Starting phenix.real_space_refine
on Wed Mar  4 04:22:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7u5j_26352/03_2026/7u5j_26352.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7u5j_26352/03_2026/7u5j_26352.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.96
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7u5j_26352/03_2026/7u5j_26352.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7u5j_26352/03_2026/7u5j_26352.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7u5j_26352/03_2026/7u5j_26352.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7u5j_26352/03_2026/7u5j_26352.map"
  }
  resolution = 2.96
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.069
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      48      5.16       5
     C    6628      2.51       5
     N    1860      2.21       5
     O    2268      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 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: 10804
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2630
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 344, 2630
          Classifications: {'peptide': 344}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 324}
    Chain: "B"
      Number of atoms: 2630
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 344, 2630
          Classifications: {'peptide': 344}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 324}
    Chain: "C"
      Number of atoms: 2630
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 344, 2630
          Classifications: {'peptide': 344}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 324}
    Chain: "D"
      Number of atoms: 2630
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 344, 2630
          Classifications: {'peptide': 344}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 324}
    Chain: "A"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 70, 70
          Classifications: {'water': 70}
          Link IDs: {None: 69}
    Chain: "B"
      Number of atoms: 68
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 68
          Classifications: {'water': 68}
          Link IDs: {None: 67}
    Chain: "C"
      Number of atoms: 73
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 73
          Classifications: {'water': 73}
          Link IDs: {None: 72}
    Chain: "D"
      Number of atoms: 73
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 73
          Classifications: {'water': 73}
          Link IDs: {None: 72}
  Time building chain proxies: 2.41, per 1000 atoms: 0.22
  Number of scatterers: 10804
  At special positions: 0
  Unit cell: (95.23, 80.25, 103.79, 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      48     16.00
     O    2268      8.00
     N    1860      7.00
     C    6628      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: 0.80
  Conformation dependent library (CDL) restraints added in 449.8 milliseconds
  

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2528

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 8 sheets defined
      53.5% alpha, 13.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 24
    Processing helix  chain 'A' and resid 36 through 47
    Processing helix  chain 'A' and resid 52 through 64
    Processing helix  chain 'A' and resid 67 through 71
      removed outlier: 3.932A  pdb=" N   VAL A  70 " --> pdb=" O   ASP A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 86
    Processing helix  chain 'A' and resid 93 through 102
    Processing helix  chain 'A' and resid 130 through 141
    Processing helix  chain 'A' and resid 160 through 180
    Processing helix  chain 'A' and resid 198 through 220
    Processing helix  chain 'A' and resid 223 through 227
    Processing helix  chain 'A' and resid 245 through 261
    Processing helix  chain 'A' and resid 276 through 289
    Processing helix  chain 'A' and resid 307 through 315
    Processing helix  chain 'A' and resid 320 through 339
      removed outlier: 4.097A  pdb=" N   ALA A 334 " --> pdb=" O   LYS A 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 9 through 24
    Processing helix  chain 'B' and resid 36 through 47
    Processing helix  chain 'B' and resid 52 through 64
    Processing helix  chain 'B' and resid 67 through 71
      removed outlier: 3.920A  pdb=" N   VAL B  70 " --> pdb=" O   ASP B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 86
    Processing helix  chain 'B' and resid 93 through 102
    Processing helix  chain 'B' and resid 130 through 141
    Processing helix  chain 'B' and resid 160 through 180
    Processing helix  chain 'B' and resid 198 through 220
    Processing helix  chain 'B' and resid 223 through 227
    Processing helix  chain 'B' and resid 245 through 261
    Processing helix  chain 'B' and resid 276 through 289
    Processing helix  chain 'B' and resid 307 through 315
    Processing helix  chain 'B' and resid 320 through 339
      removed outlier: 4.088A  pdb=" N   ALA B 334 " --> pdb=" O   LYS B 330 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 9 through 24
    Processing helix  chain 'C' and resid 36 through 47
    Processing helix  chain 'C' and resid 52 through 64
    Processing helix  chain 'C' and resid 67 through 71
