Starting phenix.real_space_refine
on Wed Mar  4 01:14:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v4j_31713/03_2026/7v4j_31713.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v4j_31713/03_2026/7v4j_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v4j_31713/03_2026/7v4j_31713.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v4j_31713/03_2026/7v4j_31713.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v4j_31713/03_2026/7v4j_31713.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v4j_31713/03_2026/7v4j_31713.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.52, per 1000 atoms: 0.26
  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: 0.57
  Conformation dependent library (CDL) restraints added in 496.9 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 15 sheets defined
      31.8% alpha, 12.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  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: 1.32

  Time building geometry restraints manager: 0.76 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: 0.01
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:             14.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.160
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.410
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.60 (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
 ARG   0.008   0.001   ARG D 107 
 TYR   0.019   0.001   TYR C 181 
 PHE   0.014   0.002   PHE B  82 
 TRP   0.027   0.002   TRP A  53 
 HIS   0.006   0.001   HIS A 249 

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

*********************** 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  : 0.348 
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: 0.0885
  time to fit residues: 21.2072
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  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 108 optimal weight:    0.3980
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    8.9990
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 123 optimal weight:   20.0000
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    7.9990
   overall best weight:    2.4788

-------------------------------------------------------------------------------
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 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 HIS
** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
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**
** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5268 r_free = 0.5268 target = 0.208114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4744 r_free = 0.4744 target = 0.162819 restraints weight = 14470.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4755 r_free = 0.4755 target = 0.165264 restraints weight = 12330.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4779 r_free = 0.4779 target = 0.166722 restraints weight = 10716.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4790 r_free = 0.4790 target = 0.167597 restraints weight = 9555.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4795 r_free = 0.4795 target = 0.167994 restraints weight = 9274.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.4815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5737
moved from start:          0.1642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  10090  Z= 0.193
  Angle     :  0.707   6.983  13705  Z= 0.373
  Chirality :  0.049   0.220   1470
  Planarity :  0.007   0.071   1775
  Dihedral  :  5.038  25.830   1365
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 20.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.22 %
    Favored  : 90.78 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 11.23 %
    Favored  : 87.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.62 (0.24), residues: 1225
  helix:  0.90 (0.27), residues: 340
  sheet: -2.13 (0.30), residues: 280
  loop : -1.70 (0.26), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 107 
 TYR   0.018   0.002   TYR D 176 
 PHE   0.016   0.003   PHE B 167 
 TRP   0.020   0.002   TRP E 198 
 HIS   0.005   0.001   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 (10090)
  covalent geometry    : angle       0.70674 (13705)
  hydrogen bonds       : bond        0.05023 (  318)
  hydrogen bonds       : angle       6.02745 (  915)

*********************** 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  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LEU cc_start: 0.7925 (mt) cc_final: 0.7398 (mt)
REVERT: D  112 LYS cc_start: 0.7672 (pptt) cc_final: 0.7269 (pptt)
  outliers start: 9
  outliers final: 3
  residues processed: 149
  average time/residue: 0.0840
  time to fit residues: 18.4704
Evaluate side-chains
  134 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 131
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  199 GLU
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 16 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 93 optimal weight:    0.6980
   chunk 118 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 87 optimal weight:   10.0000
   chunk 78 optimal weight:    0.3980
   chunk 86 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0050
   overall best weight:    0.7596

-------------------------------------------------------------------------------
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 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 = 0.5291 r_free = 0.5291 target = 0.211750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4771 r_free = 0.4771 target = 0.165577 restraints weight = 14473.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4784 r_free = 0.4784 target = 0.168011 restraints weight = 12486.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4821 r_free = 0.4821 target = 0.170505 restraints weight = 10583.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4829 r_free = 0.4829 target = 0.171289 restraints weight = 9143.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4831 r_free = 0.4831 target = 0.171484 restraints weight = 8731.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.4850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5584
moved from start:          0.1835

