Starting phenix.real_space_refine
on Thu Mar  5 06:10:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6j99_9783/03_2026/6j99_9783.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6j99_9783/03_2026/6j99_9783.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6j99_9783/03_2026/6j99_9783.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6j99_9783/03_2026/6j99_9783.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6j99_9783/03_2026/6j99_9783.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6j99_9783/03_2026/6j99_9783.map"
  }
  resolution = 4.1
  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=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5830 atoms to isotropic.
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     289      5.49       5
     S      29      5.16       5
     C    8711      2.51       5
     N    2824      2.21       5
     O    3413      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15266
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 698
          Classifications: {'peptide': 86}
          Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 83}
    Chain: "C"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 834
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 738
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 738
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 648
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 648
          Classifications: {'peptide': 81}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "G"
      Number of atoms: 809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 809
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 742
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 742
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 2935
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 2935
          Classifications: {'DNA': 144}
          Link IDs: {'rna3p': 143}
    Chain: "J"
      Number of atoms: 2990
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2990
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "L"
      Number of atoms: 603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 603
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "K"
      Number of atoms: 2665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 325, 2665
          Classifications: {'peptide': 325}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 306}
          Chain breaks: 1
  Time building chain proxies: 3.36, per 1000 atoms: 0.22
  Number of scatterers: 15266
  At special positions: 0
  Unit cell: (132.6, 137.8, 114.4, 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      29     16.00
     P     289     15.00
     O    3413      8.00
     N    2824      7.00
     C    8711      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 4.01
  Conformation dependent library (CDL) restraints added in 363.2 milliseconds
  

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2194

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 10 sheets defined
      62.3% alpha, 3.9% beta
      143 base pairs and 248 stacking pairs defined.
    Time for finding SS restraints: 2.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 4.928A  pdb=" N   GLU A  50 " --> pdb=" O   VAL A  46 " (cutoff:3.500A)
      removed outlier: 6.171A  pdb=" N   ARG A  53 " --> pdb=" O   ARG A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.508A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.841A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.794A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.649A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.347A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.793A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 101 through 120
      removed outlier: 3.973A  pdb=" N   SER D 109 " --> pdb=" O   LYS D 105 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   SER D 120 " --> pdb=" O   THR D 116 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 4.928A  pdb=" N   GLU E  50 " --> pdb=" O   VAL E  46 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   ARG E  53 " --> pdb=" O   ARG E  49 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.507A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.840A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.749A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.852A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.651A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ASN G  68 " --> pdb=" O   GLU G  64 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ALA G  69 " --> pdb=" O   LEU G  65 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 91 through 97
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 121
    Processing helix  chain 'L' and resid 22 through 35
      removed outlier: 3.588A  pdb=" N   VAL L  26 " --> pdb=" O   THR L  22 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 32 through 46
      removed outlier: 3.548A  pdb=" N   ILE K  37 " --> pdb=" O   ALA K  33 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ILE K  38 " --> pdb=" O   ALA K  34 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 51 through 56
    Processing helix  chain 'K' and resid 67 through 90
    Processing helix  chain 'K' and resid 103 through 119
    Processing helix  chain 'K' and resid 121 through 127
      removed outlier: 3.625A  pdb=" N   LEU K 125 " --> pdb=" O   ASP K 121 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 140 through 151
      removed outlier: 4.054A  pdb=" N   VAL K 144 " --> pdb=" O   SER K 140 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 167 through 177
    Processing helix  chain 'K' and resid 188 through 209
    Processing helix  chain 'K' and resid 225 through 235
    Processing helix  chain 'K' and resid 241 through 245
      removed outlier: 4.552A  pdb=" N   ALA K 244 " --> pdb=" O   ASN K 241 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 246 through 258
    Processing helix  chain 'K' and resid 281 through 285
      removed outlier: 3.960A  pdb=" N   LEU K 284 " --> pdb=" O   SER K 281 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   SER K 285 " --> pdb=" O   ARG K 282 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 281 through 285'
    Processing helix  chain 'K' and resid 287 through 289
      No H-bonds generated for 'chain 'K' and resid 287 through 289'
    Processing helix  chain 'K' and resid 319 through 331
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.398A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97
      removed outlier: 6.260A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.448A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.089A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 6
      removed outlier: 3.639A  pdb=" N   LEU L  69 " --> pdb=" O   LYS L   6 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'K' and resid 217 through 218
      removed outlier: 6.583A  pdb=" N   HIS K 182 " --> pdb=" O   THR K 217 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   PHE K 159 " --> pdb=" O   TYR K 183 " (cutoff:3.500A)
      removed outlier: 8.449A  pdb=" N   VAL K 185 " --> pdb=" O   PHE K 159 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ASP K 161 " --> pdb=" O   VAL K 185 " (cutoff:3.500A)
      removed outlier: 5.710A  pdb=" N   VAL K 160 " --> pdb=" O   PHE K 239 " (cutoff:3.500A)
      removed outlier: 5.891A  pdb=" N   ILE K 238 " --> pdb=" O   VAL K 267 " (cutoff:3.500A)

    521 hydrogen bonds defined for protein.
    1542 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      366 hydrogen bonds
      728 hydrogen bond angles
      0 basepair planarities
      143 basepair parallelities
      248 stacking parallelities
  Total time for adding SS restraints: 2.37

  Time building geometry restraints manager: 1.80 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2782
