Starting phenix.real_space_refine
on Sun Jul 27 22:46:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v4j_31713/07_2025/7v4j_31713.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v4j_31713/07_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_31713/07_2025/7v4j_31713.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v4j_31713/07_2025/7v4j_31713.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v4j_31713/07_2025/7v4j_31713.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v4j_31713/07_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 8.57, per 1000 atoms: 0.87
  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: 2.99
  Conformation dependent library (CDL) restraints added in 1.3 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: 1.10
  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: 2.59

  Time building geometry restraints manager: 3.25 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:             65.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     28.060
  Find NCS groups from input model:        0.370
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   97.040
-------------------------------------------------------------------------------
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= 0.141
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23438 (  318)
  hydrogen bonds       : angle       8.14952 (  915)
  covalent geometry    : bond        0.00329 (10090)
  covalent geometry    : angle       0.67038 (13705)

*********************** 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  : 1.016 
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: 0.2102
  time to fit residues: 49.5080
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  : 1.017 
-------------------------------------------------------------------------------
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 = 0.162845 restraints weight = 14451.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4748 r_free = 0.4748 target = 0.164604 restraints weight = 12637.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4782 r_free = 0.4782 target = 0.167013 restraints weight = 10812.217|
|-----------------------------------------------------------------------------|
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= 0.191
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04938 (  318)
  hydrogen bonds       : angle       5.98878 (  915)
  covalent geometry    : bond        0.00451 (10090)
  covalent geometry    : angle       0.70512 (13705)

*********************** 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  : 1.126 
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: 0.2000
  time to fit residues: 43.4100
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  : 1.044 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 14 optimal weight:    7.9990
   chunk 46 optimal weight:    4.9990
   chunk 105 optimal weight:    6.9990
   chunk 100 optimal weight:    5.9990
   chunk 79 optimal weight:    9.9990
   chunk 69 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   chunk 5 optimal weight:    0.7980
   chunk 109 optimal weight:    7.9990
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
** 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 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 = 0.5234 r_free = 0.5234 target = 0.205983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4741 r_free = 0.4741 target = 0.162876 restraints weight = 14972.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4727 r_free = 0.4727 target = 0.163114 restraints weight = 12406.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4750 r_free = 0.4750 target = 0.164983 restraints weight = 11488.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.4767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5755
moved from start:          0.1960

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= 0.167
  Angle     :  0.668   8.768  13705  Z= 0.348
  Chirality :  0.048   0.179   1470
  Planarity :  0.006   0.069   1775
  Dihedral  :  4.963  26.585   1365
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 17.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 14.43 %
    Favored  : 83.96 %
  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: -1.64 (0.24), residues: 1225
  helix:  0.97 (0.27), residues: 340
  sheet: -2.20 (0.30), residues: 275
  loop : -1.73 (0.26), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  53 
 HIS   0.005   0.001   HIS B 249 
 PHE   0.015   0.002   PHE B 167 
 TYR   0.017   0.002   TYR D 176 
 ARG   0.004   0.001   ARG D  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04637 (  318)
  hydrogen bonds       : angle       5.72154 (  915)
  covalent geometry    : bond        0.00397 (10090)
  covalent geometry    : angle       0.66805 (13705)

*********************** 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
  148 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 0.996 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 SER cc_start: 0.7343 (t) cc_final: 0.6892 (p)
REVERT: B   53 TRP cc_start: 0.6839 (t60) cc_final: 0.6196 (t60)
REVERT: B  135 LEU cc_start: 0.3903 (mt) cc_final: 0.3475 (mp)
REVERT: B  338 MET cc_start: 0.4583 (tpt) cc_final: 0.3214 (tpt)
REVERT: D  112 LYS cc_start: 0.7725 (pptt) cc_final: 0.7413 (pptt)
REVERT: D  252 TYR cc_start: 0.5543 (t80) cc_final: 0.4860 (m-80)
REVERT: E   70 VAL cc_start: 0.6586 (OUTLIER) cc_final: 0.5171 (t)
REVERT: E  194 MET cc_start: 0.3508 (tmm) cc_final: 0.3083 (tpp)
  outliers start: 17
  outliers final: 11
  residues processed: 143
  average time/residue: 0.1900
  time to fit residues: 40.1460
Evaluate side-chains
  139 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 127
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
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   11 ASN
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   53 TRP
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:    3.9990
   chunk 30 optimal weight:    0.0000
   chunk 32 optimal weight:    0.9980
   chunk 6 optimal weight:    0.3980
   chunk 104 optimal weight:    0.5980
   chunk 34 optimal weight:    8.9990
   chunk 72 optimal weight:    4.9990
   chunk 12 optimal weight:    0.8980
   chunk 65 optimal weight:    8.9990
   chunk 115 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.5384

