Starting phenix.real_space_refine
on Fri Feb 14 04:45:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v4j_31713/02_2025/7v4j_31713.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v4j_31713/02_2025/7v4j_31713.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v4j_31713/02_2025/7v4j_31713.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v4j_31713/02_2025/7v4j_31713.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v4j_31713/02_2025/7v4j_31713.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v4j_31713/02_2025/7v4j_31713.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C    6265      2.51       5
     N    1625      2.21       5
     O    1900      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9850
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 1970
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 18, 'TRANS': 236}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 1970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 1970
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 18, 'TRANS': 236}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 1970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 1970
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 18, 'TRANS': 236}
          Chain breaks: 4
    Chain: "D"
      Number of atoms: 1970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 1970
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 18, 'TRANS': 236}
          Chain breaks: 4
    Chain: "E"
      Number of atoms: 1970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 1970
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 18, 'TRANS': 236}
          Chain breaks: 4
  Time building chain proxies: 7.80, per 1000 atoms: 0.79
  Number of scatterers: 9850
  At special positions: 0
  Unit cell: (120.19, 122.715, 58.075, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      60     16.00
     O    1900      8.00
     N    1625      7.00
     C    6265      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.33
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2310

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 15 sheets defined
      31.8% alpha, 12.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 9
    Processing helix  chain 'A' and resid 46 through 50
      removed outlier: 3.537A  pdb=" N   LEU A  50 " --> pdb=" O   PRO A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 61
    Processing helix  chain 'A' and resid 107 through 115
    Processing helix  chain 'A' and resid 116 through 122
    Processing helix  chain 'A' and resid 168 through 182
      removed outlier: 3.663A  pdb=" N   VAL A 172 " --> pdb=" O   GLY A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 229
    Processing helix  chain 'A' and resid 339 through 352
      removed outlier: 3.769A  pdb=" N   ILE A 347 " --> pdb=" O   VAL A 343 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ALA A 348 " --> pdb=" O   THR A 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 50
      removed outlier: 3.516A  pdb=" N   LEU B  50 " --> pdb=" O   PRO B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 61
    Processing helix  chain 'B' and resid 107 through 116
    Processing helix  chain 'B' and resid 116 through 123
    Processing helix  chain 'B' and resid 168 through 182
      removed outlier: 4.217A  pdb=" N   VAL B 172 " --> pdb=" O   GLY B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 229
    Processing helix  chain 'B' and resid 339 through 352
    Processing helix  chain 'C' and resid 4 through 9
    Processing helix  chain 'C' and resid 46 through 50
      removed outlier: 3.547A  pdb=" N   LEU C  50 " --> pdb=" O   PRO C  47 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 56 through 61
      removed outlier: 3.641A  pdb=" N   THR C  60 " --> pdb=" O   ASP C  56 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 107 through 115
    Processing helix  chain 'C' and resid 116 through 123
    Processing helix  chain 'C' and resid 168 through 180
      removed outlier: 3.835A  pdb=" N   VAL C 172 " --> pdb=" O   GLY C 168 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 207 through 229
      removed outlier: 3.704A  pdb=" N   GLY C 211 " --> pdb=" O   GLY C 207 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 339 through 352
      removed outlier: 3.602A  pdb=" N   VAL C 343 " --> pdb=" O   ASP C 339 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ILE C 347 " --> pdb=" O   VAL C 343 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ALA C 348 " --> pdb=" O   THR C 344 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 56 through 61
    Processing helix  chain 'D' and resid 107 through 116
    Processing helix  chain 'D' and resid 116 through 123
    Processing helix  chain 'D' and resid 168 through 182
      removed outlier: 3.797A  pdb=" N   VAL D 172 " --> pdb=" O   GLY D 168 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 207 through 229
      removed outlier: 3.672A  pdb=" N   GLY D 211 " --> pdb=" O   GLY D 207 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 339 through 352
      removed outlier: 3.546A  pdb=" N   VAL D 343 " --> pdb=" O   ASP D 339 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ILE D 347 " --> pdb=" O   VAL D 343 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ALA D 348 " --> pdb=" O   THR D 344 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 50
    Processing helix  chain 'E' and resid 56 through 61
      removed outlier: 3.547A  pdb=" N   THR E  60 " --> pdb=" O   ASP E  56 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 107 through 115
    Processing helix  chain 'E' and resid 116 through 121
    Processing helix  chain 'E' and resid 168 through 183
      removed outlier: 3.768A  pdb=" N   VAL E 172 " --> pdb=" O   GLY E 168 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLY E 183 " --> pdb=" O   CYS E 179 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 206 through 229
    Processing helix  chain 'E' and resid 339 through 352
      removed outlier: 3.577A  pdb=" N   VAL E 343 " --> pdb=" O   ASP E 339 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 39
      removed outlier: 3.578A  pdb=" N   ARG A  34 " --> pdb=" O   TRP A  25 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LYS A  36 " --> pdb=" O   TYR A  23 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ILE A  88 " --> pdb=" O   ILE A  20 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   ILE A  26 " --> pdb=" O   CYS A  92 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   TYR A  78 " --> pdb=" O   LEU A  89 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56
      removed outlier: 3.611A  pdb=" N   TRP A  53 " --> pdb=" O   LEU A  72 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 95 through 96
      removed outlier: 3.682A  pdb=" N   GLU A 100 " --> pdb=" O   THR A  96 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 188 through 189
      removed outlier: 3.818A  pdb=" N   GLY A 188 " --> pdb=" O   GLN A 201 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   HIS A 249 " --> pdb=" O   GLU A 129 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 33 through 38
      removed outlier: 3.503A  pdb=" N   LYS B  36 " --> pdb=" O   TYR B  23 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   GLU B  22 " --> pdb=" O   ILE B  88 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 188 through 189
      removed outlier: 4.191A  pdb=" N   GLY B 188 " --> pdb=" O   GLN B 201 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   GLN B 201 " --> pdb=" O   GLY B 188 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   TYR B 132 " --> pdb=" O   TRP B 198 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   PHE B 200 " --> pdb=" O   GLN B 130 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   THR B 133 " --> pdb=" O   SER B 233 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 188 through 189
      removed outlier: 4.191A  pdb=" N   GLY B 188 " --> pdb=" O   GLN B 201 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   GLN B 201 " --> pdb=" O   GLY B 188 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   TYR B 132 " --> pdb=" O   TRP B 198 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   PHE B 200 " --> pdb=" O   GLN B 130 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   GLU B 129 " --> pdb=" O   HIS B 249 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   HIS B 249 " --> pdb=" O   GLU B 129 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 33 through 38
      removed outlier: 3.589A  pdb=" N   LYS C  36 " --> pdb=" O   TYR C  23 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLU C  22 " --> pdb=" O   ILE C  88 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 71 through 72
      removed outlier: 3.548A  pdb=" N   TYR C  95 " --> pdb=" O   ILE C  71 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 186 through 191
      removed outlier: 4.844A  pdb=" N   GLN C 201 " --> pdb=" O   SER C 187 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   ILE C 189 " --> pdb=" O   GLU C 199 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   GLU C 199 " --> pdb=" O   ILE C 189 " (cutoff:3.500A)
      removed outlier: 5.226A  pdb=" N   GLY C 191 " --> pdb=" O   GLN C 197 " (cutoff:3.500A)
      removed outlier: 7.865A  pdb=" N   GLN C 197 " --> pdb=" O   GLY C 191 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   HIS C 249 " --> pdb=" O   GLU C 129 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 33 through 37
      removed outlier: 3.763A  pdb=" N   ARG D  34 " --> pdb=" O   TRP D  25 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LYS D  36 " --> pdb=" O   TYR D  23 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 187 through 190
      removed outlier: 4.493A  pdb=" N   ILE D 189 " --> pdb=" O   GLU D 199 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   GLU D 199 " --> pdb=" O   ILE D 189 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLN D 130 " --> pdb=" O   PHE D 200 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 33 through 38
      removed outlier: 3.741A  pdb=" N   ARG E  34 " --> pdb=" O   TRP E  25 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   TRP E  25 " --> pdb=" O   ARG E  34 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LYS E  36 " --> pdb=" O   TYR E  23 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 72 through 73
      removed outlier: 4.189A  pdb=" N   TYR E  73 " --> pdb=" O   ASP E  93 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   ASP E  93 " --> pdb=" O   TYR E  73 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'E' and resid 188 through 191
      removed outlier: 3.564A  pdb=" N   GLY E 188 " --> pdb=" O   GLN E 201 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   GLN E 130 " --> pdb=" O   PHE E 200 " (cutoff:3.500A)

