and resid 38 through 50
    Processing helix  chain 'D' and resid 56 through 85
      removed outlier: 3.864A  pdb=" N   ASN D  68 " --> pdb=" O   ASN D  64 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ASN D  85 " --> pdb=" O   LEU D  81 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 91 through 103
    Processing helix  chain 'D' and resid 104 through 125
      removed outlier: 3.815A  pdb=" N   SER D 113 " --> pdb=" O   LYS D 109 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 45 through 58
      removed outlier: 3.569A  pdb=" N   ARG E  50 " --> pdb=" O   THR E  46 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 64 through 77
      removed outlier: 3.555A  pdb=" N   GLN E  77 " --> pdb=" O   ARG E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 86 through 115
      removed outlier: 3.863A  pdb=" N   VAL E  90 " --> pdb=" O   GLN E  86 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   MET E  91 " --> pdb=" O   SER E  87 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   LEU E 110 " --> pdb=" O   GLU E 106 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ALA E 115 " --> pdb=" O   CYS E 111 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 121 through 133
      removed outlier: 3.668A  pdb=" N   ILE E 125 " --> pdb=" O   MET E 121 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 30
      removed outlier: 4.140A  pdb=" N   ILE F  27 " --> pdb=" O   ARG F  24 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 31 through 42
    Processing helix  chain 'F' and resid 50 through 77
      removed outlier: 3.836A  pdb=" N   GLU F  54 " --> pdb=" O   LEU F  50 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   VAL F  61 " --> pdb=" O   GLY F  57 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   PHE F  62 " --> pdb=" O   VAL F  58 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ASP F  69 " --> pdb=" O   ASN F  65 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 83 through 95
      removed outlier: 3.639A  pdb=" N   VAL F  87 " --> pdb=" O   THR F  83 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 17 through 23
    Processing helix  chain 'G' and resid 27 through 37
    Processing helix  chain 'G' and resid 47 through 73
    Processing helix  chain 'G' and resid 80 through 90
    Processing helix  chain 'G' and resid 93 through 98
    Processing helix  chain 'H' and resid 38 through 50
    Processing helix  chain 'H' and resid 56 through 85
      removed outlier: 3.510A  pdb=" N   ILE H  62 " --> pdb=" O   LYS H  58 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   VAL H  67 " --> pdb=" O   MET H  63 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ASN H  68 " --> pdb=" O   ASN H  64 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 91 through 103
    Processing helix  chain 'H' and resid 104 through 125
      removed outlier: 3.657A  pdb=" N   LYS H 109 " --> pdb=" O   GLY H 105 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   HIS H 110 " --> pdb=" O   GLU H 106 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85
      removed outlier: 6.590A  pdb=" N   ARG A  84 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120
      removed outlier: 3.525A  pdb=" N   ILE A 120 " --> pdb=" O   ARG B  46 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99
    Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44
      removed outlier: 7.099A  pdb=" N   ARG C  43 " --> pdb=" O   ILE D  90 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103
    Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85
      removed outlier: 6.953A  pdb=" N   ARG E  84 " --> pdb=" O   VAL F  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120
    Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44
      removed outlier: 7.219A  pdb=" N   ARG G  43 " --> pdb=" O   ILE H  90 " (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

    376 hydrogen bonds defined for protein.