        1.33 -     1.45: 5098
        1.45 -     1.57: 7638
        1.57 -     1.69: 577
        1.69 -     1.81: 50
  Bond restraints: 16145
  Sorted by residual:
  bond pdb=" C8  SAH K 501 "
       pdb=" N7  SAH K 501 "
    ideal  model  delta    sigma   weight residual
    1.299  1.357 -0.058 2.00e-02 2.50e+03 8.29e+00
  bond pdb=" C2  SAH K 501 "
       pdb=" N3  SAH K 501 "
    ideal  model  delta    sigma   weight residual
    1.322  1.367 -0.045 2.00e-02 2.50e+03 5.02e+00
  bond pdb=" C3'  DT J  15 "
       pdb=" O3'  DT J  15 "
    ideal  model  delta    sigma   weight residual
    1.422  1.488 -0.066 3.00e-02 1.11e+03 4.78e+00
  bond pdb=" C3'  DC J 126 "
       pdb=" O3'  DC J 126 "
    ideal  model  delta    sigma   weight residual
    1.422  1.487 -0.065 3.00e-02 1.11e+03 4.74e+00
  bond pdb=" C   LYS B  31 "
       pdb=" N   PRO B  32 "
    ideal  model  delta    sigma   weight residual
    1.337  1.361 -0.024 1.24e-02 6.50e+03 3.78e+00
  ... (remaining 16140 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 22306
        2.38 -     4.76: 680
        4.76 -     7.14: 47
        7.14 -     9.52: 18
        9.52 -    11.90: 4
  Bond angle restraints: 23055
  Sorted by residual:
  angle pdb=" C   LEU K 299 "
        pdb=" N   LYS K 300 "
        pdb=" CA  LYS K 300 "
      ideal   model   delta    sigma   weight residual
     121.70  132.86  -11.16 1.80e+00 3.09e-01 3.84e+01
  angle pdb=" N   GLY L  75 "
        pdb=" CA  GLY L  75 "
        pdb=" C   GLY L  75 "
      ideal   model   delta    sigma   weight residual
     113.18  102.30   10.88 2.37e+00 1.78e-01 2.11e+01
  angle pdb=" C   THR B  30 "
        pdb=" N   LYS B  31 "
        pdb=" CA  LYS B  31 "
      ideal   model   delta    sigma   weight residual
     120.97  127.28   -6.31 1.48e+00 4.57e-01 1.82e+01
  angle pdb=" C   ARG E  49 "
        pdb=" N   GLU E  50 "
        pdb=" CA  GLU E  50 "
      ideal   model   delta    sigma   weight residual
     126.45  133.50   -7.05 1.77e+00 3.19e-01 1.59e+01
  angle pdb=" C   ARG A  49 "
        pdb=" N   GLU A  50 "
        pdb=" CA  GLU A  50 "
      ideal   model   delta    sigma   weight residual
     126.45  133.46   -7.01 1.77e+00 3.19e-01 1.57e+01
  ... (remaining 23050 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.05: 7058
       30.05 -    60.09: 1830
       60.09 -    90.14: 85
       90.14 -   120.18: 1
      120.18 -   150.23: 2
  Dihedral angle restraints: 8976
    sinusoidal: 5583
      harmonic: 3393
  Sorted by residual:
  dihedral pdb=" CA  PRO H 100 "
           pdb=" C   PRO H 100 "
           pdb=" N   GLY H 101 "
           pdb=" CA  GLY H 101 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -145.87  -34.13     0      5.00e+00 4.00e-02 4.66e+01
  dihedral pdb=" CA  SER K 304 "
           pdb=" C   SER K 304 "
           pdb=" N   TRP K 305 "
           pdb=" CA  TRP K 305 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.77   31.23     0      5.00e+00 4.00e-02 3.90e+01
  dihedral pdb=" CA  ARG L  74 "
           pdb=" C   ARG L  74 "
           pdb=" N   GLY L  75 "
           pdb=" CA  GLY L  75 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.47   29.53     0      5.00e+00 4.00e-02 3.49e+01
  ... (remaining 8973 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1840
       0.050 -    0.100: 620
       0.100 -    0.150: 121
       0.150 -    0.200: 21
       0.200 -    0.250: 5
  Chirality restraints: 2607
  Sorted by residual:
  chirality pdb=" P    DT J  83 "
            pdb=" OP1  DT J  83 "
            pdb=" OP2  DT J  83 "
            pdb=" O5'  DT J  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.60   -0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" C1'  DG J  82 "
            pdb=" O4'  DG J  82 "
            pdb=" C2'  DG J  82 "
            pdb=" N9   DG J  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    2.18    0.23 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CB  ILE L  13 "
            pdb=" CA  ILE L  13 "
            pdb=" CG1 ILE L  13 "
            pdb=" CG2 ILE L  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.21 2.00e-01 2.50e+01 1.15e+00
  ... (remaining 2604 not shown)

  Planarity restraints: 1920
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR E  45 "    0.014 2.00e-02 2.50e+03   2.87e-02 8.22e+00
        pdb=" C   THR E  45 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   THR E  45 "    0.019 2.00e-02 2.50e+03
        pdb=" N   VAL E  46 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A  50 "    0.014 2.00e-02 2.50e+03   2.84e-02 8.05e+00
        pdb=" C   GLU A  50 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   GLU A  50 "    0.018 2.00e-02 2.50e+03
        pdb=" N   ILE A  51 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU E  50 "   -0.014 2.00e-02 2.50e+03   2.83e-02 8.01e+00
        pdb=" C   GLU E  50 "    0.049 2.00e-02 2.50e+03
        pdb=" O   GLU E  50 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   ILE E  51 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1917 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1901
        2.74 -     3.28: 14252
        3.28 -     3.82: 32196
        3.82 -     4.36: 36012
        4.36 -     4.90: 51791
  Nonbonded interactions: 136152
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 123 "
            pdb=" NE2 HIS E 113 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" OG1 THR H  87 "
            pdb=" OE1 GLU H  90 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OD1 ASN K 242 "
            pdb=" OG  SER K 269 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O2   DC I  95 "
            pdb=" N2   DG J  53 "
     model   vdw
     2.260 2.496
  nonbonded pdb=" OH  TYR D  37 "
            pdb=" OP1  DG J 122 "
     model   vdw
     2.271 3.040
  ... (remaining 136147 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' and resid 21 through 101)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 13 through 117)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 28 through 120)
  selection = (chain 'H' and resid 28 through 120)
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.060
  Process input model:                     15.270
  Find NCS groups from input model:        0.140
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5209
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      :  0.008   0.066  16146  Z= 0.363
  Angle     :  0.978  11.900  23055  Z= 0.559
  Chirality :  0.051   0.250   2607
  Planarity :  0.007   0.066   1920
  Dihedral  : 27.095 150.230   6782
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -2.88 (0.21), residues: 1143
  helix: -1.35 (0.16), residues: 694
  sheet: -3.97 (0.63), residues: 37
  loop : -2.49 (0.28), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG K  80 
 TYR   0.041   0.004   TYR G  39 
 PHE   0.027   0.004   PHE K 245 
 TRP   0.024   0.004   TRP K 228 
 HIS   0.019   0.003   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00791 (16145)
  covalent geometry    : angle       0.97848 (23055)
  hydrogen bonds       : bond        0.12316 (  887)
  hydrogen bonds       : angle       5.58243 ( 2270)
  Misc. bond           : bond        0.00203 (    1)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  379 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 379
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.5261 (mt) cc_final: 0.4373 (mt)
REVERT: A   93 GLN cc_start: 0.4178 (tt0) cc_final: 0.3885 (tt0)
REVERT: C   57 TYR cc_start: 0.8736 (t80) cc_final: 0.8101 (t80)
REVERT: C   75 LYS cc_start: 0.7886 (mmtp) cc_final: 0.7655 (mmtt)
REVERT: D   90 GLU cc_start: 0.7424 (mp0) cc_final: 0.7196 (mp0)
REVERT: D  106 HIS cc_start: 0.7983 (m-70) cc_final: 0.7263 (m-70)
REVERT: G   68 ASN cc_start: 0.8396 (m-40) cc_final: 0.8071 (m-40)
REVERT: G   72 ASP cc_start: 0.9244 (m-30) cc_final: 0.8871 (m-30)