    320 hydrogen bonds defined for protein.
    915 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.45

  Time building geometry restraints manager: 2.70 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3147
        1.34 -     1.46: 1594
        1.46 -     1.57: 5248
        1.57 -     1.69: 1
        1.69 -     1.81: 100
  Bond restraints: 10090
  Sorted by residual:
  bond pdb=" CB  PRO E 101 "
       pdb=" CG  PRO E 101 "
    ideal  model  delta    sigma   weight residual
    1.492  1.584 -0.092 5.00e-02 4.00e+02 3.35e+00
  bond pdb=" CG  PRO E 101 "
       pdb=" CD  PRO E 101 "
    ideal  model  delta    sigma   weight residual
    1.503  1.472  0.031 3.40e-02 8.65e+02 8.21e-01
  bond pdb=" CA  GLU D 123 "
       pdb=" CB  GLU D 123 "
    ideal  model  delta    sigma   weight residual
    1.530  1.543 -0.014 1.58e-02 4.01e+03 7.33e-01
  bond pdb=" C   LYS D 237 "
       pdb=" O   LYS D 237 "
    ideal  model  delta    sigma   weight residual
    1.238  1.249 -0.011 1.28e-02 6.10e+03 7.30e-01
  bond pdb=" N   GLN E 136 "
       pdb=" CA  GLN E 136 "
    ideal  model  delta    sigma   weight residual
    1.457  1.468 -0.011 1.29e-02 6.01e+03 6.64e-01
  ... (remaining 10085 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 13077
        1.38 -     2.76: 482
        2.76 -     4.14: 111
        4.14 -     5.52: 26
        5.52 -     6.89: 9
  Bond angle restraints: 13705
  Sorted by residual:
  angle pdb=" N   MET C  31 "
        pdb=" CA  MET C  31 "
        pdb=" C   MET C  31 "
      ideal   model   delta    sigma   weight residual
     114.56  109.11    5.45 1.27e+00 6.20e-01 1.84e+01
  angle pdb=" CA  PRO E 101 "
        pdb=" N   PRO E 101 "
        pdb=" CD  PRO E 101 "
      ideal   model   delta    sigma   weight residual
     112.00  106.92    5.08 1.40e+00 5.10e-01 1.32e+01
  angle pdb=" N   GLY D 188 "
        pdb=" CA  GLY D 188 "
        pdb=" C   GLY D 188 "
      ideal   model   delta    sigma   weight residual
     112.65  116.97   -4.32 1.30e+00 5.92e-01 1.10e+01
  angle pdb=" N   ARG C 107 "
        pdb=" CA  ARG C 107 "
        pdb=" C   ARG C 107 "
      ideal   model   delta    sigma   weight residual
     113.18  108.84    4.34 1.33e+00 5.65e-01 1.06e+01
  angle pdb=" CA  TRP C  53 "
        pdb=" CB  TRP C  53 "
        pdb=" CG  TRP C  53 "
      ideal   model   delta    sigma   weight residual
     113.60  119.57   -5.97 1.90e+00 2.77e-01 9.87e+00
  ... (remaining 13700 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.54: 5369
       17.54 -    35.07: 520
       35.07 -    52.61: 72
       52.61 -    70.15: 14
       70.15 -    87.68: 10
  Dihedral angle restraints: 5985
    sinusoidal: 2355
      harmonic: 3630
  Sorted by residual:
  dihedral pdb=" CA  GLN E 136 "
           pdb=" C   GLN E 136 "
           pdb=" N   LYS E 137 "
           pdb=" CA  LYS E 137 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.64   26.36     0      5.00e+00 4.00e-02 2.78e+01
  dihedral pdb=" CA  GLN B 136 "
           pdb=" C   GLN B 136 "
           pdb=" N   LYS B 137 "
           pdb=" CA  LYS B 137 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.90   25.10     0      5.00e+00 4.00e-02 2.52e+01
  dihedral pdb=" CA  TYR D  95 "
           pdb=" C   TYR D  95 "
           pdb=" N   THR D  96 "
           pdb=" CA  THR D  96 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.42   20.58     0      5.00e+00 4.00e-02 1.69e+01
  ... (remaining 5982 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 941
       0.041 -    0.082: 394
       0.082 -    0.122: 112
       0.122 -    0.163: 18
       0.163 -    0.204: 5
  Chirality restraints: 1470
  Sorted by residual:
  chirality pdb=" CB  ILE E  24 "
            pdb=" CA  ILE E  24 "
            pdb=" CG1 ILE E  24 "
            pdb=" CG2 ILE E  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CB  ILE D  24 "
            pdb=" CA  ILE D  24 "
            pdb=" CG1 ILE D  24 "
            pdb=" CG2 ILE D  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CB  ILE A  24 "
            pdb=" CA  ILE A  24 "
            pdb=" CG1 ILE A  24 "
            pdb=" CG2 ILE A  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.80e-01
  ... (remaining 1467 not shown)