-------------------------------------------------------------------------------
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 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5300 r_free = 0.5300 target = 0.213178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4820 r_free = 0.4820 target = 0.169308 restraints weight = 14332.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4815 r_free = 0.4815 target = 0.170477 restraints weight = 11216.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4842 r_free = 0.4842 target = 0.172877 restraints weight = 10024.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.4861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5557
moved from start:          0.2181

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= 0.111
  Angle     :  0.588   5.990  13705  Z= 0.302
  Chirality :  0.045   0.176   1470
  Planarity :  0.006   0.067   1775
  Dihedral  :  4.455  23.989   1365
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 15.94 %
    Favored  : 82.08 %
  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: -1.32 (0.24), residues: 1225
  helix:  1.34 (0.27), residues: 340
  sheet: -2.13 (0.29), residues: 275
  loop : -1.54 (0.26), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  53 
 HIS   0.006   0.001   HIS B 249 
 PHE   0.015   0.002   PHE A 200 
 TYR   0.012   0.001   TYR D  78 
 ARG   0.003   0.000   ARG D 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03419 (  318)
  hydrogen bonds       : angle       5.00284 (  915)
  covalent geometry    : bond        0.00254 (10090)
  covalent geometry    : angle       0.58783 (13705)

*********************** 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
  168 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 147
  time to evaluate  : 1.012 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 MET cc_start: 0.4934 (tpt) cc_final: 0.4729 (mmm)
REVERT: B    1 MET cc_start: 0.5896 (ppp) cc_final: 0.5631 (ppp)
REVERT: B  135 LEU cc_start: 0.3302 (mt) cc_final: 0.2924 (mp)
REVERT: B  338 MET cc_start: 0.4518 (tpt) cc_final: 0.3244 (tpt)
REVERT: C  190 ASN cc_start: 0.7426 (t0) cc_final: 0.7049 (t0)
REVERT: C  197 GLN cc_start: 0.7740 (tm-30) cc_final: 0.7373 (tm-30)
REVERT: D   35 SER cc_start: 0.7031 (t) cc_final: 0.6402 (p)
REVERT: D  112 LYS cc_start: 0.7750 (pptt) cc_final: 0.7495 (pptt)
REVERT: E   70 VAL cc_start: 0.6343 (OUTLIER) cc_final: 0.4974 (t)
  outliers start: 21
  outliers final: 10
  residues processed: 162
  average time/residue: 0.2071
  time to fit residues: 48.5438
Evaluate side-chains
  145 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 134
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
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   39 THR
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   52 GLN
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain E residue   93 ASP
Chi-restraints excluded: chain E residue  199 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 71 optimal weight:    6.9990
   chunk 42 optimal weight:    5.9990
   chunk 17 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9990
   chunk 112 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 110 optimal weight:    0.5980
   chunk 103 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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**
** 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 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 = 0.5285 r_free = 0.5285 target = 0.211625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4755 r_free = 0.4755 target = 0.164598 restraints weight = 14410.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4770 r_free = 0.4770 target = 0.167259 restraints weight = 12676.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4814 r_free = 0.4814 target = 0.170471 restraints weight = 10483.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.4834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5604
moved from start:          0.2306

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= 0.116
  Angle     :  0.597   8.159  13705  Z= 0.304
  Chirality :  0.046   0.202   1470
  Planarity :  0.006   0.064   1775
  Dihedral  :  4.341  23.336   1365
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 18.30 %
    Favored  : 79.53 %
  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: -1.21 (0.25), residues: 1225
  helix:  1.47 (0.27), residues: 340
  sheet: -2.09 (0.28), residues: 285
  loop : -1.47 (0.27), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  53 
 HIS   0.003   0.001   HIS E 175 
 PHE   0.014   0.002   PHE A 200 
 TYR   0.020   0.001   TYR D 176 
 ARG   0.003   0.000   ARG D 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03420 (  318)
  hydrogen bonds       : angle       4.93319 (  915)
  covalent geometry    : bond        0.00274 (10090)
  covalent geometry    : angle       0.59658 (13705)