    1107 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      362 hydrogen bonds
      724 hydrogen bond angles
      0 basepair planarities
      141 basepair parallelities
      262 stacking parallelities
  Total time for adding SS restraints: 4.82

  Time building geometry restraints manager: 2.76 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 9463
        1.03 -     1.23: 111
        1.23 -     1.42: 5353
        1.42 -     1.61: 7117
        1.61 -     1.81: 24
  Bond restraints: 22068
  Sorted by residual:
  bond pdb=" N   SER D  33 "
       pdb=" CA  SER D  33 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.14e+00
  bond pdb=" N   ARG F  24 "
       pdb=" CA  ARG F  24 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.14e+00
  bond pdb=" N   ASP B  25 "
       pdb=" CA  ASP B  25 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.00e+00
  bond pdb=" N   SER H  33 "
       pdb=" CA  SER H  33 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.94e+00
  bond pdb=" N   ARG C  12 "
       pdb=" CA  ARG C  12 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.85e+00
  ... (remaining 22063 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 34973
        1.32 -     2.63: 4630
        2.63 -     3.95: 365
        3.95 -     5.27: 31
        5.27 -     6.58: 3
  Bond angle restraints: 40002
  Sorted by residual:
  angle pdb=" C4'  DC I  21 "
        pdb=" O4'  DC I  21 "
        pdb=" C1'  DC I  21 "
      ideal   model   delta    sigma   weight residual
     109.70  104.25    5.45 1.50e+00 4.44e-01 1.32e+01
  angle pdb=" C4'  DC I  66 "
        pdb=" O4'  DC I  66 "
        pdb=" C1'  DC I  66 "
      ideal   model   delta    sigma   weight residual
     109.70  104.37    5.33 1.50e+00 4.44e-01 1.26e+01
  angle pdb=" C2'  DC I  69 "
        pdb=" C1'  DC I  69 "
        pdb=" N1   DC I  69 "
      ideal   model   delta    sigma   weight residual
     113.50  118.53   -5.03 1.50e+00 4.44e-01 1.13e+01
  angle pdb=" N   GLY H 105 "
        pdb=" CA  GLY H 105 "
        pdb=" C   GLY H 105 "
      ideal   model   delta    sigma   weight residual
     112.83  116.83   -4.00 1.22e+00 6.72e-01 1.07e+01
  angle pdb=" O4'  DC I  66 "
        pdb=" C1'  DC I  66 "
        pdb=" N1   DC I  66 "
      ideal   model   delta    sigma   weight residual
     108.40  113.13   -4.73 1.50e+00 4.44e-01 9.96e+00
  ... (remaining 39997 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.18: 6425
       17.18 -    34.35: 1201
       34.35 -    51.53: 919
       51.53 -    68.70: 606
       68.70 -    85.88: 13
  Dihedral angle restraints: 9164
    sinusoidal: 6728
      harmonic: 2436
  Sorted by residual:
  dihedral pdb=" CG  ARG H 100 "
           pdb=" CD  ARG H 100 "
           pdb=" NE  ARG H 100 "
           pdb=" CZ  ARG H 100 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -43.87  -46.13     2      1.50e+01 4.44e-03 1.11e+01
  dihedral pdb=" CG  ARG F  56 "
           pdb=" CD  ARG F  56 "
           pdb=" NE  ARG F  56 "
           pdb=" CZ  ARG F  56 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.60   44.40     2      1.50e+01 4.44e-03 1.04e+01
  dihedral pdb=" CG  ARG G  33 "
           pdb=" CD  ARG G  33 "
           pdb=" NE  ARG G  33 "
           pdb=" CZ  ARG G  33 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -133.75   43.75     2      1.50e+01 4.44e-03 1.02e+01
  ... (remaining 9161 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1452
       0.048 -    0.095: 508
       0.095 -    0.143: 94
       0.143 -    0.191: 14
       0.191 -    0.238: 4
  Chirality restraints: 2072
  Sorted by residual:
  chirality pdb=" C1'  DC I  66 "
            pdb=" O4'  DC I  66 "
            pdb=" C2'  DC I  66 "
            pdb=" N1   DC I  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.23    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" C4'  DC I  69 "
            pdb=" C5'  DC I  69 "
            pdb=" O4'  DC I  69 "
            pdb=" C3'  DC I  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.32   -0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" C4'  DC I  21 "
            pdb=" C5'  DC I  21 "
            pdb=" O4'  DC I  21 "
            pdb=" C3'  DC I  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.32   -0.21 2.00e-01 2.50e+01 1.07e+00
  ... (remaining 2069 not shown)

  Planarity restraints: 2263
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C  33 "    0.023 9.50e-02 1.11e+02   3.93e-02 3.35e+01
        pdb=" NE  ARG C  33 "   -0.034 2.00e-02 2.50e+03
        pdb=" CZ  ARG C  33 "    0.031 2.00e-02 2.50e+03
        pdb=" NH1 ARG C  33 "    0.072 2.00e-02 2.50e+03
        pdb=" NH2 ARG C  33 "   -0.018 2.00e-02 2.50e+03
        pdb="HH11 ARG C  33 "    0.002 2.00e-02 2.50e+03
        pdb="HH12 ARG C  33 "   -0.073 2.00e-02 2.50e+03
        pdb="HH21 ARG C  33 "   -0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG C  33 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG H  87 "   -0.409 9.50e-02 1.11e+02   1.39e-01 3.28e+01
        pdb=" NE  ARG H  87 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  ARG H  87 "    0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG H  87 "    0.035 2.00e-02 2.50e+03
        pdb=" NH2 ARG H  87 "    0.046 2.00e-02 2.50e+03
        pdb="HH11 ARG H  87 "    0.000 2.00e-02 2.50e+03
        pdb="HH12 ARG H  87 "   -0.018 2.00e-02 2.50e+03
        pdb="HH21 ARG H  87 "    0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG H  87 "   -0.046 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J  60 "   -0.034 2.00e-02 2.50e+03   2.61e-02 1.87e+01