REVERT: G  115 LEU cc_start: 0.6386 (mt) cc_final: 0.5924 (tt)
REVERT: H   90 GLU cc_start: 0.6324 (mp0) cc_final: 0.5989 (mt-10)
REVERT: H  100 PRO cc_start: 0.4871 (Cg_endo) cc_final: 0.4579 (Cg_exo)
REVERT: L    1 MET cc_start: 0.2615 (ttp) cc_final: 0.1894 (ttt)
REVERT: L    6 LYS cc_start: 0.8999 (tttt) cc_final: 0.8753 (tptt)
REVERT: L   71 LEU cc_start: 0.8587 (mp) cc_final: 0.7850 (mt)
REVERT: K   53 LEU cc_start: 0.5821 (tp) cc_final: 0.5537 (pp)
REVERT: K   66 LYS cc_start: 0.7634 (mppt) cc_final: 0.7180 (pttt)
REVERT: K   96 MET cc_start: -0.0461 (ttp) cc_final: -0.1120 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 379
  average time/residue: 0.1664
  time to fit residues: 83.1159
Evaluate side-chains
  237 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:   30.0000
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    9.9990
   overall best weight:    4.3388

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  18 HIS
** C  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 ASN
** C  94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  79 HIS
D  81 ASN
** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
F  25 ASN
G  31 HIS
K  35 HIS
K 112 GLN
K 126 ASN
K 146 GLN
K 213 HIS
K 234 ASN
K 251 HIS
K 252 GLN
K 315 HIS
K 331 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.166225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.136239 restraints weight = 53630.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.139108 restraints weight = 32446.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.140848 restraints weight = 23162.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.141968 restraints weight = 18898.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.142631 restraints weight = 16818.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.4158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6697
moved from start:          0.6401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.122  16146  Z= 0.348
  Angle     :  0.994  16.145  23055  Z= 0.544
  Chirality :  0.051   0.266   2607
  Planarity :  0.008   0.060   1920
  Dihedral  : 32.360 148.779   4447
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 24.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  6.31 %
    Favored  : 93.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.18 %
    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 (0.23), residues: 1143
  helix: -0.47 (0.18), residues: 697
  sheet: -3.21 (0.60), residues: 53
  loop : -2.29 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG E 129 
 TYR   0.043   0.003   TYR B  51 
 PHE   0.061   0.005   PHE E  67 
 TRP   0.028   0.003   TRP K 205 
 HIS   0.010   0.003   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00770 (16145)
  covalent geometry    : angle       0.99398 (23055)
  hydrogen bonds       : bond        0.08269 (  887)
  hydrogen bonds       : angle       5.05600 ( 2270)
  Misc. bond           : bond        0.00162 (    1)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  366 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 365
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 TYR cc_start: 0.6458 (m-10) cc_final: 0.6082 (m-80)
REVERT: A   62 ILE cc_start: 0.8250 (mt) cc_final: 0.7970 (mt)
REVERT: A   93 GLN cc_start: 0.7907 (tt0) cc_final: 0.7638 (tt0)
REVERT: B   52 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6360 (mp0)
REVERT: B   88 TYR cc_start: 0.8635 (m-80) cc_final: 0.8427 (m-80)
REVERT: C   15 LYS cc_start: 0.6464 (tmtt) cc_final: 0.5998 (mmtm)
REVERT: C   75 LYS cc_start: 0.7960 (mmtp) cc_final: 0.7628 (mmmt)
REVERT: D   80 TYR cc_start: 0.8136 (m-10) cc_final: 0.7281 (m-10)
REVERT: D   82 LYS cc_start: 0.8912 (mtpt) cc_final: 0.8590 (mmtt)
REVERT: D   96 ARG cc_start: 0.8243 (ttm170) cc_final: 0.7986 (mtp85)
REVERT: D  106 HIS cc_start: 0.7777 (m-70) cc_final: 0.6773 (m-70)
REVERT: E   82 LEU cc_start: 0.5711 (mt) cc_final: 0.5487 (mt)
REVERT: E   99 TYR cc_start: 0.9285 (t80) cc_final: 0.8644 (t80)
REVERT: E  106 ASP cc_start: 0.8644 (m-30) cc_final: 0.7920 (m-30)
REVERT: E  123 ASP cc_start: 0.7848 (m-30) cc_final: 0.7549 (m-30)
REVERT: F   80 THR cc_start: 0.6483 (m) cc_final: 0.5692 (p)
REVERT: F   84 MET cc_start: 0.8593 (mmp) cc_final: 0.7228 (mmm)
REVERT: G   82 HIS cc_start: 0.8257 (m170) cc_final: 0.7905 (m90)
REVERT: G  104 GLN cc_start: 0.8331 (mp10) cc_final: 0.8007 (mp10)
REVERT: L    1 MET cc_start: 0.2080 (ttp) cc_final: 0.1329 (ttt)
REVERT: L   24 GLU cc_start: 0.8317 (tt0) cc_final: 0.7649 (mm-30)
REVERT: L   39 ASP cc_start: 0.7864 (p0) cc_final: 0.7547 (p0)
REVERT: K   66 LYS cc_start: 0.7981 (mppt) cc_final: 0.7529 (pttt)
REVERT: K   96 MET cc_start: 0.0927 (ttp) cc_final: -0.0312 (tpt)
REVERT: K  173 VAL cc_start: 0.9062 (t) cc_final: 0.8814 (m)
REVERT: K  179 CYS cc_start: 0.3439 (m) cc_final: 0.2953 (m)
REVERT: K  205 TRP cc_start: 0.7585 (m100) cc_final: 0.7252 (m100)
REVERT: K  278 ARG cc_start: 0.6931 (tmt170) cc_final: 0.6714 (tmt170)
REVERT: K  289 THR cc_start: 0.8102 (p) cc_final: 0.7862 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 366
  average time/residue: 0.1510
  time to fit residues: 75.3601
Evaluate side-chains
  274 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 274
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 133 optimal weight:   30.0000
   chunk 99 optimal weight:   10.0000
   chunk 44 optimal weight:    0.7980
   chunk 112 optimal weight:    6.9990
   chunk 87 optimal weight:   10.0000
   chunk 93 optimal weight:    7.9990
   chunk 92 optimal weight:    4.9990
   chunk 82 optimal weight:    7.9990
   chunk 38 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 0 optimal weight:    9.9990
   overall best weight:    3.7386

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  93 GLN
C  24 GLN
C  68 ASN
C 112 GLN
D  60 ASN
D  81 ASN
D 106 HIS
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  68 ASN
H  46 HIS
L  49 GLN
K 241 ASN
** K 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.150397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.119171 restraints weight = 50773.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.122009 restraints weight = 28880.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.123691 restraints weight = 20125.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.124703 restraints weight = 16308.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.125124 restraints weight = 14453.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7208
moved from start:          0.9190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.076  16146  Z= 0.307
  Angle     :  0.891  16.299  23055  Z= 0.489
  Chirality :  0.048   0.276   2607
  Planarity :  0.008   0.140   1920
  Dihedral  : 32.243 148.618   4447
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 22.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  5.51 %
    Favored  : 93.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.18 %
    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: -1.36 (0.23), residues: 1143
  helix: -0.10 (0.18), residues: 717
  sheet: -2.16 (0.95), residues: 28
  loop : -2.22 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.031   0.001   ARG F  92 
 TYR   0.046   0.003   TYR B  51 
 PHE   0.046   0.003   PHE F 100 
 TRP   0.017   0.002   TRP K 305 
 HIS   0.014   0.002   HIS K 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00677 (16145)
  covalent geometry    : angle       0.89068 (23055)
  hydrogen bonds       : bond        0.06724 (  887)
  hydrogen bonds       : angle       4.51582 ( 2270)
  Misc. bond           : bond        0.00066 (    1)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  391 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 383
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 TYR cc_start: 0.7166 (m-10) cc_final: 0.6538 (m-80)
REVERT: A   60 LEU cc_start: 0.8433 (mp) cc_final: 0.8111 (mm)