      removed outlier: 3.928A  pdb=" N   VAL C  70 " --> pdb=" O   ASP C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 86
    Processing helix  chain 'C' and resid 93 through 102
    Processing helix  chain 'C' and resid 130 through 141
    Processing helix  chain 'C' and resid 160 through 180
    Processing helix  chain 'C' and resid 198 through 220
    Processing helix  chain 'C' and resid 223 through 227
    Processing helix  chain 'C' and resid 245 through 261
    Processing helix  chain 'C' and resid 276 through 289
    Processing helix  chain 'C' and resid 307 through 315
    Processing helix  chain 'C' and resid 320 through 339
      removed outlier: 4.095A  pdb=" N   ALA C 334 " --> pdb=" O   LYS C 330 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 9 through 24
    Processing helix  chain 'D' and resid 36 through 47
    Processing helix  chain 'D' and resid 52 through 64
    Processing helix  chain 'D' and resid 67 through 71
      removed outlier: 3.926A  pdb=" N   VAL D  70 " --> pdb=" O   ASP D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 80 through 86
    Processing helix  chain 'D' and resid 93 through 102
    Processing helix  chain 'D' and resid 130 through 141
    Processing helix  chain 'D' and resid 160 through 180
    Processing helix  chain 'D' and resid 198 through 220
    Processing helix  chain 'D' and resid 223 through 227
    Processing helix  chain 'D' and resid 245 through 261
    Processing helix  chain 'D' and resid 276 through 289
    Processing helix  chain 'D' and resid 307 through 315
    Processing helix  chain 'D' and resid 320 through 339
      removed outlier: 4.110A  pdb=" N   ALA D 334 " --> pdb=" O   LYS D 330 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32
      removed outlier: 6.129A  pdb=" N   GLY A  29 " --> pdb=" O   GLY A  76 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   ILE A  78 " --> pdb=" O   GLY A  29 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   LEU A  31 " --> pdb=" O   ILE A  78 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   VAL A 105 " --> pdb=" O   ASP A 144 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   ALA A 146 " --> pdb=" O   VAL A 105 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   ILE A 107 " --> pdb=" O   ALA A 146 " (cutoff:3.500A)
      removed outlier: 6.049A  pdb=" N   TRP A 148 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 7.134A  pdb=" N   ASP A 144 " --> pdb=" O   VAL A 184 " (cutoff:3.500A)
      removed outlier: 8.072A  pdb=" N   ILE A 186 " --> pdb=" O   ASP A 144 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ALA A 146 " --> pdb=" O   ILE A 186 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   GLU A 188 " --> pdb=" O   ALA A 146 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   TRP A 148 " --> pdb=" O   GLU A 188 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   GLU A 190 " --> pdb=" O   TRP A 148 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   CYS A 150 " --> pdb=" O   GLU A 190 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   LEU A 192 " --> pdb=" O   CYS A 150 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   LEU A 152 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   LEU A 229 " --> pdb=" O   THR A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 115
    Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 32
      removed outlier: 6.127A  pdb=" N   GLY B  29 " --> pdb=" O   GLY B  76 " (cutoff:3.500A)
      removed outlier: 7.910A  pdb=" N   ILE B  78 " --> pdb=" O   GLY B  29 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   LEU B  31 " --> pdb=" O   ILE B  78 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   VAL B 105 " --> pdb=" O   ASP B 144 " (cutoff:3.500A)
      removed outlier: 6.044A  pdb=" N   ALA B 146 " --> pdb=" O   VAL B 105 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   ILE B 107 " --> pdb=" O   ALA B 146 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   TRP B 148 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   ASP B 144 " --> pdb=" O   VAL B 184 " (cutoff:3.500A)
      removed outlier: 8.062A  pdb=" N   ILE B 186 " --> pdb=" O   ASP B 144 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   ALA B 146 " --> pdb=" O   ILE B 186 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   GLU B 188 " --> pdb=" O   ALA B 146 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   TRP B 148 " --> pdb=" O   GLU B 188 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   GLU B 190 " --> pdb=" O   TRP B 148 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   CYS B 150 " --> pdb=" O   GLU B 190 " (cutoff:3.500A)
      removed outlier: 7.197A  pdb=" N   LEU B 192 " --> pdb=" O   CYS B 150 " (cutoff:3.500A)
      removed outlier: 7.606A  pdb=" N   LEU B 152 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   LEU B 229 " --> pdb=" O   THR B 269 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 113 through 115
    Processing sheet with id=AA5, first strand: chain 'C' and resid 29 through 32
      removed outlier: 6.135A  pdb=" N   GLY C  29 " --> pdb=" O   GLY C  76 " (cutoff:3.500A)