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= 0.118
  Angle     :  0.613   8.453  13705  Z= 0.315
  Chirality :  0.046   0.168   1470
  Planarity :  0.006   0.068   1775
  Dihedral  :  4.610  24.910   1365
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 14.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 13.58 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.35 (0.24), residues: 1225
  helix:  1.26 (0.27), residues: 340
  sheet: -2.07 (0.29), residues: 275
  loop : -1.56 (0.26), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 107 
 TYR   0.014   0.001   TYR D 176 
 PHE   0.013   0.002   PHE A 200 
 TRP   0.019   0.001   TRP A  53 
 HIS   0.005   0.001   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (10090)
  covalent geometry    : angle       0.61305 (13705)
  hydrogen bonds       : bond        0.03864 (  318)
  hydrogen bonds       : angle       5.32781 (  915)

*********************** 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
  163 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 147
  time to evaluate  : 0.433 
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  137 LYS cc_start: 0.5506 (mppt) cc_final: 0.5028 (mmtt)
REVERT: A  338 MET cc_start: 0.4930 (tpt) cc_final: 0.4707 (mmm)
REVERT: B    1 MET cc_start: 0.5900 (ppp) cc_final: 0.5595 (ppp)
REVERT: B   53 TRP cc_start: 0.6751 (t60) cc_final: 0.6033 (t60)
REVERT: B  135 LEU cc_start: 0.3613 (mt) cc_final: 0.3272 (mp)
REVERT: B  338 MET cc_start: 0.4550 (tpt) cc_final: 0.3218 (tpt)
REVERT: D  112 LYS cc_start: 0.7728 (pptt) cc_final: 0.7453 (pptt)
REVERT: D  252 TYR cc_start: 0.5551 (t80) cc_final: 0.5019 (m-80)
REVERT: E   70 VAL cc_start: 0.6270 (OUTLIER) cc_final: 0.4922 (t)
  outliers start: 16
  outliers final: 10
  residues processed: 157
  average time/residue: 0.0865
  time to fit residues: 19.9229
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  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 GLU
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue  213 GLN
Chi-restraints excluded: chain C residue   53 TRP
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  213 GLN
Chi-restraints excluded: chain C residue  250 THR
Chi-restraints excluded: chain E residue   52 GLN
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain E residue   93 ASP
Chi-restraints excluded: chain E residue  213 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 111 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   chunk 67 optimal weight:    2.9990
   chunk 35 optimal weight:    9.9990
   chunk 25 optimal weight:    0.9990
   chunk 84 optimal weight:    7.9990
   chunk 31 optimal weight:    0.5980
   chunk 39 optimal weight:    0.4980
   chunk 121 optimal weight:    0.7980
   chunk 109 optimal weight:    0.9980
   chunk 14 optimal weight:   10.0000
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 HIS
** 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 = 0.5298 r_free = 0.5298 target = 0.212960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4769 r_free = 0.4769 target = 0.165607 restraints weight = 14515.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4789 r_free = 0.4789 target = 0.168735 restraints weight = 12828.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4832 r_free = 0.4832 target = 0.171339 restraints weight = 10488.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4836 r_free = 0.4836 target = 0.171903 restraints weight = 9331.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4844 r_free = 0.4844 target = 0.172669 restraints weight = 8659.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.4864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5561
moved from start:          0.2128

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= 0.112
  Angle     :  0.596   7.921  13705  Z= 0.305
  Chirality :  0.046   0.186   1470
  Planarity :  0.006   0.066   1775
  Dihedral  :  4.413  23.968   1365
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 15.47 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.22 (0.24), residues: 1225
  helix:  1.44 (0.27), residues: 340
  sheet: -2.09 (0.28), residues: 285
  loop : -1.45 (0.26), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  83 
 TYR   0.019   0.001   TYR D 176 
 PHE   0.016   0.002   PHE A 200 
 TRP   0.023   0.001   TRP A  53 
 HIS   0.006   0.001   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (10090)
  covalent geometry    : angle       0.59629 (13705)
  hydrogen bonds       : bond        0.03455 (  318)
  hydrogen bonds       : angle       5.01254 (  915)