REVERT: A   90 MET cc_start: 0.8242 (ppp) cc_final: 0.7813 (tmm)
REVERT: A   93 GLN cc_start: 0.8441 (tt0) cc_final: 0.7810 (tt0)
REVERT: B   67 ARG cc_start: 0.8945 (ttm110) cc_final: 0.8655 (ttm110)
REVERT: B   91 LYS cc_start: 0.9171 (tptt) cc_final: 0.8876 (tttp)
REVERT: B   95 ARG cc_start: 0.8954 (ptp-110) cc_final: 0.8615 (ptp-110)
REVERT: B  100 PHE cc_start: 0.8626 (m-10) cc_final: 0.8162 (m-10)
REVERT: C   33 LEU cc_start: 0.9085 (mt) cc_final: 0.8865 (mt)
REVERT: C   56 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8109 (mm-30)
REVERT: C   75 LYS cc_start: 0.8586 (mmtp) cc_final: 0.7922 (mmmm)
REVERT: D   73 GLU cc_start: 0.8082 (tp30) cc_final: 0.7730 (tp30)
REVERT: D  103 LEU cc_start: 0.9163 (tp) cc_final: 0.8707 (tp)
REVERT: D  106 HIS cc_start: 0.7847 (m90) cc_final: 0.7491 (m90)
REVERT: E   51 ILE cc_start: 0.6437 (mt) cc_final: 0.5635 (mt)
REVERT: E   55 GLN cc_start: 0.7956 (pp30) cc_final: 0.7576 (pp30)
REVERT: E   85 GLN cc_start: 0.7560 (tt0) cc_final: 0.7297 (tt0)
REVERT: E   94 GLU cc_start: 0.9083 (tp30) cc_final: 0.8766 (tm-30)
REVERT: E   99 TYR cc_start: 0.9102 (t80) cc_final: 0.8684 (t80)
REVERT: E  120 MET cc_start: 0.7706 (pmm) cc_final: 0.7289 (mtm)
REVERT: E  122 LYS cc_start: 0.8437 (pttp) cc_final: 0.7845 (ptpp)
REVERT: F   29 ILE cc_start: 0.5715 (mm) cc_final: 0.5396 (mm)
REVERT: F   39 ARG cc_start: 0.7527 (mpt180) cc_final: 0.7244 (mmp80)
REVERT: F   97 LEU cc_start: 0.9278 (tp) cc_final: 0.8970 (tp)
REVERT: G   75 LYS cc_start: 0.8306 (mmtt) cc_final: 0.7999 (mmtt)
REVERT: G   82 HIS cc_start: 0.8486 (m170) cc_final: 0.7904 (m90)
REVERT: H   76 ARG cc_start: 0.8512 (ttm110) cc_final: 0.8044 (ttm110)
REVERT: L    1 MET cc_start: 0.1791 (ttp) cc_final: 0.0839 (ttt)
REVERT: L   62 GLN cc_start: 0.7702 (tp40) cc_final: 0.7399 (tp40)
REVERT: K   53 LEU cc_start: 0.6152 (tp) cc_final: 0.5521 (mt)
REVERT: K   55 MET cc_start: 0.7769 (mmp) cc_final: 0.7415 (mtm)
REVERT: K   66 LYS cc_start: 0.8086 (mppt) cc_final: 0.7574 (pttt)
REVERT: K   96 MET cc_start: 0.0508 (ttp) cc_final: -0.0647 (tpt)
REVERT: K  170 VAL cc_start: 0.6240 (t) cc_final: 0.5872 (t)
REVERT: K  205 TRP cc_start: 0.7363 (m100) cc_final: 0.7157 (m100)
REVERT: K  281 SER cc_start: 0.9246 (t) cc_final: 0.8815 (m)
  outliers start: 8
  outliers final: 2
  residues processed: 385
  average time/residue: 0.1540
  time to fit residues: 81.3187
Evaluate side-chains
  307 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 305
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 88 optimal weight:   10.0000
   chunk 18 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 52 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 60 optimal weight:    7.9990
   chunk 71 optimal weight:    8.9990
   chunk 6 optimal weight:    0.7980
   chunk 102 optimal weight:   20.0000
   chunk 3 optimal weight:    0.7980
   chunk 101 optimal weight:    3.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 113 HIS
A 125 GLN
B  25 ASN
B  75 HIS
** C  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 ASN
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  92 GLN
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  84 GLN
** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  46 HIS
K 234 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.153068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.122512 restraints weight = 50120.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.125475 restraints weight = 27952.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.127302 restraints weight = 19285.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.128380 restraints weight = 15417.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.128914 restraints weight = 13598.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7121
moved from start:          0.9631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  16146  Z= 0.172
  Angle     :  0.693  12.529  23055  Z= 0.392
  Chirality :  0.042   0.247   2607
  Planarity :  0.005   0.060   1920
  Dihedral  : 32.005 146.240   4447
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 16.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.18 %
    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: -0.65 (0.24), residues: 1143
  helix:  0.60 (0.19), residues: 712
  sheet: -2.87 (0.68), residues: 48
  loop : -2.04 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  92 
 TYR   0.030   0.002   TYR B  51 
 PHE   0.062   0.002   PHE E  67 
 TRP   0.007   0.001   TRP K 208 
 HIS   0.004   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (16145)
  covalent geometry    : angle       0.69280 (23055)
  hydrogen bonds       : bond        0.04984 (  887)
  hydrogen bonds       : angle       3.98766 ( 2270)
  Misc. bond           : bond        0.00018 (    1)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  374 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 374
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.8178 (mp) cc_final: 0.7729 (mm)
REVERT: A   93 GLN cc_start: 0.8163 (tt0) cc_final: 0.7628 (tt0)
REVERT: B   74 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7899 (mt-10)
REVERT: B   91 LYS cc_start: 0.9049 (tptt) cc_final: 0.8825 (tttp)
REVERT: B   95 ARG cc_start: 0.8887 (ptp-110) cc_final: 0.8523 (ptp-110)
REVERT: C   24 GLN cc_start: 0.7674 (tt0) cc_final: 0.7275 (tt0)
REVERT: C   33 LEU cc_start: 0.9077 (mt) cc_final: 0.8751 (mt)
REVERT: C   54 VAL cc_start: 0.9562 (t) cc_final: 0.9223 (p)
REVERT: C   75 LYS cc_start: 0.8542 (mmtp) cc_final: 0.7957 (mmmm)
REVERT: D   82 LYS cc_start: 0.9168 (mtmt) cc_final: 0.8720 (mmtt)
REVERT: D   92 GLN cc_start: 0.8673 (pt0) cc_final: 0.8291 (pt0)
REVERT: D  103 LEU cc_start: 0.9046 (tp) cc_final: 0.8790 (tp)
REVERT: D  106 HIS cc_start: 0.7912 (m90) cc_final: 0.7314 (m90)
REVERT: E   55 GLN cc_start: 0.7926 (pp30) cc_final: 0.7466 (pp30)
REVERT: E   68 GLN cc_start: 0.8258 (pt0) cc_final: 0.7948 (mp10)
REVERT: E   85 GLN cc_start: 0.7842 (tt0) cc_final: 0.7428 (tt0)
REVERT: E   99 TYR cc_start: 0.9119 (t80) cc_final: 0.8428 (t80)
REVERT: F   29 ILE cc_start: 0.5866 (mm) cc_final: 0.5601 (mm)
REVERT: F   84 MET cc_start: 0.8763 (mmp) cc_final: 0.8265 (mmp)
REVERT: F   92 ARG cc_start: 0.7909 (tmm160) cc_final: 0.7265 (ttp80)
REVERT: G   75 LYS cc_start: 0.8351 (mmtt) cc_final: 0.7914 (mmtt)
REVERT: G   76 THR cc_start: 0.9006 (p) cc_final: 0.8687 (t)
REVERT: G   78 ILE cc_start: 0.6290 (mt) cc_final: 0.6025 (mt)
REVERT: G   82 HIS cc_start: 0.8457 (m170) cc_final: 0.7950 (m90)
REVERT: G   84 GLN cc_start: 0.8178 (tp-100) cc_final: 0.7635 (tm-30)
REVERT: L    1 MET cc_start: 0.2093 (ttp) cc_final: 0.1347 (ttt)
REVERT: L   62 GLN cc_start: 0.7891 (tp40) cc_final: 0.7584 (tp40)
REVERT: K   53 LEU cc_start: 0.6022 (tp) cc_final: 0.5584 (mt)
REVERT: K   66 LYS cc_start: 0.8036 (mppt) cc_final: 0.7561 (pttt)
REVERT: K   96 MET cc_start: 0.0228 (ttp) cc_final: -0.0749 (tpt)
REVERT: K  205 TRP cc_start: 0.7345 (m100) cc_final: 0.7048 (m100)
REVERT: K  248 GLU cc_start: 0.8491 (tt0) cc_final: 0.8226 (mp0)
REVERT: K  281 SER cc_start: 0.9151 (t) cc_final: 0.8697 (m)
REVERT: K  295 GLU cc_start: 0.6973 (tm-30) cc_final: 0.6729 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 374
  average time/residue: 0.1516
  time to fit residues: 77.6744
Evaluate side-chains
  297 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 297
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 47 optimal weight:    5.9990
   chunk 44 optimal weight:    0.7980
   chunk 18 optimal weight:    5.9990
   chunk 87 optimal weight:   10.0000
   chunk 59 optimal weight:    0.8980
   chunk 42 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 45 optimal weight:    7.9990
   chunk 72 optimal weight:   10.0000
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  46 HIS
L  49 GLN