*********************** 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
  160 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 137
  time to evaluate  : 1.128 
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: 0.3395 (OUTLIER) cc_final: 0.3181 (tt)
REVERT: A  338 MET cc_start: 0.5012 (tpt) cc_final: 0.4785 (mmm)
REVERT: B    1 MET cc_start: 0.5867 (ppp) cc_final: 0.5589 (ppp)
REVERT: B  102 ILE cc_start: 0.3028 (OUTLIER) cc_final: 0.2805 (tt)
REVERT: B  338 MET cc_start: 0.4425 (tpt) cc_final: 0.3218 (tpt)
REVERT: C  197 GLN cc_start: 0.7711 (tm-30) cc_final: 0.7411 (tm-30)
REVERT: D   35 SER cc_start: 0.7042 (t) cc_final: 0.6411 (p)
REVERT: D  112 LYS cc_start: 0.7780 (pptt) cc_final: 0.7547 (pptt)
REVERT: E   35 SER cc_start: 0.7010 (t) cc_final: 0.6476 (t)
REVERT: E   70 VAL cc_start: 0.6314 (OUTLIER) cc_final: 0.4990 (t)
REVERT: E  194 MET cc_start: 0.3539 (tmm) cc_final: 0.2983 (tpp)
  outliers start: 23
  outliers final: 14
  residues processed: 153
  average time/residue: 0.1938
  time to fit residues: 43.3310
Evaluate side-chains
  150 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 133
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
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  137 LYS
Chi-restraints excluded: chain B residue  213 GLN
Chi-restraints excluded: chain C residue   39 THR
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   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  254 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 116 optimal weight:    0.6980
   chunk 91 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0980
   chunk 30 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 47 optimal weight:    9.9990
   chunk 123 optimal weight:   30.0000
   chunk 16 optimal weight:    1.9990
   chunk 67 optimal weight:    0.5980
   chunk 110 optimal weight:    9.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 201 GLN ** 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 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 136 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 = 0.5289 r_free = 0.5289 target = 0.211842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4771 r_free = 0.4771 target = 0.165723 restraints weight = 14435.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4791 r_free = 0.4791 target = 0.168838 restraints weight = 12025.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4823 r_free = 0.4823 target = 0.171172 restraints weight = 9861.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.4842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5592
moved from start:          0.2454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10090  Z= 0.113
  Angle     :  0.597   8.532  13705  Z= 0.303
  Chirality :  0.046   0.189   1470
  Planarity :  0.006   0.063   1775
  Dihedral  :  4.267  22.956   1365
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 14.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 19.43 %
    Favored  : 78.30 %
  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: -1.12 (0.25), residues: 1225
  helix:  1.53 (0.27), residues: 340
  sheet: -2.00 (0.28), residues: 285
  loop : -1.41 (0.27), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  53 
 HIS   0.007   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 A  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03300 (  318)
  hydrogen bonds       : angle       4.78423 (  915)
  covalent geometry    : bond        0.00265 (10090)
  covalent geometry    : angle       0.59735 (13705)