*********************** 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
  166 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 145
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 MET cc_start: 0.5006 (tpt) cc_final: 0.4794 (mmm)
REVERT: B    1 MET cc_start: 0.5896 (ppp) cc_final: 0.5612 (ppp)
REVERT: B  135 LEU cc_start: 0.3505 (mt) cc_final: 0.3102 (mp)
REVERT: B  338 MET cc_start: 0.4449 (tpt) cc_final: 0.3194 (tpt)
REVERT: C  190 ASN cc_start: 0.7386 (t0) cc_final: 0.7031 (t0)
REVERT: C  250 THR cc_start: 0.5990 (OUTLIER) cc_final: 0.5783 (t)
REVERT: D   35 SER cc_start: 0.7034 (t) cc_final: 0.6537 (p)
REVERT: D  112 LYS cc_start: 0.7684 (pptt) cc_final: 0.7426 (pptt)
REVERT: E   35 SER cc_start: 0.6974 (t) cc_final: 0.6764 (t)
REVERT: E   70 VAL cc_start: 0.6287 (OUTLIER) cc_final: 0.4961 (t)
REVERT: E  194 MET cc_start: 0.3409 (tmm) cc_final: 0.2877 (tpp)
  outliers start: 21
  outliers final: 15
  residues processed: 158
  average time/residue: 0.0811
  time to fit residues: 19.0576
Evaluate side-chains
  151 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
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 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 C residue  250 THR
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 101 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 62 optimal weight:    9.9990
   chunk 34 optimal weight:    9.9990
   chunk 35 optimal weight:    5.9990
   chunk 87 optimal weight:    1.9990
   chunk 51 optimal weight:    9.9990
   chunk 103 optimal weight:    0.8980
   chunk 57 optimal weight:    5.9990
   chunk 124 optimal weight:    8.9990
   overall best weight:    3.1788

-------------------------------------------------------------------------------
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
** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 136 GLN
** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 201 GLN ** 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 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 105 ASN
** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5229 r_free = 0.5229 target = 0.204265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4700 r_free = 0.4700 target = 0.159759 restraints weight = 14808.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4696 r_free = 0.4696 target = 0.160329 restraints weight = 12406.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4720 r_free = 0.4720 target = 0.162195 restraints weight = 11212.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4728 r_free = 0.4728 target = 0.162755 restraints weight = 10259.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4731 r_free = 0.4731 target = 0.163030 restraints weight = 9809.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.4748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5846
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  10090  Z= 0.225
  Angle     :  0.738   7.834  13705  Z= 0.385
  Chirality :  0.050   0.164   1470
  Planarity :  0.007   0.066   1775
  Dihedral  :  5.196  27.008   1365
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 22.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.61 %
    Favored  : 89.39 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 17.45 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.77 (0.24), residues: 1225
  helix:  0.76 (0.27), residues: 340
  sheet: -2.25 (0.30), residues: 275
  loop : -1.76 (0.26), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  83 
 TYR   0.016   0.002   TYR D 176 
 PHE   0.017   0.003   PHE A 200 
 TRP   0.012   0.002   TRP A  53 
 HIS   0.021   0.002   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 (10090)
  covalent geometry    : angle       0.73805 (13705)
  hydrogen bonds       : bond        0.05232 (  318)
  hydrogen bonds       : angle       5.87606 (  915)

*********************** 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
  176 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 144
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ILE cc_start: 0.3893 (OUTLIER) cc_final: 0.3661 (tt)
REVERT: B  102 ILE cc_start: 0.3503 (OUTLIER) cc_final: 0.3260 (tt)
REVERT: B  338 MET cc_start: 0.4544 (tpt) cc_final: 0.3236 (tpt)
REVERT: D   35 SER cc_start: 0.7244 (t) cc_final: 0.6738 (t)
REVERT: D  112 LYS cc_start: 0.7772 (pptt) cc_final: 0.7458 (pptt)
REVERT: E   12 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6927 (pp)
REVERT: E   70 VAL cc_start: 0.6716 (OUTLIER) cc_final: 0.5247 (t)
REVERT: E  194 MET cc_start: 0.3668 (tmm) cc_final: 0.3333 (tpp)
  outliers start: 32
  outliers final: 16
  residues processed: 165
  average time/residue: 0.0837
  time to fit residues: 20.4338
Evaluate side-chains
  149 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
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  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    9 ASN
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   53 TRP
Chi-restraints excluded: chain C residue  108 PHE
Chi-restraints excluded: chain C residue  198 TRP
Chi-restraints excluded: chain C residue  213 GLN
Chi-restraints excluded: chain D residue   95 TYR
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   53 TRP
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain E residue   93 ASP
Chi-restraints excluded: chain E residue  173 ASP
Chi-restraints excluded: chain E residue  213 GLN
Chi-restraints excluded: chain E residue  352 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 123 optimal weight:    5.9990
   chunk 37 optimal weight:    7.9990
   chunk 115 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 30 optimal weight:    8.9990
   chunk 46 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 120 optimal weight:    0.5980
   chunk 11 optimal weight:    9.9990
   chunk 44 optimal weight:    7.9990
   chunk 12 optimal weight:    9.9990
   overall best weight:    2.1186