K 213 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.152290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.122072 restraints weight = 50043.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.125026 restraints weight = 27312.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.126802 restraints weight = 18706.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 68)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.127851 restraints weight = 14971.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.128371 restraints weight = 13228.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7123
moved from start:          1.0019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  16146  Z= 0.173
  Angle     :  0.685  11.255  23055  Z= 0.385
  Chirality :  0.040   0.185   2607
  Planarity :  0.005   0.073   1920
  Dihedral  : 31.701 145.780   4447
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 16.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.18 %
    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: -0.35 (0.25), residues: 1143
  helix:  0.87 (0.19), residues: 709
  sheet: -2.13 (0.89), residues: 38
  loop : -2.08 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B  92 
 TYR   0.034   0.002   TYR B  51 
 PHE   0.019   0.002   PHE D  62 
 TRP   0.008   0.001   TRP K 208 
 HIS   0.004   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (16145)
  covalent geometry    : angle       0.68544 (23055)
  hydrogen bonds       : bond        0.04643 (  887)
  hydrogen bonds       : angle       3.83379 ( 2270)
  Misc. bond           : bond        0.00022 (    1)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  371 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 371
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.8441 (mp) cc_final: 0.7988 (mm)
REVERT: A   86 SER cc_start: 0.8547 (p) cc_final: 0.8323 (p)
REVERT: A   90 MET cc_start: 0.8278 (ppp) cc_final: 0.7855 (tmm)
REVERT: A   93 GLN cc_start: 0.8296 (tt0) cc_final: 0.7901 (tt0)
REVERT: B   59 LYS cc_start: 0.8761 (tttt) cc_final: 0.8395 (tppt)
REVERT: B   63 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8000 (mt-10)
REVERT: B   67 ARG cc_start: 0.9056 (ttm110) cc_final: 0.8785 (ttm110)
REVERT: B   74 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7900 (mt-10)
REVERT: B   95 ARG cc_start: 0.8939 (ptp-110) cc_final: 0.8592 (ptp-110)
REVERT: B  100 PHE cc_start: 0.8009 (m-10) cc_final: 0.7437 (m-10)
REVERT: C   33 LEU cc_start: 0.9089 (mt) cc_final: 0.8724 (mt)
REVERT: C   75 LYS cc_start: 0.8567 (mmtp) cc_final: 0.8058 (mmmm)
REVERT: D   92 GLN cc_start: 0.8711 (pt0) cc_final: 0.8375 (pt0)
REVERT: D  103 LEU cc_start: 0.8966 (tp) cc_final: 0.8492 (tp)
REVERT: D  106 HIS cc_start: 0.7714 (m90) cc_final: 0.7452 (m170)
REVERT: E   55 GLN cc_start: 0.7829 (pp30) cc_final: 0.7513 (pp30)
REVERT: E   85 GLN cc_start: 0.8027 (tt0) cc_final: 0.7611 (tt0)
REVERT: E   94 GLU cc_start: 0.8664 (tp30) cc_final: 0.8328 (tm-30)
REVERT: E   99 TYR cc_start: 0.9099 (t80) cc_final: 0.8472 (t80)
REVERT: F   31 LYS cc_start: 0.8355 (tttm) cc_final: 0.7906 (tttm)
REVERT: F   68 ASP cc_start: 0.7386 (m-30) cc_final: 0.5323 (m-30)
REVERT: F   84 MET cc_start: 0.8761 (mmp) cc_final: 0.8265 (mmp)
REVERT: F   92 ARG cc_start: 0.7584 (ttp80) cc_final: 0.7094 (tmm160)
REVERT: G   76 THR cc_start: 0.9077 (p) cc_final: 0.8732 (t)
REVERT: G   78 ILE cc_start: 0.6254 (mt) cc_final: 0.6035 (mt)
REVERT: G   81 ARG cc_start: 0.8554 (tpt-90) cc_final: 0.8350 (tpt170)
REVERT: G   82 HIS cc_start: 0.8436 (m170) cc_final: 0.7901 (m90)
REVERT: G   84 GLN cc_start: 0.8084 (tp-100) cc_final: 0.7488 (tm-30)
REVERT: H   56 MET cc_start: 0.7669 (tmm) cc_final: 0.7436 (tmm)
REVERT: L    1 MET cc_start: 0.1981 (ttp) cc_final: 0.1101 (ttt)
REVERT: L   39 ASP cc_start: 0.8225 (p0) cc_final: 0.7084 (p0)
REVERT: L   62 GLN cc_start: 0.7970 (tp40) cc_final: 0.7671 (tp40)
REVERT: K   53 LEU cc_start: 0.6060 (tp) cc_final: 0.5622 (mt)
REVERT: K   66 LYS cc_start: 0.8020 (mppt) cc_final: 0.7568 (pttt)
REVERT: K   96 MET cc_start: 0.0026 (ttp) cc_final: -0.0486 (tpp)
REVERT: K  147 MET cc_start: 0.5238 (mmt) cc_final: 0.4922 (mmt)
REVERT: K  248 GLU cc_start: 0.8438 (tt0) cc_final: 0.8224 (mp0)
REVERT: K  281 SER cc_start: 0.9141 (t) cc_final: 0.8804 (m)
REVERT: K  291 MET cc_start: 0.6871 (ptp) cc_final: 0.6499 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 371
  average time/residue: 0.1508
  time to fit residues: 76.6554
Evaluate side-chains
  307 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 307
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 130 optimal weight:    6.9990
   chunk 75 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 129 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 131 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 111 optimal weight:    5.9990
   chunk 80 optimal weight:    5.9990
   chunk 73 optimal weight:   10.0000
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  68 GLN
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  89 ASN
D  60 ASN
** E  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 GLN
F  75 HIS
G 104 GLN
H  81 ASN
** L  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.137592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.105192 restraints weight = 49985.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.107830 restraints weight = 27564.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.109432 restraints weight = 19077.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 58)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.110342 restraints weight = 15495.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.110845 restraints weight = 13840.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          1.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063  16146  Z= 0.267
  Angle     :  0.811  15.877  23055  Z= 0.454
  Chirality :  0.047   0.566   2607
  Planarity :  0.006   0.054   1920
  Dihedral  : 31.792 147.077   4447
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 21.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.11 %
    Favored  : 96.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.18 %
    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: -0.85 (0.24), residues: 1143
  helix:  0.38 (0.19), residues: 705
  sheet: -2.07 (0.90), residues: 38
  loop : -2.10 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG E  63 
 TYR   0.045   0.003   TYR B  72 
 PHE   0.053   0.003   PHE E  67 
 TRP   0.015   0.002   TRP K 208 
 HIS   0.010   0.001   HIS K 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00592 (16145)
  covalent geometry    : angle       0.81064 (23055)
  hydrogen bonds       : bond        0.06554 (  887)
  hydrogen bonds       : angle       4.26576 ( 2270)
  Misc. bond           : bond        0.00051 (    1)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  370 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 369
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.7295 (m-30) cc_final: 0.7062 (m-30)
REVERT: A   90 MET cc_start: 0.8295 (ppp) cc_final: 0.8031 (tmm)
REVERT: A   93 GLN cc_start: 0.8786 (tt0) cc_final: 0.8341 (tt0)
REVERT: B   39 ARG cc_start: 0.8439 (mmt90) cc_final: 0.8106 (mmt90)
REVERT: B   53 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8229 (mm-30)
REVERT: B   73 THR cc_start: 0.9365 (m) cc_final: 0.9028 (t)
REVERT: B   74 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7997 (mt-10)
REVERT: B  100 PHE cc_start: 0.8638 (m-80) cc_final: 0.8242 (m-10)
REVERT: C   15 LYS cc_start: 0.6701 (tmtt) cc_final: 0.6375 (mmtm)
REVERT: C   64 GLU cc_start: 0.8736 (pt0) cc_final: 0.8466 (pt0)
REVERT: C   75 LYS cc_start: 0.8963 (mmtp) cc_final: 0.8512 (mmmm)
REVERT: C   77 ARG cc_start: 0.7506 (mtt90) cc_final: 0.7065 (mtp85)
REVERT: C   93 LEU cc_start: 0.9412 (mm) cc_final: 0.9181 (mm)
REVERT: C  110 ASN cc_start: 0.6906 (t0) cc_final: 0.6692 (t0)