  Planarity restraints: 1775
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU E 100 "    0.070 5.00e-02 4.00e+02   1.04e-01 1.74e+01
        pdb=" N   PRO E 101 "   -0.180 5.00e-02 4.00e+02
        pdb=" CA  PRO E 101 "    0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO E 101 "    0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D 102 "   -0.048 5.00e-02 4.00e+02   7.23e-02 8.36e+00
        pdb=" N   PRO D 103 "    0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO D 103 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO D 103 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 102 "    0.047 5.00e-02 4.00e+02   7.21e-02 8.32e+00
        pdb=" N   PRO A 103 "   -0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO A 103 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 103 "    0.040 5.00e-02 4.00e+02
  ... (remaining 1772 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 236
        2.65 -     3.22: 9801
        3.22 -     3.78: 16131
        3.78 -     4.34: 21550
        4.34 -     4.90: 34287
  Nonbonded interactions: 82005
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 137 "
            pdb=" O   GLY A 229 "
     model   vdw
     2.092 3.120
  nonbonded pdb=" OG  SER C 205 "
            pdb=" OG  SER C 209 "
     model   vdw
     2.119 3.040
  nonbonded pdb=" NE2 GLN D  52 "
            pdb=" O   LEU D  72 "
     model   vdw
     2.175 3.120
  nonbonded pdb=" O   TYR B 181 "
            pdb=" OG  SER E  15 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" OH  TYR D  55 "
            pdb=" OE1 GLN D  62 "
     model   vdw
     2.215 3.040
  ... (remaining 82000 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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:             11.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     25.200
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5235
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      :  0.003   0.092  10090  Z= 0.219
  Angle     :  0.670   6.894  13705  Z= 0.354
  Chirality :  0.048   0.204   1470
  Planarity :  0.007   0.104   1775
  Dihedral  : 13.953  87.681   3675
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 19.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.16 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.24), residues: 1225
  helix:  0.49 (0.25), residues: 395
  sheet: -2.13 (0.30), residues: 275
  loop : -1.56 (0.27), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A  53 
 HIS   0.006   0.001   HIS A 249 
 PHE   0.014   0.002   PHE B  82 
 TYR   0.019   0.001   TYR C 181 
 ARG   0.008   0.001   ARG D 107 

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 1.058 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LEU cc_start: 0.7145 (mt) cc_final: 0.6942 (mt)
REVERT: C  216 MET cc_start: 0.5703 (mtm) cc_final: 0.5491 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.2199
  time to fit residues: 51.8050
Evaluate side-chains
  135 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 105 optimal weight:    9.9990
   chunk 94 optimal weight:   10.0000
   chunk 52 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0270
   chunk 63 optimal weight:    0.9980
   chunk 50 optimal weight:    7.9990
   chunk 97 optimal weight:    8.9990
   chunk 37 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 72 optimal weight:   20.0000
   chunk 113 optimal weight:    1.9990
   overall best weight:    2.4044

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  87 ASN
** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 HIS
** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 249 HIS
** D  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  62 GLN
E  87 ASN
** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5269 r_free = 0.5269 target = 0.208232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4746 r_free = 0.4746 target = 0.162847 restraints weight = 14451.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4748 r_free = 0.4748 target = 0.164586 restraints weight = 12637.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4782 r_free = 0.4782 target = 0.167012 restraints weight = 10809.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.4802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5753
moved from start:          0.1663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  10090  Z= 0.293
  Angle     :  0.705   6.846  13705  Z= 0.372
  Chirality :  0.049   0.225   1470
  Planarity :  0.007   0.071   1775
  Dihedral  :  5.026  25.716   1365
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 20.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.14 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 11.13 %
    Favored  : 88.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.24), residues: 1225
  helix:  0.92 (0.27), residues: 340
  sheet: -2.13 (0.30), residues: 280
  loop : -1.69 (0.26), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP E 198 
 HIS   0.005   0.001   HIS B 249 
 PHE   0.016   0.003   PHE B 167 
 TYR   0.021   0.002   TYR D 176 
 ARG   0.006   0.001   ARG D 107 