*********************** 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
  162 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 138
  time to evaluate  : 0.997 
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: 0.3435 (OUTLIER) cc_final: 0.3207 (tt)
REVERT: A  338 MET cc_start: 0.5045 (tpt) cc_final: 0.4828 (mmm)
REVERT: B    1 MET cc_start: 0.5863 (ppp) cc_final: 0.5603 (ppp)
REVERT: B   53 TRP cc_start: 0.6878 (t60) cc_final: 0.6371 (t60)
REVERT: B  102 ILE cc_start: 0.3102 (OUTLIER) cc_final: 0.2873 (tt)
REVERT: B  338 MET cc_start: 0.4428 (tpt) cc_final: 0.3239 (tpt)
REVERT: C  197 GLN cc_start: 0.7740 (tm-30) cc_final: 0.7417 (tm-30)
REVERT: D   35 SER cc_start: 0.6969 (t) cc_final: 0.6346 (p)
REVERT: D  112 LYS cc_start: 0.7791 (pptt) cc_final: 0.7573 (pptt)
REVERT: E   35 SER cc_start: 0.6912 (t) cc_final: 0.6692 (t)
REVERT: E   70 VAL cc_start: 0.6329 (OUTLIER) cc_final: 0.4985 (t)
  outliers start: 24
  outliers final: 18
  residues processed: 153
  average time/residue: 0.1977
  time to fit residues: 43.9428
Evaluate side-chains
  152 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  216 MET
Chi-restraints excluded: chain B residue   52 GLN
Chi-restraints excluded: chain B residue  102 ILE
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 B residue  249 HIS
Chi-restraints excluded: chain C residue   39 THR
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   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  254 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 100 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 87 optimal weight:    0.7980
   chunk 82 optimal weight:    0.3980
   chunk 101 optimal weight:    6.9990
   chunk 91 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   chunk 24 optimal weight:    7.9990
   chunk 31 optimal weight:    0.0060
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.8400

-------------------------------------------------------------------------------
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 201 GLN
B 249 HIS
** 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 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 = 0.5291 r_free = 0.5291 target = 0.212013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4770 r_free = 0.4770 target = 0.165756 restraints weight = 14611.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4792 r_free = 0.4792 target = 0.169131 restraints weight = 12028.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4822 r_free = 0.4822 target = 0.171074 restraints weight = 9959.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.4842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5589
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10090  Z= 0.115
  Angle     :  0.615  10.200  13705  Z= 0.309
  Chirality :  0.046   0.191   1470
  Planarity :  0.006   0.063   1775
  Dihedral  :  4.246  22.503   1365
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 14.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 20.47 %
    Favored  : 76.89 %
  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: -1.10 (0.25), residues: 1225
  helix:  1.53 (0.27), residues: 340
  sheet: -2.01 (0.29), residues: 285
  loop : -1.37 (0.27), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  53 
 HIS   0.013   0.001   HIS B 249 
 PHE   0.013   0.001   PHE A 200 
 TYR   0.020   0.001   TYR D 176 
 ARG   0.003   0.000   ARG A  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03264 (  318)
  hydrogen bonds       : angle       4.72752 (  915)
  covalent geometry    : bond        0.00270 (10090)
  covalent geometry    : angle       0.61506 (13705)

*********************** 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
  168 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 140
  time to evaluate  : 1.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ILE cc_start: 0.3497 (OUTLIER) cc_final: 0.3257 (tt)
REVERT: A  338 MET cc_start: 0.5048 (tpt) cc_final: 0.4837 (mmm)
REVERT: B    1 MET cc_start: 0.5846 (ppp) cc_final: 0.5578 (ppp)
REVERT: B   53 TRP cc_start: 0.6884 (t60) cc_final: 0.6370 (t60)
REVERT: B  102 ILE cc_start: 0.3205 (OUTLIER) cc_final: 0.2966 (tt)
REVERT: B  338 MET cc_start: 0.4408 (tpt) cc_final: 0.3224 (tpt)
REVERT: C  197 GLN cc_start: 0.7753 (tm-30) cc_final: 0.7429 (tm-30)
REVERT: D   35 SER cc_start: 0.6967 (t) cc_final: 0.6316 (p)
REVERT: D  112 LYS cc_start: 0.7814 (pptt) cc_final: 0.7612 (pptt)
REVERT: E   35 SER cc_start: 0.6956 (t) cc_final: 0.6747 (t)
REVERT: E   70 VAL cc_start: 0.6310 (OUTLIER) cc_final: 0.4979 (t)
REVERT: E  194 MET cc_start: 0.3722 (tmm) cc_final: 0.3068 (tpp)
REVERT: E  338 MET cc_start: 0.3787 (tpt) cc_final: 0.2661 (tpt)
  outliers start: 28
  outliers final: 16
  residues processed: 158
  average time/residue: 0.1989
  time to fit residues: 46.1846
Evaluate side-chains
  153 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 1.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  216 MET
Chi-restraints excluded: chain B residue  102 ILE
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   39 THR
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 C residue  216 MET
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   52 GLN
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  213 GLN
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:    8.9990
   chunk 114 optimal weight:    7.9990
   chunk 37 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 98 optimal weight:    8.9990
   chunk 8 optimal weight:    3.9990
   chunk 67 optimal weight:    9.9990
   chunk 10 optimal weight:    0.3980
   chunk 40 optimal weight:   10.0000
   chunk 100 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   overall best weight:    2.0386