REVERT: D   54 LYS cc_start: 0.8400 (ptmt) cc_final: 0.8024 (mttp)
REVERT: D   99 LEU cc_start: 0.9374 (mt) cc_final: 0.9160 (mt)
REVERT: D  103 LEU cc_start: 0.8945 (tp) cc_final: 0.8530 (tp)
REVERT: E   51 ILE cc_start: 0.7634 (mt) cc_final: 0.7412 (mt)
REVERT: E   64 LYS cc_start: 0.6815 (mppt) cc_final: 0.6510 (mppt)
REVERT: E  104 PHE cc_start: 0.9509 (m-80) cc_final: 0.9272 (m-10)
REVERT: F   84 MET cc_start: 0.8850 (mmp) cc_final: 0.8436 (mmp)
REVERT: G   82 HIS cc_start: 0.8576 (m170) cc_final: 0.8050 (m90)
REVERT: H   54 LYS cc_start: 0.8614 (tppp) cc_final: 0.8223 (mmtp)
REVERT: H   56 MET cc_start: 0.7968 (tmm) cc_final: 0.7738 (tmm)
REVERT: H   80 TYR cc_start: 0.7548 (m-10) cc_final: 0.7228 (m-10)
REVERT: H   99 LEU cc_start: 0.8843 (mm) cc_final: 0.8512 (mm)
REVERT: L    1 MET cc_start: 0.2410 (ttp) cc_final: 0.1347 (tpp)
REVERT: L   62 GLN cc_start: 0.7967 (tp40) cc_final: 0.7491 (tp40)
REVERT: K   53 LEU cc_start: 0.6304 (tp) cc_final: 0.5620 (mt)
REVERT: K   55 MET cc_start: 0.7832 (mmp) cc_final: 0.7262 (mtm)
REVERT: K   66 LYS cc_start: 0.8122 (mppt) cc_final: 0.7620 (pttt)
REVERT: K   96 MET cc_start: 0.0637 (ttp) cc_final: -0.0223 (tpp)
REVERT: K  147 MET cc_start: 0.5407 (mmt) cc_final: 0.5024 (mmt)
REVERT: K  153 MET cc_start: 0.3344 (ppp) cc_final: 0.3011 (ppp)
REVERT: K  159 PHE cc_start: 0.7448 (t80) cc_final: 0.7046 (t80)
REVERT: K  229 ARG cc_start: 0.9223 (mmm-85) cc_final: 0.8993 (mmt180)
REVERT: K  238 ILE cc_start: 0.8020 (mt) cc_final: 0.7807 (mt)
REVERT: K  255 GLU cc_start: 0.9261 (mt-10) cc_final: 0.9054 (mt-10)
REVERT: K  281 SER cc_start: 0.9245 (t) cc_final: 0.8811 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 370
  average time/residue: 0.1451
  time to fit residues: 74.4920
Evaluate side-chains
  317 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 317
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 130 optimal weight:    6.9990
   chunk 16 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 88 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 109 optimal weight:   30.0000
   chunk 45 optimal weight:    1.9990
   chunk 15 optimal weight:    0.3980
   chunk 12 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
A 113 HIS
B  64 ASN
C  24 GLN
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 ASN
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  94 ASN
** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 106 HIS
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  46 HIS
** K 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.141901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.110532 restraints weight = 49402.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.113368 restraints weight = 26311.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.115049 restraints weight = 17920.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.116001 restraints weight = 14406.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.116446 restraints weight = 12821.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          1.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  16146  Z= 0.168
  Angle     :  0.696  12.813  23055  Z= 0.392
  Chirality :  0.041   0.168   2607
  Planarity :  0.005   0.053   1920
  Dihedral  : 31.667 146.383   4447
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 15.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.30 %
    Favored  : 98.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.18 %
    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: -0.48 (0.24), residues: 1143
  helix:  0.72 (0.19), residues: 713
  sheet: -2.33 (0.85), residues: 40
  loop : -2.05 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG D  89 
 TYR   0.031   0.002   TYR B  98 
 PHE   0.015   0.002   PHE C  25 
 TRP   0.006   0.001   TRP K 305 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (16145)
  covalent geometry    : angle       0.69585 (23055)
  hydrogen bonds       : bond        0.04636 (  887)
  hydrogen bonds       : angle       3.83549 ( 2270)
  Misc. bond           : bond        0.00009 (    1)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  379 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 378
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 LEU cc_start: 0.8730 (tt) cc_final: 0.8513 (tp)
REVERT: A   86 SER cc_start: 0.8648 (m) cc_final: 0.8420 (m)
REVERT: A   93 GLN cc_start: 0.8747 (tt0) cc_final: 0.8137 (tt0)
REVERT: A  107 THR cc_start: 0.9352 (m) cc_final: 0.8589 (m)
REVERT: B   31 LYS cc_start: 0.8925 (tppp) cc_final: 0.8648 (tppt)
REVERT: B   39 ARG cc_start: 0.8277 (mmt90) cc_final: 0.8046 (mtt-85)
REVERT: C   15 LYS cc_start: 0.6761 (tmtt) cc_final: 0.6313 (mmtm)
REVERT: C   64 GLU cc_start: 0.8780 (pt0) cc_final: 0.8426 (pt0)
REVERT: C   75 LYS cc_start: 0.8826 (mmtp) cc_final: 0.8300 (mmmm)
REVERT: C   89 ASN cc_start: 0.8635 (m110) cc_final: 0.8332 (m110)
REVERT: D   44 GLN cc_start: 0.8246 (tt0) cc_final: 0.7831 (tt0)
REVERT: D   58 ILE cc_start: 0.9078 (mm) cc_final: 0.8772 (mm)
REVERT: D   82 LYS cc_start: 0.9255 (mtpt) cc_final: 0.8824 (mmtt)
REVERT: D  103 LEU cc_start: 0.8921 (tp) cc_final: 0.8483 (tp)
REVERT: E   54 TYR cc_start: 0.7234 (m-10) cc_final: 0.6938 (m-10)
REVERT: E   56 LYS cc_start: 0.8023 (mtpt) cc_final: 0.7632 (mttp)
REVERT: E   61 LEU cc_start: 0.9202 (mt) cc_final: 0.8998 (mt)
REVERT: E   85 GLN cc_start: 0.8492 (tt0) cc_final: 0.8190 (tt0)
REVERT: E   94 GLU cc_start: 0.8608 (tp30) cc_final: 0.8340 (tp30)
REVERT: E   97 GLU cc_start: 0.8177 (tp30) cc_final: 0.7914 (tp30)
REVERT: F   40 ARG cc_start: 0.8771 (ttm170) cc_final: 0.8445 (ttm170)
REVERT: F   59 LYS cc_start: 0.9024 (mmmt) cc_final: 0.8812 (mmtm)
REVERT: F   84 MET cc_start: 0.8790 (mmp) cc_final: 0.8170 (mmm)
REVERT: G   76 THR cc_start: 0.9104 (p) cc_final: 0.8870 (t)
REVERT: G   82 HIS cc_start: 0.8513 (m170) cc_final: 0.8043 (m90)
REVERT: G   84 GLN cc_start: 0.8345 (tp-100) cc_final: 0.7663 (tm-30)
REVERT: G   92 GLU cc_start: 0.8030 (tt0) cc_final: 0.7277 (tt0)
REVERT: L    1 MET cc_start: 0.2842 (ttp) cc_final: 0.1738 (tpp)
REVERT: L   39 ASP cc_start: 0.8340 (p0) cc_final: 0.7636 (p0)
REVERT: L   62 GLN cc_start: 0.7974 (tp40) cc_final: 0.7477 (tp40)
REVERT: K   53 LEU cc_start: 0.6154 (tp) cc_final: 0.5616 (mt)
REVERT: K   66 LYS cc_start: 0.8045 (mppt) cc_final: 0.7544 (pttt)
REVERT: K   96 MET cc_start: 0.0225 (ttp) cc_final: -0.0459 (tpp)
REVERT: K  248 GLU cc_start: 0.8354 (mp0) cc_final: 0.8015 (mp0)
REVERT: K  255 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8960 (mt-10)
REVERT: K  281 SER cc_start: 0.9147 (t) cc_final: 0.8691 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 378
  average time/residue: 0.1491
  time to fit residues: 77.7823
Evaluate side-chains
  313 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 313
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 137 optimal weight:    9.9990
   chunk 125 optimal weight:    4.9990
   chunk 87 optimal weight:   10.0000
   chunk 21 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 47 optimal weight:    6.9990
   chunk 98 optimal weight:   10.0000
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 106 HIS
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  75 HIS
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  46 HIS
H  81 ASN
K 146 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.141895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.110798 restraints weight = 49678.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.113674 restraints weight = 26442.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.115396 restraints weight = 17842.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.116424 restraints weight = 14244.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.116929 restraints weight = 12577.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          1.2392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  16146  Z= 0.167