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 145
  time to evaluate  : 1.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LEU cc_start: 0.7929 (mt) cc_final: 0.7393 (mt)
REVERT: D  112 LYS cc_start: 0.7668 (pptt) cc_final: 0.7260 (pptt)
  outliers start: 9
  outliers final: 2
  residues processed: 149
  average time/residue: 0.2071
  time to fit residues: 44.7812
Evaluate side-chains
  132 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 130
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   93 ASP
Chi-restraints excluded: chain E residue  199 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 14 optimal weight:    9.9990
   chunk 46 optimal weight:    0.6980
   chunk 105 optimal weight:    6.9990
   chunk 100 optimal weight:    5.9990
   chunk 79 optimal weight:    6.9990
   chunk 69 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 109 optimal weight:    5.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 HIS
** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5272 r_free = 0.5272 target = 0.209889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4779 r_free = 0.4779 target = 0.165967 restraints weight = 14758.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4773 r_free = 0.4773 target = 0.166959 restraints weight = 11568.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4798 r_free = 0.4798 target = 0.168978 restraints weight = 10479.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.4817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5641
moved from start:          0.1852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10090  Z= 0.196
  Angle     :  0.625   8.827  13705  Z= 0.322
  Chirality :  0.047   0.167   1470
  Planarity :  0.006   0.068   1775
  Dihedral  :  4.682  25.333   1365
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 15.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 13.96 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.40 (0.24), residues: 1225
  helix:  1.19 (0.27), residues: 340
  sheet: -2.08 (0.30), residues: 275
  loop : -1.59 (0.26), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 198 
 HIS   0.005   0.001   HIS B 249 
 PHE   0.014   0.002   PHE B 167 
 TYR   0.015   0.001   TYR D 176 
 ARG   0.004   0.001   ARG D 107 

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 139
  time to evaluate  : 1.115 
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: A   35 SER cc_start: 0.7342 (t) cc_final: 0.7061 (p)
REVERT: B   53 TRP cc_start: 0.6773 (t60) cc_final: 0.6083 (t60)
REVERT: B  135 LEU cc_start: 0.3759 (mt) cc_final: 0.3385 (mp)
REVERT: B  338 MET cc_start: 0.4550 (tpt) cc_final: 0.3214 (tpt)
REVERT: C  197 GLN cc_start: 0.7835 (tm-30) cc_final: 0.7259 (tm-30)
REVERT: D  112 LYS cc_start: 0.7743 (pptt) cc_final: 0.7446 (pptt)
REVERT: E   70 VAL cc_start: 0.6432 (OUTLIER) cc_final: 0.5062 (t)
REVERT: E  194 MET cc_start: 0.3508 (tmm) cc_final: 0.3048 (tpp)
  outliers start: 15
  outliers final: 9
  residues processed: 149
  average time/residue: 0.2049
  time to fit residues: 44.2781
Evaluate side-chains
  138 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 128
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 GLU
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue  213 GLN
Chi-restraints excluded: chain C residue   53 TRP
Chi-restraints excluded: chain C residue  213 GLN
Chi-restraints excluded: chain C residue  250 THR
Chi-restraints excluded: chain E residue   52 GLN
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain E residue   93 ASP
Chi-restraints excluded: chain E residue  213 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 95 optimal weight:    4.9990
   chunk 30 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 6 optimal weight:    7.9990
   chunk 104 optimal weight:    9.9990
   chunk 34 optimal weight:    2.9990
   chunk 72 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9980
   chunk 65 optimal weight:    9.9990
   chunk 115 optimal weight:    9.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 HIS
** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 105 ASN
** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5202 r_free = 0.5202 target = 0.201678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4684 r_free = 0.4684 target = 0.158390 restraints weight = 14836.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4677 r_free = 0.4677 target = 0.158662 restraints weight = 12317.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4691 r_free = 0.4691 target = 0.159821 restraints weight = 11269.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.4706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5920
moved from start:          0.2634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  10090  Z= 0.416
  Angle     :  0.803   9.587  13705  Z= 0.422
  Chirality :  0.052   0.190   1470
  Planarity :  0.007   0.068   1775
  Dihedral  :  5.625  28.415   1365
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 26.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.57 %
    Favored  : 87.43 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 17.55 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.16 (0.24), residues: 1225
  helix:  0.43 (0.27), residues: 340
  sheet: -2.74 (0.27), residues: 325
  loop : -1.69 (0.27), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  53 
 HIS   0.006   0.002   HIS D 175 
 PHE   0.018   0.003   PHE B 167 
 TYR   0.019   0.003   TYR D 176 
 ARG   0.007   0.001   ARG B  83 