-------------------------------------------------------------------------------
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 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 136 GLN
** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 201 GLN ** 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 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 = 0.5246 r_free = 0.5246 target = 0.206356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4713 r_free = 0.4713 target = 0.161432 restraints weight = 14816.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4713 r_free = 0.4713 target = 0.162227 restraints weight = 12409.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4740 r_free = 0.4740 target = 0.164148 restraints weight = 11333.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4752 r_free = 0.4752 target = 0.165065 restraints weight = 10142.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4766 r_free = 0.4766 target = 0.166132 restraints weight = 9615.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.4784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5779
moved from start:          0.2632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10090  Z= 0.168
  Angle     :  0.683   9.367  13705  Z= 0.351
  Chirality :  0.048   0.165   1470
  Planarity :  0.006   0.064   1775
  Dihedral  :  4.938  26.044   1365
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 18.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.57 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 20.57 %
    Favored  : 76.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.71 (0.24), residues: 1225
  helix:  0.86 (0.27), residues: 340
  sheet: -2.29 (0.29), residues: 285
  loop : -1.69 (0.26), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  34 
 TYR   0.016   0.002   TYR D 176 
 PHE   0.014   0.002   PHE A 200 
 TRP   0.010   0.001   TRP B  53 
 HIS   0.002   0.001   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 (10090)
  covalent geometry    : angle       0.68346 (13705)
  hydrogen bonds       : bond        0.04367 (  318)
  hydrogen bonds       : angle       5.54653 (  915)

*********************** 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
  164 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 135
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ILE cc_start: 0.3847 (OUTLIER) cc_final: 0.3622 (tt)
REVERT: B    1 MET cc_start: 0.5885 (ppp) cc_final: 0.5654 (ppp)
REVERT: B   35 SER cc_start: 0.7354 (m) cc_final: 0.7045 (p)
REVERT: B  102 ILE cc_start: 0.3706 (OUTLIER) cc_final: 0.3446 (tt)
REVERT: B  338 MET cc_start: 0.4471 (tpt) cc_final: 0.3892 (tpt)
REVERT: C   91 MET cc_start: 0.5683 (tpt) cc_final: 0.5463 (tpt)
REVERT: C   96 THR cc_start: 0.0186 (OUTLIER) cc_final: -0.0207 (p)
REVERT: D   35 SER cc_start: 0.7156 (t) cc_final: 0.6744 (t)
REVERT: D  112 LYS cc_start: 0.7814 (pptt) cc_final: 0.7497 (pptt)
REVERT: E   70 VAL cc_start: 0.6539 (OUTLIER) cc_final: 0.5063 (t)
REVERT: E  194 MET cc_start: 0.3654 (tmm) cc_final: 0.3405 (tpp)
REVERT: E  352 ILE cc_start: 0.5692 (OUTLIER) cc_final: 0.5479 (mp)
  outliers start: 29
  outliers final: 16
  residues processed: 156
  average time/residue: 0.0788
  time to fit residues: 18.4477
Evaluate side-chains
  150 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
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  136 GLN
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   96 THR
Chi-restraints excluded: chain C residue  198 TRP
Chi-restraints excluded: chain C residue  213 GLN
Chi-restraints excluded: chain D residue   95 TYR
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   53 TRP
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain E residue   93 ASP
Chi-restraints excluded: chain E residue  213 GLN
Chi-restraints excluded: chain E residue  352 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 85 optimal weight:    0.7980
   chunk 28 optimal weight:    6.9990
   chunk 29 optimal weight:    6.9990
   chunk 88 optimal weight:    0.9980
   chunk 120 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 48 optimal weight:   10.0000
   chunk 5 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 201 GLN
** 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 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 = 0.5262 r_free = 0.5262 target = 0.209189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4778 r_free = 0.4778 target = 0.165813 restraints weight = 14650.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4770 r_free = 0.4770 target = 0.166956 restraints weight = 11867.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4801 r_free = 0.4801 target = 0.169444 restraints weight = 10587.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4802 r_free = 0.4802 target = 0.169443 restraints weight = 9243.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4809 r_free = 0.4809 target = 0.170132 restraints weight = 9229.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.4828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5657
moved from start:          0.2652