-------------------------------------------------------------------------------
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 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 105 ASN ** 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 = 0.5239 r_free = 0.5239 target = 0.206592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4739 r_free = 0.4739 target = 0.162929 restraints weight = 14733.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4727 r_free = 0.4727 target = 0.163576 restraints weight = 12194.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4752 r_free = 0.4752 target = 0.165550 restraints weight = 11157.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.4770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5745
moved from start:          0.2654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10090  Z= 0.164
  Angle     :  0.686  10.228  13705  Z= 0.348
  Chirality :  0.047   0.187   1470
  Planarity :  0.006   0.064   1775
  Dihedral  :  4.680  24.234   1365
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 17.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.82 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 21.23 %
    Favored  : 76.51 %
  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: -1.29 (0.25), residues: 1225
  helix:  1.21 (0.27), residues: 340
  sheet: -1.87 (0.31), residues: 260
  loop : -1.57 (0.26), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  53 
 HIS   0.003   0.001   HIS D 175 
 PHE   0.014   0.002   PHE A 200 
 TYR   0.025   0.002   TYR D 176 
 ARG   0.004   0.001   ARG E 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04157 (  318)
  hydrogen bonds       : angle       5.14853 (  915)
  covalent geometry    : bond        0.00388 (10090)
  covalent geometry    : angle       0.68579 (13705)

*********************** 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
  157 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 133
  time to evaluate  : 1.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ILE cc_start: 0.3807 (OUTLIER) cc_final: 0.3534 (tt)
REVERT: A  194 MET cc_start: 0.3498 (tpp) cc_final: 0.3038 (mtp)
REVERT: A  338 MET cc_start: 0.5062 (tpt) cc_final: 0.4862 (mmm)
REVERT: B    1 MET cc_start: 0.5918 (ppp) cc_final: 0.5644 (ppp)
REVERT: B   35 SER cc_start: 0.7368 (m) cc_final: 0.7109 (p)
REVERT: B  102 ILE cc_start: 0.3547 (OUTLIER) cc_final: 0.3268 (tt)
REVERT: B  106 LYS cc_start: 0.6591 (mmtm) cc_final: 0.6138 (mptt)
REVERT: B  338 MET cc_start: 0.4456 (tpt) cc_final: 0.4024 (tpt)
REVERT: C  136 GLN cc_start: 0.5397 (tm-30) cc_final: 0.5113 (tm-30)
REVERT: D  112 LYS cc_start: 0.7834 (pptt) cc_final: 0.7572 (pptt)
REVERT: E   35 SER cc_start: 0.7084 (t) cc_final: 0.6421 (t)
REVERT: E   70 VAL cc_start: 0.6608 (OUTLIER) cc_final: 0.5194 (t)
REVERT: E  194 MET cc_start: 0.3893 (tmm) cc_final: 0.3278 (tpp)
  outliers start: 24
  outliers final: 14
  residues processed: 151
  average time/residue: 0.1920
  time to fit residues: 42.8946
Evaluate side-chains
  147 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
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  213 GLN
Chi-restraints excluded: chain C residue   39 THR
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 D residue  173 ASP
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  213 GLN
Chi-restraints excluded: chain E residue  352 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 106 optimal weight:    0.0000
   chunk 112 optimal weight:    8.9990
   chunk 89 optimal weight:    0.5980
   chunk 70 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 82 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 92 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    1.3188