  Angle     :  0.682  12.471  23055  Z= 0.386
  Chirality :  0.040   0.156   2607
  Planarity :  0.005   0.054   1920
  Dihedral  : 31.425 145.508   4447
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 15.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.40 %
    Favored  : 98.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.18 %
    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: -0.49 (0.24), residues: 1143
  helix:  0.71 (0.19), residues: 717
  sheet: -2.26 (0.84), residues: 40
  loop : -2.08 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F  36 
 TYR   0.031   0.002   TYR B  98 
 PHE   0.015   0.002   PHE D  62 
 TRP   0.008   0.001   TRP K 305 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (16145)
  covalent geometry    : angle       0.68195 (23055)
  hydrogen bonds       : bond        0.04591 (  887)
  hydrogen bonds       : angle       3.84897 ( 2270)
  Misc. bond           : bond        0.00011 (    1)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  371 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 370
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 LEU cc_start: 0.8432 (tp) cc_final: 0.8215 (tp)
REVERT: A   93 GLN cc_start: 0.8769 (tt0) cc_final: 0.8078 (tt0)
REVERT: A  125 GLN cc_start: 0.8583 (mp10) cc_final: 0.7736 (mm-40)
REVERT: B   92 ARG cc_start: 0.8358 (tpp80) cc_final: 0.7953 (tpp80)
REVERT: C   15 LYS cc_start: 0.6657 (tmtt) cc_final: 0.6349 (mmtm)
REVERT: D   82 LYS cc_start: 0.9306 (mtpt) cc_final: 0.8842 (mmtt)
REVERT: D  103 LEU cc_start: 0.8882 (tp) cc_final: 0.8468 (tp)
REVERT: E   56 LYS cc_start: 0.7770 (mtpt) cc_final: 0.7489 (mtpt)
REVERT: E   61 LEU cc_start: 0.9174 (mt) cc_final: 0.8822 (mt)
REVERT: E   94 GLU cc_start: 0.8565 (tp30) cc_final: 0.8238 (tp30)
REVERT: E   97 GLU cc_start: 0.8192 (tp30) cc_final: 0.7398 (tp30)
REVERT: E  123 ASP cc_start: 0.7836 (t70) cc_final: 0.7559 (t0)
REVERT: F   40 ARG cc_start: 0.8902 (ttm170) cc_final: 0.8213 (ttm170)
REVERT: F   84 MET cc_start: 0.8769 (mmp) cc_final: 0.8252 (mmm)
REVERT: G   76 THR cc_start: 0.9063 (p) cc_final: 0.8859 (t)
REVERT: G   82 HIS cc_start: 0.8552 (m170) cc_final: 0.8078 (m90)
REVERT: G   84 GLN cc_start: 0.8445 (tp-100) cc_final: 0.7531 (tm-30)
REVERT: G   92 GLU cc_start: 0.7920 (tt0) cc_final: 0.7634 (tt0)
REVERT: H   53 SER cc_start: 0.9305 (t) cc_final: 0.9075 (p)
REVERT: H   54 LYS cc_start: 0.8455 (ttmm) cc_final: 0.8152 (mptt)
REVERT: H   90 GLU cc_start: 0.8849 (pm20) cc_final: 0.8628 (pm20)
REVERT: H  102 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7283 (mm-30)
REVERT: L    1 MET cc_start: 0.2440 (ttp) cc_final: 0.1404 (tpp)
REVERT: L   39 ASP cc_start: 0.8247 (p0) cc_final: 0.7604 (p0)
REVERT: L   62 GLN cc_start: 0.7980 (tp40) cc_final: 0.7477 (tp40)
REVERT: K   53 LEU cc_start: 0.6127 (tp) cc_final: 0.5652 (mt)
REVERT: K   66 LYS cc_start: 0.8044 (mppt) cc_final: 0.7584 (pttt)
REVERT: K   96 MET cc_start: -0.0036 (ttp) cc_final: -0.0832 (tpp)
REVERT: K  146 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7230 (pp30)
REVERT: K  205 TRP cc_start: 0.7290 (m100) cc_final: 0.6740 (m100)
REVERT: K  248 GLU cc_start: 0.8488 (mp0) cc_final: 0.8138 (mp0)
REVERT: K  255 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8927 (mt-10)
REVERT: K  281 SER cc_start: 0.9034 (t) cc_final: 0.8561 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 371
  average time/residue: 0.1385
  time to fit residues: 71.7932
Evaluate side-chains
  306 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 305
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 80 optimal weight:    6.9990
   chunk 76 optimal weight:    7.9990
   chunk 93 optimal weight:    7.9990
   chunk 32 optimal weight:    6.9990
   chunk 34 optimal weight:    0.0060
   chunk 41 optimal weight:    3.9990
   chunk 81 optimal weight:    7.9990
   chunk 74 optimal weight:    8.9990
   chunk 111 optimal weight:   10.0000
   chunk 49 optimal weight:    0.4980
   overall best weight:    2.5000

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  68 GLN
** C  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 110 ASN
C 112 GLN
D  60 ASN
D  92 GLN
D 106 HIS
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.134881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.102814 restraints weight = 49940.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.105326 restraints weight = 27503.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.106802 restraints weight = 19105.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.107594 restraints weight = 15592.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.108179 restraints weight = 14056.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          1.3224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073  16146  Z= 0.220
  Angle     :  0.758  14.018  23055  Z= 0.422
  Chirality :  0.043   0.229   2607
  Planarity :  0.006   0.106   1920
  Dihedral  : 31.423 145.801   4447
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 18.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.90 %
    Favored  : 99.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.53 (0.24), residues: 1143
  helix:  0.62 (0.19), residues: 714
  sheet: -2.21 (0.85), residues: 40
  loop : -1.93 (0.29), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.028   0.001   ARG L  72 
 TYR   0.032   0.002   TYR B  98 
 PHE   0.021   0.002   PHE D  62 
 TRP   0.008   0.001   TRP K 208 
 HIS   0.007   0.001   HIS K 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 (16145)
  covalent geometry    : angle       0.75818 (23055)
  hydrogen bonds       : bond        0.05298 (  887)
  hydrogen bonds       : angle       4.05324 ( 2270)
  Misc. bond           : bond        0.00045 (    1)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  365 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 364
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 LEU cc_start: 0.8675 (tp) cc_final: 0.8439 (tp)
REVERT: A   70 LEU cc_start: 0.8853 (tt) cc_final: 0.8586 (tt)
REVERT: B   63 GLU cc_start: 0.8607 (mp0) cc_final: 0.8195 (mp0)
REVERT: C   73 ASN cc_start: 0.9070 (m-40) cc_final: 0.8842 (m-40)
REVERT: C  104 GLN cc_start: 0.8467 (tp-100) cc_final: 0.8252 (tp40)
REVERT: C  114 VAL cc_start: 0.8586 (m) cc_final: 0.8303 (t)
REVERT: D   82 LYS cc_start: 0.9271 (mtpt) cc_final: 0.8642 (mmtt)
REVERT: D   83 ARG cc_start: 0.9091 (mmp80) cc_final: 0.8790 (mmp80)
REVERT: D   99 LEU cc_start: 0.9435 (mt) cc_final: 0.9176 (mt)
REVERT: D  103 LEU cc_start: 0.8989 (tp) cc_final: 0.8677 (tp)
REVERT: E   56 LYS cc_start: 0.8435 (mtpt) cc_final: 0.8181 (mtpt)
REVERT: E   61 LEU cc_start: 0.9258 (mt) cc_final: 0.8651 (mt)
REVERT: E   94 GLU cc_start: 0.8574 (tp30) cc_final: 0.8269 (tp30)
REVERT: E   97 GLU cc_start: 0.8086 (tp30) cc_final: 0.7752 (tp30)
REVERT: E  123 ASP cc_start: 0.7949 (t70) cc_final: 0.7615 (t0)
REVERT: F   40 ARG cc_start: 0.8934 (ttm170) cc_final: 0.8145 (ttm170)
REVERT: F   66 ILE cc_start: 0.9750 (mt) cc_final: 0.9543 (mt)
REVERT: F   84 MET cc_start: 0.8858 (mmp) cc_final: 0.8135 (mmm)
REVERT: G   92 GLU cc_start: 0.8197 (tt0) cc_final: 0.7986 (tt0)
REVERT: H   52 SER cc_start: 0.8823 (m) cc_final: 0.8563 (m)
REVERT: H   53 SER cc_start: 0.9585 (t) cc_final: 0.9364 (p)
REVERT: H   54 LYS cc_start: 0.8715 (ttmm) cc_final: 0.8223 (mttt)
REVERT: H  102 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7159 (mm-30)
REVERT: H  106 HIS cc_start: 0.8723 (m170) cc_final: 0.8452 (m-70)
REVERT: L    1 MET cc_start: 0.2127 (ttp) cc_final: 0.1190 (tpp)
REVERT: L   44 ILE cc_start: 0.6982 (mt) cc_final: 0.6768 (mt)
REVERT: L   62 GLN cc_start: 0.7945 (tp40) cc_final: 0.7452 (tp40)
REVERT: K   66 LYS cc_start: 0.8107 (mppt) cc_final: 0.7588 (pttt)
REVERT: K   96 MET cc_start: -0.0317 (ttp) cc_final: -0.1236 (tpp)