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= 0.124
  Angle     :  0.643   8.411  13705  Z= 0.327
  Chirality :  0.047   0.191   1470
  Planarity :  0.006   0.064   1775
  Dihedral  :  4.622  24.607   1365
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 15.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 21.32 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.42 (0.25), residues: 1225
  helix:  1.15 (0.27), residues: 340
  sheet: -2.15 (0.29), residues: 285
  loop : -1.53 (0.27), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  34 
 TYR   0.014   0.001   TYR D  73 
 PHE   0.015   0.002   PHE A 200 
 TRP   0.031   0.001   TRP A  53 
 HIS   0.011   0.001   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (10090)
  covalent geometry    : angle       0.64328 (13705)
  hydrogen bonds       : bond        0.03668 (  318)
  hydrogen bonds       : angle       5.12599 (  915)

*********************** 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
  159 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.294 
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: B    1 MET cc_start: 0.5939 (ppp) cc_final: 0.5717 (ppp)
REVERT: B   53 TRP cc_start: 0.6962 (t60) cc_final: 0.6558 (t60)
REVERT: B  102 ILE cc_start: 0.3517 (OUTLIER) cc_final: 0.3284 (tt)
REVERT: B  338 MET cc_start: 0.4493 (tpt) cc_final: 0.3959 (tpt)
REVERT: C   91 MET cc_start: 0.5635 (tpt) cc_final: 0.5419 (tpt)
REVERT: C  133 THR cc_start: 0.6166 (OUTLIER) cc_final: 0.5936 (p)
REVERT: D   35 SER cc_start: 0.6967 (t) cc_final: 0.6261 (p)
REVERT: D  112 LYS cc_start: 0.7820 (pptt) cc_final: 0.7568 (pptt)
REVERT: E   35 SER cc_start: 0.7003 (t) cc_final: 0.6768 (t)
REVERT: E   70 VAL cc_start: 0.6452 (OUTLIER) cc_final: 0.5012 (t)
  outliers start: 25
  outliers final: 13
  residues processed: 154
  average time/residue: 0.0878
  time to fit residues: 19.6808
Evaluate side-chains
  143 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 127
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  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  133 THR
Chi-restraints excluded: chain E residue  213 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 54 optimal weight:    0.4980
   chunk 34 optimal weight:    9.9990
   chunk 84 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 76 optimal weight:    8.9990
   chunk 18 optimal weight:    5.9990
   chunk 11 optimal weight:    7.9990
   chunk 46 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0570
   chunk 91 optimal weight:    8.9990
   chunk 35 optimal weight:   10.0000
   overall best weight:    1.8902