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 147
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 SER cc_start: 0.7375 (t) cc_final: 0.6818 (p)
REVERT: A  158 TYR cc_start: 0.4513 (t80) cc_final: 0.4258 (t80)
REVERT: A  194 MET cc_start: 0.3743 (tpp) cc_final: 0.3205 (mtp)
REVERT: A  338 MET cc_start: 0.5192 (tpt) cc_final: 0.4904 (mmm)
REVERT: D  112 LYS cc_start: 0.7744 (pptt) cc_final: 0.7418 (pptt)
REVERT: E   12 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.7045 (pp)
REVERT: E   70 VAL cc_start: 0.6805 (OUTLIER) cc_final: 0.5303 (t)
  outliers start: 26
  outliers final: 12
  residues processed: 164
  average time/residue: 0.2023
  time to fit residues: 47.5360
Evaluate side-chains
  145 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 131
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue  213 GLN
Chi-restraints excluded: chain B residue  249 HIS
Chi-restraints excluded: chain C residue    9 ASN
Chi-restraints excluded: chain C residue   53 TRP
Chi-restraints excluded: chain C residue  213 GLN
Chi-restraints excluded: chain D residue  199 GLU
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   53 TRP
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain E residue   93 ASP
Chi-restraints excluded: chain E residue  199 GLU
Chi-restraints excluded: chain E residue  213 GLN
Chi-restraints excluded: chain E residue  352 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 71 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 87 optimal weight:    0.7980
   chunk 112 optimal weight:    0.9980
   chunk 10 optimal weight:   10.0000
   chunk 110 optimal weight:    5.9990
   chunk 103 optimal weight:    2.9990
   chunk 82 optimal weight:    0.4980
   chunk 39 optimal weight:    8.9990
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5263 r_free = 0.5263 target = 0.209255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4731 r_free = 0.4731 target = 0.162811 restraints weight = 14427.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4745 r_free = 0.4745 target = 0.165247 restraints weight = 12419.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4782 r_free = 0.4782 target = 0.167938 restraints weight = 10549.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.4801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5683
moved from start:          0.2490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10090  Z= 0.185
  Angle     :  0.636   9.250  13705  Z= 0.327
  Chirality :  0.047   0.166   1470
  Planarity :  0.006   0.066   1775
  Dihedral  :  4.769  25.493   1365
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 15.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 19.53 %
    Favored  : 77.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.25), residues: 1225
  helix:  1.06 (0.27), residues: 340
  sheet: -2.23 (0.30), residues: 275
  loop : -1.64 (0.27), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A  53 
 HIS   0.014   0.001   HIS B 249 
 PHE   0.015   0.002   PHE A 200 
 TYR   0.014   0.001   TYR D 176 
 ARG   0.004   0.001   ARG D  34 

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 136
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ILE cc_start: 0.3559 (OUTLIER) cc_final: 0.3345 (tt)
REVERT: B  102 ILE cc_start: 0.3140 (OUTLIER) cc_final: 0.2912 (tt)
REVERT: B  338 MET cc_start: 0.4398 (tpt) cc_final: 0.3116 (tpt)
REVERT: C   96 THR cc_start: 0.0232 (OUTLIER) cc_final: -0.0092 (p)
REVERT: C  197 GLN cc_start: 0.7756 (tm-30) cc_final: 0.7305 (tm-30)
REVERT: D   52 GLN cc_start: 0.8027 (tp40) cc_final: 0.7815 (mm-40)
REVERT: D  112 LYS cc_start: 0.7843 (pptt) cc_final: 0.7551 (pptt)
REVERT: D  252 TYR cc_start: 0.5472 (t80) cc_final: 0.4705 (m-80)
REVERT: E   35 SER cc_start: 0.6988 (t) cc_final: 0.6697 (t)
REVERT: E   70 VAL cc_start: 0.6328 (OUTLIER) cc_final: 0.4899 (t)
REVERT: E  194 MET cc_start: 0.3741 (tmm) cc_final: 0.3275 (tpp)
  outliers start: 29
  outliers final: 14
  residues processed: 159
  average time/residue: 0.1957
  time to fit residues: 45.2004
Evaluate side-chains
  143 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  137 LYS
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  213 GLN
Chi-restraints excluded: chain C residue   53 TRP
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain C residue  198 TRP
Chi-restraints excluded: chain C residue  213 GLN
Chi-restraints excluded: chain D residue   95 TYR
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   53 TRP
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain E residue   93 ASP
Chi-restraints excluded: chain E residue  133 THR
Chi-restraints excluded: chain E residue  213 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 116 optimal weight:    0.5980
   chunk 91 optimal weight:    7.9990
   chunk 54 optimal weight:    0.6980
   chunk 30 optimal weight:    7.9990
   chunk 26 optimal weight:    0.0050
   chunk 46 optimal weight:    0.0670
   chunk 47 optimal weight:    0.0070
   chunk 123 optimal weight:   20.0000
   chunk 16 optimal weight:    1.9990
   chunk 67 optimal weight:   10.0000
   chunk 110 optimal weight:    7.9990
   overall best weight:    0.2750

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

Flipped N/Q/H residues before XYZ refinement:
** A  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 136 GLN
B 201 GLN
B 249 HIS
** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   9 ASN
** D  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 136 GLN
** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5314 r_free = 0.5314 target = 0.214876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4838 r_free = 0.4838 target = 0.171146 restraints weight = 14287.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4836 r_free = 0.4836 target = 0.172694 restraints weight = 11014.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4868 r_free = 0.4868 target = 0.175420 restraints weight = 9631.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.4887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5505
moved from start:          0.2692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  10090  Z= 0.160
  Angle     :  0.607   7.555  13705  Z= 0.308
  Chirality :  0.046   0.195   1470
  Planarity :  0.006   0.065   1775
  Dihedral  :  4.285  22.610   1365
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 20.66 %
    Favored  : 76.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.24), residues: 1225
  helix:  0.91 (0.26), residues: 375
  sheet: -2.17 (0.28), residues: 285
  loop : -1.52 (0.27), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A  53 
 HIS   0.004   0.001   HIS B 249 
 PHE   0.014   0.001   PHE A 200 
 TYR   0.017   0.001   TYR D 176 
 ARG   0.003   0.000   ARG D 107 