REVERT: K  147 MET cc_start: 0.5543 (mmt) cc_final: 0.5154 (mmt)
REVERT: K  205 TRP cc_start: 0.7163 (m100) cc_final: 0.6604 (m100)
REVERT: K  248 GLU cc_start: 0.8584 (mp0) cc_final: 0.8234 (mp0)
REVERT: K  281 SER cc_start: 0.9271 (t) cc_final: 0.8813 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 364
  average time/residue: 0.1378
  time to fit residues: 70.6200
Evaluate side-chains
  309 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 309
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 78 optimal weight:    7.9990
   chunk 86 optimal weight:   10.0000
   chunk 30 optimal weight:    1.9990
   chunk 80 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 133 optimal weight:   30.0000
   chunk 16 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0020
   chunk 75 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 77 optimal weight:    7.9990
   overall best weight:    2.1996

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
A  68 GLN
A  93 GLN
A 108 ASN
** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  94 ASN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  81 ASN
K 146 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.133484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.101955 restraints weight = 49441.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.104502 restraints weight = 26531.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.106016 restraints weight = 18141.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.106910 restraints weight = 14685.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.107325 restraints weight = 13117.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          1.3720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064  16146  Z= 0.201
  Angle     :  0.740  12.253  23055  Z= 0.411
  Chirality :  0.042   0.208   2607
  Planarity :  0.006   0.045   1920
  Dihedral  : 31.390 145.636   4447
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 17.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.60 %
    Favored  : 99.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.18 %
    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: -0.60 (0.24), residues: 1143
  helix:  0.57 (0.19), residues: 714
  sheet: -2.17 (0.85), residues: 40
  loop : -1.99 (0.29), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G  35 
 TYR   0.032   0.002   TYR B  98 
 PHE   0.018   0.002   PHE A  67 
 TRP   0.010   0.001   TRP K 305 
 HIS   0.013   0.001   HIS D 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 (16145)
  covalent geometry    : angle       0.73956 (23055)
  hydrogen bonds       : bond        0.04845 (  887)
  hydrogen bonds       : angle       4.07167 ( 2270)
  Misc. bond           : bond        0.00022 (    1)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  378 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 376
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 LEU cc_start: 0.8945 (tt) cc_final: 0.8572 (tt)
REVERT: B   92 ARG cc_start: 0.8374 (tpp80) cc_final: 0.7912 (tpp80)
REVERT: C   73 ASN cc_start: 0.9082 (m-40) cc_final: 0.8849 (m-40)
REVERT: C  114 VAL cc_start: 0.8596 (m) cc_final: 0.8312 (t)
REVERT: D   58 ILE cc_start: 0.9208 (mm) cc_final: 0.8811 (mm)
REVERT: D   82 LYS cc_start: 0.9311 (mtpt) cc_final: 0.8685 (mmtt)
REVERT: D   83 ARG cc_start: 0.9137 (mmp80) cc_final: 0.8836 (mmp80)
REVERT: D   97 LEU cc_start: 0.8870 (mt) cc_final: 0.8623 (mt)
REVERT: D   99 LEU cc_start: 0.9428 (mt) cc_final: 0.9114 (mt)
REVERT: D  103 LEU cc_start: 0.8972 (tp) cc_final: 0.8601 (tp)
REVERT: E   54 TYR cc_start: 0.6872 (m-80) cc_final: 0.6631 (m-10)
REVERT: E   61 LEU cc_start: 0.9017 (mt) cc_final: 0.8385 (mt)
REVERT: E   64 LYS cc_start: 0.8070 (mppt) cc_final: 0.7582 (mmtp)
REVERT: E   68 GLN cc_start: 0.8345 (pt0) cc_final: 0.8021 (pt0)
REVERT: E   94 GLU cc_start: 0.8525 (tp30) cc_final: 0.8143 (tp30)
REVERT: E   97 GLU cc_start: 0.8150 (tp30) cc_final: 0.7382 (tp30)
REVERT: E  123 ASP cc_start: 0.7930 (t70) cc_final: 0.7620 (t0)
REVERT: F   37 LEU cc_start: 0.9573 (mm) cc_final: 0.9233 (mm)
REVERT: F   40 ARG cc_start: 0.9001 (ttm170) cc_final: 0.8318 (ttm170)
REVERT: F   75 HIS cc_start: 0.8038 (t-170) cc_final: 0.7675 (t-170)
REVERT: F   84 MET cc_start: 0.8860 (mmp) cc_final: 0.8388 (mmm)
REVERT: G   39 TYR cc_start: 0.8628 (m-80) cc_final: 0.8401 (m-80)
REVERT: H   52 SER cc_start: 0.8743 (m) cc_final: 0.8478 (m)
REVERT: H   53 SER cc_start: 0.9526 (t) cc_final: 0.9272 (p)
REVERT: H   54 LYS cc_start: 0.8632 (ttmm) cc_final: 0.8337 (mptt)
REVERT: H  102 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7449 (mm-30)
REVERT: H  106 HIS cc_start: 0.8702 (m170) cc_final: 0.8331 (m170)
REVERT: H  108 VAL cc_start: 0.8821 (t) cc_final: 0.8562 (t)
REVERT: L    1 MET cc_start: 0.2078 (ttp) cc_final: 0.1036 (tpp)
REVERT: L   44 ILE cc_start: 0.7050 (mt) cc_final: 0.6733 (mt)
REVERT: L   62 GLN cc_start: 0.7990 (tp40) cc_final: 0.7478 (tp40)
REVERT: K   66 LYS cc_start: 0.8131 (mppt) cc_final: 0.7614 (pttt)
REVERT: K   73 ARG cc_start: 0.7407 (mmp80) cc_final: 0.6872 (ptt180)
REVERT: K   96 MET cc_start: -0.0404 (ttp) cc_final: -0.1223 (tpp)
REVERT: K  146 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.7060 (pp30)
REVERT: K  205 TRP cc_start: 0.7156 (m100) cc_final: 0.6606 (m100)
REVERT: K  248 GLU cc_start: 0.8634 (mp0) cc_final: 0.8217 (mp0)
REVERT: K  281 SER cc_start: 0.9069 (t) cc_final: 0.8616 (m)
  outliers start: 2
  outliers final: 0
  residues processed: 377
  average time/residue: 0.1422
  time to fit residues: 75.2236
Evaluate side-chains
  321 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 320
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 22 optimal weight:    4.9990
   chunk 60 optimal weight:    0.3980
   chunk 38 optimal weight:    0.0670
   chunk 33 optimal weight:    1.9990
   chunk 116 optimal weight:    6.9990
   chunk 98 optimal weight:   10.0000
   chunk 114 optimal weight:    6.9990
   chunk 125 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.8320

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
A 125 GLN
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 146 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.135669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.104517 restraints weight = 49611.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.107159 restraints weight = 26618.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.108724 restraints weight = 18100.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.109624 restraints weight = 14597.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.110154 restraints weight = 13053.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          1.3916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  16146  Z= 0.163
  Angle     :  0.716  15.734  23055  Z= 0.397
  Chirality :  0.041   0.166   2607
  Planarity :  0.005   0.046   1920
  Dihedral  : 31.245 144.815   4447
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 16.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.30 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.18 %
    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: -0.52 (0.24), residues: 1143
  helix:  0.62 (0.19), residues: 715
  sheet: -2.00 (0.89), residues: 40
  loop : -1.96 (0.28), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  45 
 TYR   0.029   0.002   TYR B  98 
 PHE   0.017   0.002   PHE G  25 
 TRP   0.008   0.001   TRP K 305 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (16145)
  covalent geometry    : angle       0.71557 (23055)
  hydrogen bonds       : bond        0.04408 (  887)
  hydrogen bonds       : angle       3.98187 ( 2270)
  Misc. bond           : bond        0.00010 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3004.63 seconds
wall clock time: 52 minutes 39.26 seconds (3159.26 seconds total)