        pdb=" N1   DC J  60 "    0.072 2.00e-02 2.50e+03
        pdb=" C2   DC J  60 "   -0.033 2.00e-02 2.50e+03
        pdb=" O2   DC J  60 "    0.006 2.00e-02 2.50e+03
        pdb=" N3   DC J  60 "    0.003 2.00e-02 2.50e+03
        pdb=" C4   DC J  60 "   -0.002 2.00e-02 2.50e+03
        pdb=" N4   DC J  60 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5   DC J  60 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DC J  60 "    0.002 2.00e-02 2.50e+03
        pdb=" H5   DC J  60 "   -0.006 2.00e-02 2.50e+03
        pdb=" H6   DC J  60 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 2260 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 595
        2.19 -     2.79: 34680
        2.79 -     3.39: 49566
        3.39 -     4.00: 70495
        4.00 -     4.60: 111624
  Nonbonded interactions: 266960
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU E  74 "
            pdb="HD21 ASN F  26 "
     model   vdw
     1.586 2.450
  nonbonded pdb=" OD2 ASP E 107 "
            pdb="HH11 ARG E 132 "
     model   vdw
     1.603 2.450
  nonbonded pdb=" OD2 ASP D  69 "
            pdb=" HH  TYR F  99 "
     model   vdw
     1.611 2.450
  nonbonded pdb=" O   LEU C  86 "
            pdb="HD21 ASN C  90 "
     model   vdw
     1.636 2.450
  nonbonded pdb="HE21 GLN C  25 "
            pdb=" OE1 GLN D  48 "
     model   vdw
     1.651 2.450
  ... (remaining 266955 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'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 25 through 102)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             5.210
  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:             0.120
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.410
  Find NCS groups from input model:        0.170
  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:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
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      :  0.005   0.069  12601  Z= 0.249
  Angle     :  0.912   6.584  18242  Z= 0.589
  Chirality :  0.049   0.238   2072
  Planarity :  0.013   0.152   1318
  Dihedral  : 26.172  85.877   5435
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 1.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  3.22 %
    Favored  : 96.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.27), residues: 736
  helix:  0.46 (0.20), residues: 531
  sheet:  None (None), residues: 0
  loop : -0.33 (0.35), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.027   0.003   ARG E  64 
 TYR   0.020   0.005   TYR G  58 
 PHE   0.017   0.003   PHE D  66 
 HIS   0.012   0.003   HIS D 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 (12601)
  covalent geometry    : angle       0.91167 (18242)
  hydrogen bonds       : bond        0.13252 (  738)
  hydrogen bonds       : angle       3.78051 ( 1831)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.443 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 104
  average time/residue: 0.4276
  time to fit residues: 54.6154
Evaluate side-chains
  55 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
B  26 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.081023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.057021 restraints weight = 69930.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.2898 rms_B_bonded: 1.57
r_work: 0.2766 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2647 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8756
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  12601  Z= 0.228
  Angle     :  0.655   5.933  18242  Z= 0.409
  Chirality :  0.041   0.138   2072
  Planarity :  0.005   0.052   1318
  Dihedral  : 29.181  83.532   3959
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 2.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  5.48 %
    Favored  : 93.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.69 (0.30), residues: 736
  helix:  1.94 (0.23), residues: 536
  sheet:  None (None), residues: 0
  loop : -1.19 (0.34), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H 100 
 TYR   0.011   0.001   TYR F  73 
 PHE   0.014   0.001   PHE D  66 
 HIS   0.005   0.001   HIS E 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 (12601)
  covalent geometry    : angle       0.65512 (18242)
  hydrogen bonds       : bond        0.07281 (  738)
  hydrogen bonds       : angle       3.22556 ( 1831)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.413 
Fit side-chains
REVERT: D   77 GLU cc_start: 0.8926 (tp30) cc_final: 0.8623 (tp30)
REVERT: F   25 ASP cc_start: 0.7788 (t70) cc_final: 0.7501 (t0)
  outliers start: 4
  outliers final: 4
  residues processed: 58
  average time/residue: 0.2101
  time to fit residues: 17.0928
Evaluate side-chains
  57 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain D residue   72 GLU
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain G residue   42 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   chunk 67 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 16 optimal weight:    7.9990
   overall best weight:    1.9588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.080271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.056064 restraints weight = 69331.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 1.55
r_work: 0.2728 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2611 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8780
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  12601  Z= 0.203
  Angle     :  0.614   4.374  18242  Z= 0.386
  Chirality :  0.039   0.140   2072
  Planarity :  0.005   0.047   1318
  Dihedral  : 29.005  80.496   3959