-------------------------------------------------------------------------------
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 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  62 GLN
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 HIS
** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D   9 ASN
** D  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5231 r_free = 0.5231 target = 0.205861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4732 r_free = 0.4732 target = 0.162293 restraints weight = 14710.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4720 r_free = 0.4720 target = 0.162916 restraints weight = 12212.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4744 r_free = 0.4744 target = 0.164899 restraints weight = 11126.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4751 r_free = 0.4751 target = 0.165280 restraints weight = 10010.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4760 r_free = 0.4760 target = 0.166062 restraints weight = 9904.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.4777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5749
moved from start:          0.2809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10090  Z= 0.162
  Angle     :  0.699   9.561  13705  Z= 0.355
  Chirality :  0.048   0.185   1470
  Planarity :  0.006   0.066   1775
  Dihedral  :  4.818  24.569   1365
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 17.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.06 %
    Favored  : 90.94 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 21.89 %
    Favored  : 75.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.53 (0.25), residues: 1225
  helix:  1.01 (0.27), residues: 340
  sheet: -2.24 (0.29), residues: 285
  loop : -1.54 (0.27), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 107 
 TYR   0.012   0.002   TYR D 176 
 PHE   0.015   0.002   PHE A 200 
 TRP   0.029   0.001   TRP A  53 
 HIS   0.005   0.001   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (10090)
  covalent geometry    : angle       0.69948 (13705)
  hydrogen bonds       : bond        0.04116 (  318)
  hydrogen bonds       : angle       5.34983 (  915)

*********************** 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
  165 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 133
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.3826 (tpp) cc_final: 0.3237 (mtp)
REVERT: B    1 MET cc_start: 0.5991 (ppp) cc_final: 0.5755 (ppp)
REVERT: B   35 SER cc_start: 0.7313 (m) cc_final: 0.7096 (p)
REVERT: B  102 ILE cc_start: 0.3715 (OUTLIER) cc_final: 0.3474 (tt)
REVERT: B  338 MET cc_start: 0.4493 (tpt) cc_final: 0.3951 (tpt)
REVERT: C   96 THR cc_start: -0.0231 (OUTLIER) cc_final: -0.0647 (p)
REVERT: D   35 SER cc_start: 0.7088 (t) cc_final: 0.6660 (t)
REVERT: D  112 LYS cc_start: 0.7858 (pptt) cc_final: 0.7600 (pptt)
REVERT: E   35 SER cc_start: 0.7085 (t) cc_final: 0.6426 (t)
REVERT: E   70 VAL cc_start: 0.6568 (OUTLIER) cc_final: 0.5136 (t)
REVERT: E  194 MET cc_start: 0.3879 (tmm) cc_final: 0.3331 (tpp)
REVERT: E  352 ILE cc_start: 0.5534 (OUTLIER) cc_final: 0.5327 (mp)
  outliers start: 32
  outliers final: 22
  residues processed: 156
  average time/residue: 0.0792
  time to fit residues: 18.5053
Evaluate side-chains
  157 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 131
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 LYS
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  137 LYS
Chi-restraints excluded: chain B residue  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   96 THR
Chi-restraints excluded: chain C residue  108 PHE
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain C residue  198 TRP
Chi-restraints excluded: chain C residue  213 GLN
Chi-restraints excluded: chain D residue   12 LEU
Chi-restraints excluded: chain D residue   95 TYR
Chi-restraints excluded: chain D residue  210 SER
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   52 GLN
Chi-restraints excluded: chain E residue   53 TRP
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain E residue   93 ASP
Chi-restraints excluded: chain E residue  133 THR
Chi-restraints excluded: chain E residue  213 GLN
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 30 optimal weight:    9.9990
   chunk 62 optimal weight:    3.9990
   chunk 109 optimal weight:    3.9990
   chunk 46 optimal weight:    0.2980
   chunk 82 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 115 optimal weight:    1.9990
   chunk 47 optimal weight:    0.2980
   chunk 84 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9980
   chunk 18 optimal weight:    4.9990
   overall best weight:    0.6180