-------------------------------------------------------------------------------
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**
** 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 136 GLN ** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5262 r_free = 0.5262 target = 0.208966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4756 r_free = 0.4756 target = 0.164337 restraints weight = 14597.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4750 r_free = 0.4750 target = 0.165512 restraints weight = 11545.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4774 r_free = 0.4774 target = 0.167491 restraints weight = 10452.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.4793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5680
moved from start:          0.2736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10090  Z= 0.137
  Angle     :  0.671  10.287  13705  Z= 0.338
  Chirality :  0.047   0.218   1470
  Planarity :  0.006   0.063   1775
  Dihedral  :  4.540  23.501   1365
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 16.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 21.70 %
    Favored  : 76.32 %
  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: -1.27 (0.25), residues: 1225
  helix:  1.27 (0.27), residues: 340
  sheet: -2.07 (0.29), residues: 285
  loop : -1.43 (0.27), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  53 
 HIS   0.002   0.001   HIS C 249 
 PHE   0.014   0.002   PHE A 200 
 TYR   0.025   0.001   TYR D 176 
 ARG   0.003   0.000   ARG E 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03681 (  318)
  hydrogen bonds       : angle       5.00264 (  915)
  covalent geometry    : bond        0.00326 (10090)
  covalent geometry    : angle       0.67066 (13705)

*********************** 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
  159 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 138
  time to evaluate  : 1.072 
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: 0.3652 (OUTLIER) cc_final: 0.3401 (tt)
REVERT: A  194 MET cc_start: 0.3581 (tpp) cc_final: 0.3055 (mtp)
REVERT: B    1 MET cc_start: 0.5897 (ppp) cc_final: 0.5624 (ppp)
REVERT: B   53 TRP cc_start: 0.7033 (t60) cc_final: 0.6535 (t60)
REVERT: B  102 ILE cc_start: 0.3323 (OUTLIER) cc_final: 0.3026 (tt)
REVERT: B  106 LYS cc_start: 0.6560 (mmtm) cc_final: 0.6025 (mptt)
REVERT: B  338 MET cc_start: 0.4453 (tpt) cc_final: 0.4027 (tpt)
REVERT: C  197 GLN cc_start: 0.7799 (tm-30) cc_final: 0.7400 (tm-30)
REVERT: D  112 LYS cc_start: 0.7846 (pptt) cc_final: 0.7616 (pptt)
REVERT: E   35 SER cc_start: 0.7067 (t) cc_final: 0.6455 (t)
REVERT: E   70 VAL cc_start: 0.6403 (OUTLIER) cc_final: 0.4970 (t)
REVERT: E  194 MET cc_start: 0.4020 (tmm) cc_final: 0.3468 (tpp)
REVERT: E  338 MET cc_start: 0.3853 (tpt) cc_final: 0.2558 (tpt)
  outliers start: 21
  outliers final: 16
  residues processed: 153
  average time/residue: 0.2302
  time to fit residues: 51.3607
Evaluate side-chains
  151 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 132
  time to evaluate  : 1.361 
-------------------------------------------------------------------------------
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   39 THR
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   53 TRP
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain E residue   93 ASP
Chi-restraints excluded: chain E residue  120 VAL
Chi-restraints excluded: chain E residue  213 GLN
Chi-restraints excluded: chain E residue  352 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 69 optimal weight:    8.9990
   chunk 85 optimal weight:    9.9990
   chunk 86 optimal weight:    6.9990
   chunk 83 optimal weight:    2.9990
   chunk 105 optimal weight:    2.9990
   chunk 72 optimal weight:    6.9990
   chunk 49 optimal weight:   10.0000
   chunk 110 optimal weight:    7.9990
   chunk 12 optimal weight:    4.9990
   chunk 36 optimal weight:    0.0870
   overall best weight:    3.0166

-------------------------------------------------------------------------------
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**
** 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 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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5231 r_free = 0.5231 target = 0.204725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4713 r_free = 0.4713 target = 0.160729 restraints weight = 14764.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4708 r_free = 0.4708 target = 0.161379 restraints weight = 12156.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4732 r_free = 0.4732 target = 0.163317 restraints weight = 10858.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.4749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5835
moved from start:          0.2994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  10090  Z= 0.218
  Angle     :  0.783  13.604  13705  Z= 0.397
  Chirality :  0.050   0.188   1470
  Planarity :  0.007   0.063   1775
  Dihedral  :  5.165  24.856   1365
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 22.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.94 %
    Favored  : 89.06 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 22.26 %
    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: -1.73 (0.24), residues: 1225
  helix:  0.83 (0.26), residues: 340
  sheet: -2.55 (0.27), residues: 335
  loop : -1.39 (0.28), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  53 
 HIS   0.005   0.001   HIS D 175 
 PHE   0.016   0.003   PHE B 114 
 TYR   0.025   0.002   TYR D 176 
 ARG   0.005   0.001   ARG E 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04818 (  318)
  hydrogen bonds       : angle       5.61568 (  915)
  covalent geometry    : bond        0.00520 (10090)
  covalent geometry    : angle       0.78275 (13705)