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 1.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  5.48 %
    Favored  : 93.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.81 (0.31), residues: 736
  helix:  2.18 (0.23), residues: 536
  sheet:  None (None), residues: 0
  loop : -1.63 (0.34), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 100 
 TYR   0.009   0.001   TYR F  73 
 PHE   0.012   0.001   PHE D  66 
 HIS   0.004   0.001   HIS E 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 (12601)
  covalent geometry    : angle       0.61416 (18242)
  hydrogen bonds       : bond        0.06721 (  738)
  hydrogen bonds       : angle       3.01305 ( 1831)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.441 
Fit side-chains
REVERT: D   77 GLU cc_start: 0.8930 (tp30) cc_final: 0.8649 (tp30)
REVERT: F   25 ASP cc_start: 0.7725 (t70) cc_final: 0.7475 (t0)
  outliers start: 6
  outliers final: 2
  residues processed: 58
  average time/residue: 0.2743
  time to fit residues: 21.0582
Evaluate side-chains
  52 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 50
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain G residue   42 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 92 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 27 optimal weight:    0.5980
   chunk 96 optimal weight:    5.9990
   chunk 95 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    1.2386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.080664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.056549 restraints weight = 69683.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.2881 rms_B_bonded: 1.55
r_work: 0.2747 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2628 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8768
moved from start:          0.2439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12601  Z= 0.177
  Angle     :  0.595   4.334  18242  Z= 0.377
  Chirality :  0.037   0.138   2072
  Planarity :  0.004   0.051   1318
  Dihedral  : 29.006  80.825   3959
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 1.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  6.28 %
    Favored  : 93.40 %
  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 are not related in a simple way.
  whole:  1.85 (0.31), residues: 736
  helix:  2.24 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -1.73 (0.34), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  72 
 TYR   0.007   0.001   TYR A 100 
 PHE   0.012   0.001   PHE D  66 
 HIS   0.003   0.001   HIS C  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (12601)
  covalent geometry    : angle       0.59517 (18242)
  hydrogen bonds       : bond        0.06194 (  738)
  hydrogen bonds       : angle       2.97294 ( 1831)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 51
  time to evaluate  : 0.440 
Fit side-chains
REVERT: D   77 GLU cc_start: 0.8940 (tp30) cc_final: 0.8670 (tp30)
REVERT: F   25 ASP cc_start: 0.7729 (t70) cc_final: 0.7460 (t0)
  outliers start: 2
  outliers final: 1
  residues processed: 53
  average time/residue: 0.2362
  time to fit residues: 17.6834
Evaluate side-chains
  53 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 52
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   42 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 7 optimal weight:    2.9990
   chunk 93 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 98 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.8986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.078826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.054899 restraints weight = 70256.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.2822 rms_B_bonded: 1.59
r_work: 0.2680 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2559 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8770
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12601  Z= 0.202
  Angle     :  0.592   4.179  18242  Z= 0.372
  Chirality :  0.039   0.139   2072
  Planarity :  0.005   0.049   1318
  Dihedral  : 28.999  81.269   3959
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 1.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  7.73 %
    Favored  : 91.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.81 (0.31), residues: 736
  helix:  2.27 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -1.95 (0.34), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  72 
 TYR   0.008   0.001   TYR A 100 
 PHE   0.013   0.001   PHE D  66 
 HIS   0.004   0.001   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 (12601)
  covalent geometry    : angle       0.59161 (18242)
  hydrogen bonds       : bond        0.06482 (  738)
  hydrogen bonds       : angle       2.95952 ( 1831)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 52
  time to evaluate  : 0.450 
Fit side-chains
REVERT: F   25 ASP cc_start: 0.7728 (t70) cc_final: 0.7460 (t0)
  outliers start: 2
  outliers final: 2
  residues processed: 54
  average time/residue: 0.2685
  time to fit residues: 20.2103
Evaluate side-chains
  52 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 50
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain G residue   42 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 95 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   chunk 73 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 50 optimal weight:    0.5980
   chunk 23 optimal weight:    0.5980
   overall best weight:    1.4384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.080625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.056666 restraints weight = 69663.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.2884 rms_B_bonded: 1.55