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 140
  time to evaluate  : 1.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ILE cc_start: 0.3388 (OUTLIER) cc_final: 0.3154 (tt)
REVERT: A  137 LYS cc_start: 0.5729 (OUTLIER) cc_final: 0.5506 (mmtt)
REVERT: B   53 TRP cc_start: 0.6889 (t60) cc_final: 0.6429 (t60)
REVERT: B  102 ILE cc_start: 0.3005 (OUTLIER) cc_final: 0.2770 (tt)
REVERT: B  338 MET cc_start: 0.4449 (tpt) cc_final: 0.3233 (tpt)
REVERT: C   53 TRP cc_start: 0.6635 (OUTLIER) cc_final: 0.6179 (t60)
REVERT: C  190 ASN cc_start: 0.7449 (t0) cc_final: 0.6983 (t0)
REVERT: D   35 SER cc_start: 0.7040 (t) cc_final: 0.6441 (p)
REVERT: D  112 LYS cc_start: 0.7856 (pptt) cc_final: 0.7646 (pptt)
REVERT: E   70 VAL cc_start: 0.6259 (OUTLIER) cc_final: 0.4957 (t)
REVERT: E  170 ASP cc_start: 0.5866 (p0) cc_final: 0.4791 (t0)
REVERT: E  194 MET cc_start: 0.3777 (tmm) cc_final: 0.3329 (tpp)
REVERT: E  338 MET cc_start: 0.3843 (tpt) cc_final: 0.2650 (tpt)
  outliers start: 31
  outliers final: 13
  residues processed: 165
  average time/residue: 0.1986
  time to fit residues: 47.4342
Evaluate side-chains
  146 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 SER
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  137 LYS
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  137 LYS
Chi-restraints excluded: chain B residue  213 GLN
Chi-restraints excluded: chain B residue  249 HIS
Chi-restraints excluded: chain C residue   53 TRP
Chi-restraints excluded: chain C residue  198 TRP
Chi-restraints excluded: chain C residue  213 GLN
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   52 GLN
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain E residue   93 ASP
Chi-restraints excluded: chain E residue  129 GLU
Chi-restraints excluded: chain E residue  254 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 63 optimal weight:    0.6980
   chunk 87 optimal weight:    7.9990
   chunk 82 optimal weight:    0.9980
   chunk 101 optimal weight:    6.9990
   chunk 91 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 24 optimal weight:    8.9990
   chunk 31 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 HIS
** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5280 r_free = 0.5280 target = 0.211161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4756 r_free = 0.4756 target = 0.164653 restraints weight = 14609.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4768 r_free = 0.4768 target = 0.167220 restraints weight = 12207.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4816 r_free = 0.4816 target = 0.170499 restraints weight = 10271.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.4834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5610
moved from start:          0.2720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10090  Z= 0.198
  Angle     :  0.646  10.245  13705  Z= 0.324
  Chirality :  0.046   0.183   1470
  Planarity :  0.006   0.064   1775
  Dihedral  :  4.357  22.820   1365
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 14.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 21.89 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.25), residues: 1225
  helix:  1.36 (0.27), residues: 340
  sheet: -2.13 (0.29), residues: 285
  loop : -1.42 (0.27), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A  53 
 HIS   0.006   0.001   HIS B 249 
 PHE   0.013   0.001   PHE A 200 
 TYR   0.012   0.001   TYR D 176 
 ARG   0.003   0.000   ARG A  34 

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 128
  time to evaluate  : 1.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.3515 (tpp) cc_final: 0.2997 (mtp)
REVERT: B   53 TRP cc_start: 0.6964 (t60) cc_final: 0.6552 (t60)
REVERT: B  102 ILE cc_start: 0.3155 (OUTLIER) cc_final: 0.2919 (tt)
REVERT: B  338 MET cc_start: 0.4389 (tpt) cc_final: 0.3193 (tpt)
REVERT: C   96 THR cc_start: -0.0067 (OUTLIER) cc_final: -0.0426 (p)
REVERT: C  133 THR cc_start: 0.6199 (OUTLIER) cc_final: 0.5877 (p)
REVERT: D  112 LYS cc_start: 0.7867 (pptt) cc_final: 0.7638 (pptt)
REVERT: E   53 TRP cc_start: 0.6530 (t60) cc_final: 0.5919 (t60)
REVERT: E   70 VAL cc_start: 0.6250 (OUTLIER) cc_final: 0.4939 (t)
REVERT: E  133 THR cc_start: 0.6252 (OUTLIER) cc_final: 0.5957 (p)
REVERT: E  180 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7584 (mm)
REVERT: E  194 MET cc_start: 0.3814 (tmm) cc_final: 0.3492 (tpp)
REVERT: E  338 MET cc_start: 0.3782 (tpt) cc_final: 0.2572 (tpt)
  outliers start: 27
  outliers final: 15
  residues processed: 149
  average time/residue: 0.1881
  time to fit residues: 41.1539
Evaluate side-chains
  146 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 LYS
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  137 LYS
Chi-restraints excluded: chain B residue  213 GLN
Chi-restraints excluded: chain C residue   53 TRP
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain C residue  198 TRP
Chi-restraints excluded: chain C residue  213 GLN
Chi-restraints excluded: chain C residue  254 THR
Chi-restraints excluded: chain D residue   12 LEU
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   52 GLN
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain E residue   93 ASP
Chi-restraints excluded: chain E residue  129 GLU
Chi-restraints excluded: chain E residue  133 THR
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  254 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 114 optimal weight:    0.3980
   chunk 37 optimal weight:    8.9990
   chunk 82 optimal weight:    0.7980
   chunk 98 optimal weight:    0.0570
   chunk 8 optimal weight:    0.9980
   chunk 67 optimal weight:    5.9990
   chunk 10 optimal weight:   10.0000
   chunk 40 optimal weight:    0.4980
   chunk 100 optimal weight:    0.9990
   chunk 1 optimal weight:    8.9990
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
A  75 GLN
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 HIS
** D  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5308 r_free = 0.5308 target = 0.214023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4795 r_free = 0.4795 target = 0.167618 restraints weight = 14364.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4818 r_free = 0.4818 target = 0.171219 restraints weight = 11633.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4853 r_free = 0.4853 target = 0.173922 restraints weight = 9457.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.4872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5534
moved from start:          0.2858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10090  Z= 0.177
  Angle     :  0.658  10.522  13705  Z= 0.325
  Chirality :  0.046   0.201   1470
  Planarity :  0.006   0.063   1775
  Dihedral  :  4.277  21.872   1365
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 22.17 %
    Favored  : 75.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.25), residues: 1225
  helix:  1.41 (0.27), residues: 340
  sheet: -2.09 (0.28), residues: 285
  loop : -1.34 (0.27), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A  53 
 HIS   0.006   0.001   HIS B 249 
 PHE   0.013   0.001   PHE A 200 
 TYR   0.011   0.001   TYR D 176 
 ARG   0.002   0.000   ARG A 107 