********************** 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
  166 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 142
  time to evaluate  : 1.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ILE cc_start: 0.4049 (OUTLIER) cc_final: 0.3798 (tt)
REVERT: A  194 MET cc_start: 0.3683 (tpp) cc_final: 0.3205 (mtp)
REVERT: B    1 MET cc_start: 0.5940 (ppp) cc_final: 0.5669 (ppp)
REVERT: B  102 ILE cc_start: 0.3944 (OUTLIER) cc_final: 0.3704 (tt)
REVERT: B  106 LYS cc_start: 0.6635 (mmtm) cc_final: 0.6117 (mptt)
REVERT: B  338 MET cc_start: 0.4481 (tpt) cc_final: 0.4014 (tpt)
REVERT: C   53 TRP cc_start: 0.6940 (OUTLIER) cc_final: 0.6086 (t60)
REVERT: D   35 SER cc_start: 0.7205 (t) cc_final: 0.6716 (t)
REVERT: D  112 LYS cc_start: 0.7878 (pptt) cc_final: 0.7590 (pptt)
REVERT: E   12 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6900 (pp)
REVERT: E   70 VAL cc_start: 0.6661 (OUTLIER) cc_final: 0.5186 (t)
REVERT: E  194 MET cc_start: 0.3972 (tmm) cc_final: 0.3504 (tpp)
  outliers start: 24
  outliers final: 16
  residues processed: 161
  average time/residue: 0.2999
  time to fit residues: 68.8972
Evaluate side-chains
  154 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 133
  time to evaluate  : 1.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  137 LYS
Chi-restraints excluded: chain A residue  180 LEU
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  133 THR
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   53 TRP
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain E residue   93 ASP
Chi-restraints excluded: chain E residue  120 VAL
Chi-restraints excluded: chain E residue  213 GLN
Chi-restraints excluded: chain E residue  352 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 73 optimal weight:   20.0000
   chunk 52 optimal weight:    0.5980
   chunk 76 optimal weight:    0.0980
   chunk 82 optimal weight:    0.9990
   chunk 104 optimal weight:    0.0980
   chunk 49 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 89 optimal weight:    0.0270
   chunk 99 optimal weight:    6.9990
   overall best weight:    0.3640

-------------------------------------------------------------------------------
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  62 GLN
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  52 GLN
** C 197 GLN ** 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 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 = 0.5277 r_free = 0.5277 target = 0.211854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4756 r_free = 0.4756 target = 0.165754 restraints weight = 14602.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4772 r_free = 0.4772 target = 0.168433 restraints weight = 12222.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4810 r_free = 0.4810 target = 0.171133 restraints weight = 10272.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.4827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5576
moved from start:          0.3022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10090  Z= 0.122
  Angle     :  0.712  11.522  13705  Z= 0.350
  Chirality :  0.047   0.219   1470
  Planarity :  0.006   0.063   1775
  Dihedral  :  4.534  22.645   1365
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 15.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 23.21 %
    Favored  : 74.72 %
  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: -1.23 (0.25), residues: 1225
  helix:  1.31 (0.27), residues: 340
  sheet: -1.98 (0.30), residues: 285
  loop : -1.44 (0.27), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.001   TRP A  53 
 HIS   0.003   0.001   HIS A 175 
 PHE   0.013   0.001   PHE B 108 
 TYR   0.026   0.001   TYR D 176 
 ARG   0.006   0.001   ARG A  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03433 (  318)
  hydrogen bonds       : angle       4.85298 (  915)
  covalent geometry    : bond        0.00286 (10090)
  covalent geometry    : angle       0.71216 (13705)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4200.51 seconds
wall clock time: 77 minutes 22.70 seconds (4642.70 seconds total)