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5286 r_free = 0.5286 target = 0.211475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4765 r_free = 0.4765 target = 0.165258 restraints weight = 14414.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4787 r_free = 0.4787 target = 0.168690 restraints weight = 11886.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4815 r_free = 0.4815 target = 0.170743 restraints weight = 9797.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4827 r_free = 0.4827 target = 0.171574 restraints weight = 8722.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4832 r_free = 0.4832 target = 0.172060 restraints weight = 8489.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.4851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5588
moved from start:          0.2858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10090  Z= 0.118
  Angle     :  0.664   9.648  13705  Z= 0.331
  Chirality :  0.047   0.208   1470
  Planarity :  0.006   0.067   1775
  Dihedral  :  4.509  23.091   1365
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 14.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 22.36 %
    Favored  : 75.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.43 (0.25), residues: 1225
  helix:  0.80 (0.26), residues: 370
  sheet: -2.18 (0.29), residues: 285
  loop : -1.39 (0.28), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 107 
 TYR   0.010   0.001   TYR D  78 
 PHE   0.016   0.002   PHE A 200 
 TRP   0.037   0.001   TRP A  53 
 HIS   0.008   0.001   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (10090)
  covalent geometry    : angle       0.66428 (13705)
  hydrogen bonds       : bond        0.03414 (  318)
  hydrogen bonds       : angle       4.94565 (  915)

*********************** 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
  158 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 131
  time to evaluate  : 0.341 
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  194 MET cc_start: 0.3861 (tpp) cc_final: 0.3172 (mtp)
REVERT: A  338 MET cc_start: 0.5052 (tpt) cc_final: 0.4805 (mmm)
REVERT: B    1 MET cc_start: 0.5961 (ppp) cc_final: 0.5734 (ppp)
REVERT: B   53 TRP cc_start: 0.6971 (t60) cc_final: 0.6604 (t60)
REVERT: B  102 ILE cc_start: 0.3585 (OUTLIER) cc_final: 0.3382 (tt)
REVERT: B  338 MET cc_start: 0.4508 (tpt) cc_final: 0.4064 (tpt)
REVERT: D   35 SER cc_start: 0.6921 (t) cc_final: 0.6325 (p)
REVERT: D  112 LYS cc_start: 0.7880 (pptt) cc_final: 0.7677 (pptt)
REVERT: E   70 VAL cc_start: 0.6296 (OUTLIER) cc_final: 0.4888 (t)
REVERT: E  194 MET cc_start: 0.3880 (tmm) cc_final: 0.3371 (tpp)
  outliers start: 27
  outliers final: 20
  residues processed: 150
  average time/residue: 0.0803
  time to fit residues: 18.0564
Evaluate side-chains
  149 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 LYS
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  133 THR
Chi-restraints excluded: chain B residue  136 GLN
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  254 THR
Chi-restraints excluded: chain D residue   12 LEU
Chi-restraints excluded: chain D residue  210 SER
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 114 optimal weight:    0.2980
   chunk 88 optimal weight:    0.7980
   chunk 119 optimal weight:    2.9990
   chunk 121 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   chunk 14 optimal weight:    8.9990
   chunk 44 optimal weight:    9.9990
   chunk 111 optimal weight:    7.9990
   chunk 54 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   9 ASN
** 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 = 0.5282 r_free = 0.5282 target = 0.211244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4758 r_free = 0.4758 target = 0.164917 restraints weight = 14391.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4766 r_free = 0.4766 target = 0.167124 restraints weight = 12103.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4807 r_free = 0.4807 target = 0.170037 restraints weight = 10362.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4812 r_free = 0.4812 target = 0.170602 restraints weight = 8851.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4820 r_free = 0.4820 target = 0.171207 restraints weight = 8549.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.4839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5603
moved from start:          0.2940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10090  Z= 0.123
  Angle     :  0.664  10.135  13705  Z= 0.334
  Chirality :  0.046   0.200   1470
  Planarity :  0.006   0.066   1775
  Dihedral  :  4.444  22.696   1365
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 14.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 22.55 %
    Favored  : 75.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.25), residues: 1225
  helix:  1.28 (0.27), residues: 340
  sheet: -2.43 (0.27), residues: 335
  loop : -1.10 (0.29), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 107 
 TYR   0.010   0.001   TYR D  78 
 PHE   0.015   0.002   PHE A 200 
 TRP   0.039   0.001   TRP A  53 
 HIS   0.004   0.001   HIS E 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (10090)
  covalent geometry    : angle       0.66365 (13705)
  hydrogen bonds       : bond        0.03388 (  318)
  hydrogen bonds       : angle       4.89690 (  915)