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 129
  time to evaluate  : 1.091 
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: A  102 ILE cc_start: 0.3444 (OUTLIER) cc_final: 0.3224 (tt)
REVERT: A  194 MET cc_start: 0.3473 (tpp) cc_final: 0.2930 (mtp)
REVERT: B   53 TRP cc_start: 0.6945 (t60) cc_final: 0.6485 (t60)
REVERT: B  102 ILE cc_start: 0.3207 (OUTLIER) cc_final: 0.2965 (tt)
REVERT: B  106 LYS cc_start: 0.6552 (mmtm) cc_final: 0.6087 (mptt)
REVERT: B  338 MET cc_start: 0.4430 (tpt) cc_final: 0.4035 (tpt)
REVERT: C   53 TRP cc_start: 0.6615 (OUTLIER) cc_final: 0.6251 (t60)
REVERT: C   96 THR cc_start: -0.0047 (OUTLIER) cc_final: -0.0397 (p)
REVERT: C  133 THR cc_start: 0.6154 (OUTLIER) cc_final: 0.5905 (p)
REVERT: C  190 ASN cc_start: 0.7484 (t0) cc_final: 0.7015 (t0)
REVERT: E   53 TRP cc_start: 0.6554 (t60) cc_final: 0.6220 (t60)
REVERT: E   70 VAL cc_start: 0.6228 (OUTLIER) cc_final: 0.4919 (t)
REVERT: E  338 MET cc_start: 0.3767 (tpt) cc_final: 0.2639 (tpt)
  outliers start: 25
  outliers final: 15
  residues processed: 147
  average time/residue: 0.2048
  time to fit residues: 44.2568
Evaluate side-chains
  147 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 1.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  137 LYS
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  137 LYS
Chi-restraints excluded: chain B residue  213 GLN
Chi-restraints excluded: chain B residue  249 HIS
Chi-restraints excluded: chain C residue   53 TRP
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain C residue  198 TRP
Chi-restraints excluded: chain C residue  213 GLN
Chi-restraints excluded: chain D residue   12 LEU
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   52 GLN
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain E residue   93 ASP
Chi-restraints excluded: chain E residue  129 GLU
Chi-restraints excluded: chain E residue  213 GLN
Chi-restraints excluded: chain E residue  254 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 71 optimal weight:    0.8980
   chunk 106 optimal weight:    0.7980
   chunk 112 optimal weight:    7.9990
   chunk 89 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0370
   chunk 92 optimal weight:    3.9990
   chunk 40 optimal weight:    8.9990
   overall best weight:    0.7258

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 HIS
** D  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5304 r_free = 0.5304 target = 0.213463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4786 r_free = 0.4786 target = 0.167061 restraints weight = 14365.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4812 r_free = 0.4812 target = 0.171058 restraints weight = 11742.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4844 r_free = 0.4844 target = 0.173004 restraints weight = 9511.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.4863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5550
moved from start:          0.2949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10090  Z= 0.186
  Angle     :  0.681  11.004  13705  Z= 0.335
  Chirality :  0.046   0.229   1470
  Planarity :  0.006   0.063   1775
  Dihedral  :  4.277  21.522   1365
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 14.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 22.45 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.25), residues: 1225
  helix:  1.42 (0.27), residues: 340
  sheet: -2.08 (0.28), residues: 285
  loop : -1.34 (0.27), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.001   TRP A  53 
 HIS   0.010   0.001   HIS B 249 
 PHE   0.013   0.001   PHE A 200 
 TYR   0.013   0.001   TYR D 252 
 ARG   0.002   0.000   ARG A  34 