r_work: 0.2753 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2636 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8760
moved from start:          0.2786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  12601  Z= 0.180
  Angle     :  0.576   4.193  18242  Z= 0.364
  Chirality :  0.038   0.136   2072
  Planarity :  0.004   0.047   1318
  Dihedral  : 28.979  81.216   3959
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  8.21 %
    Favored  : 91.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.99 (0.31), residues: 736
  helix:  2.42 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -1.95 (0.35), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  72 
 TYR   0.007   0.001   TYR A 100 
 PHE   0.011   0.001   PHE D  66 
 HIS   0.003   0.001   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 (12601)
  covalent geometry    : angle       0.57608 (18242)
  hydrogen bonds       : bond        0.05934 (  738)
  hydrogen bonds       : angle       2.84758 ( 1831)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 52
  time to evaluate  : 0.461 
Fit side-chains
REVERT: E   74 GLU cc_start: 0.8730 (tt0) cc_final: 0.8490 (tt0)
REVERT: F   25 ASP cc_start: 0.7710 (t70) cc_final: 0.7500 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 53
  average time/residue: 0.2940
  time to fit residues: 21.2777
Evaluate side-chains
  52 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   42 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 94 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 71 optimal weight:   10.0000
   chunk 96 optimal weight:    4.9990
   chunk 63 optimal weight:    0.8980
   chunk 92 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 97 optimal weight:    7.9990
   chunk 60 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.077817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.054373 restraints weight = 69836.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.2835 rms_B_bonded: 1.65
r_work: 0.2681 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2557 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8755
moved from start:          0.2910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030  12601  Z= 0.212
  Angle     :  0.593   4.197  18242  Z= 0.373
  Chirality :  0.039   0.134   2072
  Planarity :  0.005   0.050   1318
  Dihedral  : 28.907  82.048   3959
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 1.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  8.37 %
    Favored  : 91.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.78 (0.31), residues: 736
  helix:  2.31 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -2.16 (0.35), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G  72 
 TYR   0.009   0.001   TYR A 100 
 PHE   0.014   0.001   PHE D  66 
 HIS   0.005   0.001   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 (12601)
  covalent geometry    : angle       0.59270 (18242)
  hydrogen bonds       : bond        0.06851 (  738)
  hydrogen bonds       : angle       2.99285 ( 1831)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 54
  time to evaluate  : 0.417 
Fit side-chains
REVERT: E   74 GLU cc_start: 0.8846 (tt0) cc_final: 0.8567 (tt0)
REVERT: F   25 ASP cc_start: 0.7793 (t70) cc_final: 0.7585 (t0)
  outliers start: 3
  outliers final: 3
  residues processed: 56
  average time/residue: 0.2473
  time to fit residues: 19.0388
Evaluate side-chains
  55 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   72 GLU
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain G residue   42 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 78 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 49 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 83 optimal weight:    5.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.078381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.054717 restraints weight = 69164.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.2822 rms_B_bonded: 1.57
r_work: 0.2680 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2559 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.2946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12601  Z= 0.166
  Angle     :  0.577   4.263  18242  Z= 0.365
  Chirality :  0.036   0.136   2072
  Planarity :  0.004   0.053   1318
  Dihedral  : 28.901  82.218   3959
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 1.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  8.21 %
    Favored  : 91.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.90 (0.31), residues: 736
  helix:  2.40 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -2.11 (0.35), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  43 
 TYR   0.007   0.001   TYR A 100 
 PHE   0.013   0.001   PHE D  66 
 HIS   0.003   0.001   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (12601)
  covalent geometry    : angle       0.57657 (18242)
  hydrogen bonds       : bond        0.06176 (  738)
  hydrogen bonds       : angle       2.89882 ( 1831)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 53
  time to evaluate  : 0.388 
Fit side-chains
REVERT: E   74 GLU cc_start: 0.8841 (tt0) cc_final: 0.8554 (tt0)
REVERT: F   25 ASP cc_start: 0.7806 (t70) cc_final: 0.7576 (t0)
REVERT: H   72 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8292 (tm-30)
  outliers start: 2
  outliers final: 1
  residues processed: 54
  average time/residue: 0.2595
  time to fit residues: 19.0196
Evaluate side-chains