********************** 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
  152 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 128
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.3883 (tpp) cc_final: 0.3185 (mtp)
REVERT: A  338 MET cc_start: 0.5046 (tpt) cc_final: 0.4822 (mmm)
REVERT: B    1 MET cc_start: 0.5953 (ppp) cc_final: 0.5725 (ppp)
REVERT: B   53 TRP cc_start: 0.7021 (t60) cc_final: 0.6655 (t60)
REVERT: B  338 MET cc_start: 0.4483 (tpt) cc_final: 0.4050 (tpt)
REVERT: C   96 THR cc_start: -0.0124 (OUTLIER) cc_final: -0.0519 (p)
REVERT: D   35 SER cc_start: 0.6946 (t) cc_final: 0.6341 (p)
REVERT: D  112 LYS cc_start: 0.7870 (pptt) cc_final: 0.7668 (pptt)
REVERT: E   70 VAL cc_start: 0.6333 (OUTLIER) cc_final: 0.4960 (t)
REVERT: E  133 THR cc_start: 0.6238 (OUTLIER) cc_final: 0.6026 (p)
REVERT: E  194 MET cc_start: 0.3929 (tmm) cc_final: 0.3391 (tpp)
  outliers start: 24
  outliers final: 20
  residues processed: 145
  average time/residue: 0.0802
  time to fit residues: 17.6420
Evaluate side-chains
  148 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 125
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 LYS
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue   93 ASP
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   96 THR
Chi-restraints excluded: chain C residue  198 TRP
Chi-restraints excluded: chain C residue  213 GLN
Chi-restraints excluded: chain C residue  254 THR
Chi-restraints excluded: chain D residue    9 ASN
Chi-restraints excluded: chain D residue   12 LEU
Chi-restraints excluded: chain D residue  210 SER
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   52 GLN
Chi-restraints excluded: chain E residue   53 TRP
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain E residue   93 ASP
Chi-restraints excluded: chain E residue  133 THR
Chi-restraints excluded: chain E residue  213 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 93 optimal weight:    4.9990
   chunk 96 optimal weight:    0.6980
   chunk 76 optimal weight:    3.9990
   chunk 16 optimal weight:    0.3980
   chunk 100 optimal weight:    0.0030
   chunk 103 optimal weight:    4.9990
   chunk 2 optimal weight:    0.7980
   chunk 6 optimal weight:    9.9990
   chunk 33 optimal weight:    0.4980
   chunk 60 optimal weight:    2.9990
   chunk 59 optimal weight:    8.9990
   overall best weight:    0.4790

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

Flipped N/Q/H residues before XYZ refinement:
B 136 GLN
** D   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 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 = 0.5305 r_free = 0.5305 target = 0.213835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4790 r_free = 0.4790 target = 0.167516 restraints weight = 14373.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4799 r_free = 0.4799 target = 0.169965 restraints weight = 11950.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4845 r_free = 0.4845 target = 0.173265 restraints weight = 10059.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4846 r_free = 0.4846 target = 0.173520 restraints weight = 8526.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4855 r_free = 0.4855 target = 0.174285 restraints weight = 8344.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.4875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5534
moved from start:          0.3055

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= 0.116
  Angle     :  0.671  10.246  13705  Z= 0.334
  Chirality :  0.046   0.199   1470
  Planarity :  0.006   0.067   1775
  Dihedral  :  4.318  21.743   1365
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 23.40 %
    Favored  : 74.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.19 (0.25), residues: 1225
  helix:  1.37 (0.27), residues: 340
  sheet: -2.36 (0.27), residues: 335
  loop : -1.02 (0.29), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 107 
 TYR   0.010   0.001   TYR D  78 
 PHE   0.015   0.001   PHE A 200 
 TRP   0.041   0.001   TRP A  53 
 HIS   0.004   0.001   HIS E 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (10090)
  covalent geometry    : angle       0.67067 (13705)
  hydrogen bonds       : bond        0.03187 (  318)
  hydrogen bonds       : angle       4.71026 (  915)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1859.60 seconds
wall clock time: 33 minutes 2.67 seconds (1982.67 seconds total)