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 125
  time to evaluate  : 1.040 
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: A  102 ILE cc_start: 0.3543 (OUTLIER) cc_final: 0.3308 (tt)
REVERT: B   53 TRP cc_start: 0.6971 (t60) cc_final: 0.6648 (t60)
REVERT: B  102 ILE cc_start: 0.3277 (OUTLIER) cc_final: 0.2994 (tt)
REVERT: B  106 LYS cc_start: 0.6573 (mmtm) cc_final: 0.6046 (mptt)
REVERT: B  338 MET cc_start: 0.4477 (tpt) cc_final: 0.4088 (tpt)
REVERT: C   53 TRP cc_start: 0.6650 (OUTLIER) cc_final: 0.6285 (t60)
REVERT: C   96 THR cc_start: -0.0087 (OUTLIER) cc_final: -0.0459 (p)
REVERT: C  133 THR cc_start: 0.6183 (OUTLIER) cc_final: 0.5863 (p)
REVERT: E   53 TRP cc_start: 0.6573 (t60) cc_final: 0.6252 (t60)
REVERT: E   70 VAL cc_start: 0.6197 (OUTLIER) cc_final: 0.4890 (t)
REVERT: E  180 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7550 (mm)
REVERT: E  194 MET cc_start: 0.3930 (tmm) cc_final: 0.3273 (tpp)
REVERT: E  338 MET cc_start: 0.3705 (tpt) cc_final: 0.2613 (tpt)
  outliers start: 27
  outliers final: 16
  residues processed: 145
  average time/residue: 0.1887
  time to fit residues: 40.3160
Evaluate side-chains
  147 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  137 LYS
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  137 LYS
Chi-restraints excluded: chain B residue  199 GLU
Chi-restraints excluded: chain B residue  213 GLN
Chi-restraints excluded: chain B residue  249 HIS
Chi-restraints excluded: chain C residue   53 TRP
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain C residue  198 TRP
Chi-restraints excluded: chain C residue  213 GLN
Chi-restraints excluded: chain D residue   12 LEU
Chi-restraints excluded: chain D residue  210 SER
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   52 GLN
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain E residue   93 ASP
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  213 GLN
Chi-restraints excluded: chain E residue  254 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 69 optimal weight:    6.9990
   chunk 85 optimal weight:    5.9990
   chunk 86 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   chunk 105 optimal weight:    0.7980
   chunk 72 optimal weight:    8.9990
   chunk 49 optimal weight:   10.0000
   chunk 110 optimal weight:    5.9990
   chunk 12 optimal weight:    8.9990
   chunk 36 optimal weight:    5.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 HIS
** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5208 r_free = 0.5208 target = 0.203423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4700 r_free = 0.4700 target = 0.159814 restraints weight = 14827.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4688 r_free = 0.4688 target = 0.160342 restraints weight = 12389.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4715 r_free = 0.4715 target = 0.162472 restraints weight = 11427.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.4731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5833
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  10090  Z= 0.334
  Angle     :  0.793  12.192  13705  Z= 0.404
  Chirality :  0.050   0.179   1470
  Planarity :  0.007   0.064   1775
  Dihedral  :  5.183  24.300   1365
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 22.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.86 %
    Favored  : 89.14 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 22.55 %
    Favored  : 75.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.74 (0.24), residues: 1225
  helix:  0.77 (0.26), residues: 340
  sheet: -2.53 (0.26), residues: 335
  loop : -1.37 (0.28), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A  53 
 HIS   0.015   0.002   HIS B 249 
 PHE   0.016   0.003   PHE B 114 
 TYR   0.016   0.002   TYR A 176 
 ARG   0.005   0.001   ARG E 218 

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 128
  time to evaluate  : 1.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ILE cc_start: 0.4003 (OUTLIER) cc_final: 0.3759 (tt)
REVERT: A  194 MET cc_start: 0.3804 (tpp) cc_final: 0.3267 (mtp)
REVERT: B  102 ILE cc_start: 0.3876 (OUTLIER) cc_final: 0.3672 (tt)
REVERT: B  338 MET cc_start: 0.4488 (tpt) cc_final: 0.4040 (tpt)
REVERT: C   53 TRP cc_start: 0.6961 (OUTLIER) cc_final: 0.6424 (t60)
REVERT: D   35 SER cc_start: 0.7132 (t) cc_final: 0.6263 (p)
REVERT: E   12 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.7000 (pp)
REVERT: E   53 TRP cc_start: 0.6851 (t60) cc_final: 0.6404 (t60)
REVERT: E   70 VAL cc_start: 0.6701 (OUTLIER) cc_final: 0.5364 (t)
REVERT: E  194 MET cc_start: 0.4010 (tmm) cc_final: 0.3459 (tpp)
  outliers start: 25
  outliers final: 15
  residues processed: 147
  average time/residue: 0.1972
  time to fit residues: 43.1515
Evaluate side-chains
  145 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 125
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  137 LYS
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  137 LYS
Chi-restraints excluded: chain B residue  199 GLU
Chi-restraints excluded: chain B residue  213 GLN
Chi-restraints excluded: chain C residue   53 TRP
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain C residue  198 TRP
Chi-restraints excluded: chain C residue  213 GLN
Chi-restraints excluded: chain C residue  254 THR
Chi-restraints excluded: chain D residue   12 LEU
Chi-restraints excluded: chain D residue  210 SER
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain E residue   93 ASP
Chi-restraints excluded: chain E residue  213 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 68 optimal weight:    3.9990
   chunk 73 optimal weight:    6.9990
   chunk 52 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 82 optimal weight:    0.6980
   chunk 104 optimal weight:    5.9990
   chunk 49 optimal weight:   10.0000
   chunk 18 optimal weight:    6.9990
   chunk 89 optimal weight:    0.5980
   chunk 99 optimal weight:    6.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5247 r_free = 0.5247 target = 0.207379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4768 r_free = 0.4768 target = 0.164883 restraints weight = 14666.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4739 r_free = 0.4739 target = 0.164471 restraints weight = 12796.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4766 r_free = 0.4766 target = 0.166760 restraints weight = 11440.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.4784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5728
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10090  Z= 0.238
  Angle     :  0.727  11.221  13705  Z= 0.363
  Chirality :  0.047   0.198   1470
  Planarity :  0.006   0.064   1775
  Dihedral  :  4.806  23.241   1365
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 18.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 23.49 %
    Favored  : 74.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.54 (0.24), residues: 1225
  helix:  1.04 (0.27), residues: 340
  sheet: -2.44 (0.26), residues: 335
  loop : -1.31 (0.28), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP A  53 
 HIS   0.002   0.001   HIS E 175 
 PHE   0.010   0.002   PHE B 114 
 TYR   0.012   0.001   TYR B  95 
 ARG   0.004   0.000   ARG E 218 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3412.29 seconds
wall clock time: 62 minutes 51.77 seconds (3771.77 seconds total)