  54 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   42 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 90 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    1.3584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.078438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.054731 restraints weight = 69746.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.2823 rms_B_bonded: 1.57
r_work: 0.2679 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2558 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.2970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  12601  Z= 0.177
  Angle     :  0.575   5.348  18242  Z= 0.363
  Chirality :  0.037   0.136   2072
  Planarity :  0.004   0.052   1318
  Dihedral  : 28.900  82.193   3959
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 1.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  7.89 %
    Favored  : 91.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.94 (0.31), residues: 736
  helix:  2.44 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -2.13 (0.35), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G  72 
 TYR   0.007   0.001   TYR A 100 
 PHE   0.012   0.001   PHE D  66 
 HIS   0.003   0.001   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (12601)
  covalent geometry    : angle       0.57512 (18242)
  hydrogen bonds       : bond        0.06183 (  738)
  hydrogen bonds       : angle       2.87987 ( 1831)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 52
  time to evaluate  : 0.421 
Fit side-chains
REVERT: E   74 GLU cc_start: 0.8857 (tt0) cc_final: 0.8557 (tt0)
REVERT: F   25 ASP cc_start: 0.7810 (t70) cc_final: 0.7579 (t0)
REVERT: H   72 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8285 (tm-30)
  outliers start: 2
  outliers final: 2
  residues processed: 54
  average time/residue: 0.2798
  time to fit residues: 20.7853
Evaluate side-chains
  54 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 52
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain G residue   42 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 95 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 92 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.7788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.078474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.054755 restraints weight = 69758.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.2824 rms_B_bonded: 1.57
r_work: 0.2682 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2561 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8691
moved from start:          0.3043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  12601  Z= 0.192
  Angle     :  0.578   4.947  18242  Z= 0.364
  Chirality :  0.038   0.135   2072
  Planarity :  0.004   0.053   1318
  Dihedral  : 28.860  82.114   3959
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 1.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  8.21 %
    Favored  : 91.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.93 (0.31), residues: 736
  helix:  2.46 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -2.23 (0.34), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G  72 
 TYR   0.008   0.001   TYR A 100 
 PHE   0.012   0.001   PHE D  66 
 HIS   0.005   0.001   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 (12601)
  covalent geometry    : angle       0.57812 (18242)
  hydrogen bonds       : bond        0.06189 (  738)
  hydrogen bonds       : angle       2.86430 ( 1831)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 53
  time to evaluate  : 0.445 
Fit side-chains
REVERT: E   74 GLU cc_start: 0.8841 (tt0) cc_final: 0.8533 (tt0)
REVERT: H   72 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8261 (tm-30)
  outliers start: 2
  outliers final: 2
  residues processed: 54
  average time/residue: 0.2261
  time to fit residues: 16.8342
Evaluate side-chains
  55 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 53
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain G residue   42 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 88 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 73 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 96 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   overall best weight:    1.2986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.078646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.054950 restraints weight = 69797.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.2830 rms_B_bonded: 1.57
r_work: 0.2687 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2567 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
moved from start:          0.3063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027  12601  Z= 0.173
  Angle     :  0.576   5.294  18242  Z= 0.363
  Chirality :  0.037   0.135   2072
  Planarity :  0.004   0.052   1318
  Dihedral  : 28.856  82.218   3959
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 1.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  7.73 %
    Favored  : 91.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.97 (0.31), residues: 736
  helix:  2.48 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -2.20 (0.35), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G  72 
 TYR   0.007   0.001   TYR A 100 
 PHE   0.011   0.001   PHE D  66 
 HIS   0.003   0.001   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (12601)
  covalent geometry    : angle       0.57565 (18242)
  hydrogen bonds       : bond        0.06017 (  738)
  hydrogen bonds       : angle       2.84623 ( 1831)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5129.86 seconds
wall clock time: 87 minutes 22.66 seconds (5242.66 seconds total)