      removed outlier: 7.915A  pdb=" N   ILE C  78 " --> pdb=" O   GLY C  29 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   LEU C  31 " --> pdb=" O   ILE C  78 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   VAL C 105 " --> pdb=" O   ASP C 144 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   ALA C 146 " --> pdb=" O   VAL C 105 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   ILE C 107 " --> pdb=" O   ALA C 146 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   TRP C 148 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   ASP C 144 " --> pdb=" O   VAL C 184 " (cutoff:3.500A)
      removed outlier: 8.071A  pdb=" N   ILE C 186 " --> pdb=" O   ASP C 144 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   ALA C 146 " --> pdb=" O   ILE C 186 " (cutoff:3.500A)
      removed outlier: 7.563A  pdb=" N   GLU C 188 " --> pdb=" O   ALA C 146 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   TRP C 148 " --> pdb=" O   GLU C 188 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   GLU C 190 " --> pdb=" O   TRP C 148 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   CYS C 150 " --> pdb=" O   GLU C 190 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   LEU C 192 " --> pdb=" O   CYS C 150 " (cutoff:3.500A)
      removed outlier: 7.601A  pdb=" N   LEU C 152 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 6.024A  pdb=" N   LEU C 229 " --> pdb=" O   THR C 269 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 113 through 115
    Processing sheet with id=AA7, first strand: chain 'D' and resid 29 through 32
      removed outlier: 6.134A  pdb=" N   GLY D  29 " --> pdb=" O   GLY D  76 " (cutoff:3.500A)
      removed outlier: 7.915A  pdb=" N   ILE D  78 " --> pdb=" O   GLY D  29 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   LEU D  31 " --> pdb=" O   ILE D  78 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   VAL D 105 " --> pdb=" O   ASP D 144 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   ALA D 146 " --> pdb=" O   VAL D 105 " (cutoff:3.500A)
      removed outlier: 6.073A  pdb=" N   ILE D 107 " --> pdb=" O   ALA D 146 " (cutoff:3.500A)
      removed outlier: 6.056A  pdb=" N   TRP D 148 " --> pdb=" O   ILE D 107 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   ASP D 144 " --> pdb=" O   VAL D 184 " (cutoff:3.500A)
      removed outlier: 8.064A  pdb=" N   ILE D 186 " --> pdb=" O   ASP D 144 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ALA D 146 " --> pdb=" O   ILE D 186 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   GLU D 188 " --> pdb=" O   ALA D 146 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   TRP D 148 " --> pdb=" O   GLU D 188 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   GLU D 190 " --> pdb=" O   TRP D 148 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   CYS D 150 " --> pdb=" O   GLU D 190 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   LEU D 192 " --> pdb=" O   CYS D 150 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   LEU D 152 " --> pdb=" O   LEU D 192 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   LEU D 229 " --> pdb=" O   THR D 269 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 113 through 115

    568 hydrogen bonds defined for protein.
    1656 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: 1.82

  Time building geometry restraints manager: 1.12 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3516
        1.34 -     1.46: 1636
        1.46 -     1.57: 5512
        1.57 -     1.69: 0
        1.69 -     1.81: 60
  Bond restraints: 10724
  Sorted by residual:
  bond pdb=" C   ASN A  71 "
       pdb=" N   PRO A  72 "
    ideal  model  delta    sigma   weight residual
    1.337  1.354 -0.017 1.24e-02 6.50e+03 1.93e+00
  bond pdb=" C   ASN D  71 "
       pdb=" N   PRO D  72 "
    ideal  model  delta    sigma   weight residual
    1.337  1.354 -0.017 1.24e-02 6.50e+03 1.79e+00
  bond pdb=" C   ASN B  71 "
       pdb=" N   PRO B  72 "
    ideal  model  delta    sigma   weight residual
    1.337  1.354 -0.016 1.24e-02 6.50e+03 1.76e+00
  bond pdb=" C   ASN C  71 "
       pdb=" N   PRO C  72 "
    ideal  model  delta    sigma   weight residual
    1.337  1.353 -0.016 1.24e-02 6.50e+03 1.67e+00
  bond pdb=" CA  PHE A  58 "
       pdb=" CB  PHE A  58 "
    ideal  model  delta    sigma   weight residual
    1.530  1.547 -0.017 1.68e-02 3.54e+03 9.90e-01
  ... (remaining 10719 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.05: 13697
        1.05 -     2.10: 674
        2.10 -     3.15: 134
        3.15 -     4.20: 23
        4.20 -     5.25: 8
  Bond angle restraints: 14536
  Sorted by residual:
  angle pdb=" CA  PHE D  58 "
        pdb=" CB  PHE D  58 "
        pdb=" CG  PHE D  58 "
      ideal   model   delta    sigma   weight residual
     113.80  116.26   -2.46 1.00e+00 1.00e+00 6.03e+00
  angle pdb=" CA  PHE B  58 "
        pdb=" CB  PHE B  58 "
        pdb=" CG  PHE B  58 "
      ideal   model   delta    sigma   weight residual
     113.80  116.25   -2.45 1.00e+00 1.00e+00 6.01e+00
  angle pdb=" CA  PHE A  58 "
        pdb=" CB  PHE A  58 "
        pdb=" CG  PHE A  58 "
      ideal   model   delta    sigma   weight residual
     113.80  116.23   -2.43 1.00e+00 1.00e+00 5.91e+00
  angle pdb=" CA  PHE C  58 "
        pdb=" CB  PHE C  58 "
        pdb=" CG  PHE C  58 "
      ideal   model   delta    sigma   weight residual
     113.80  116.14   -2.34 1.00e+00 1.00e+00 5.50e+00
  angle pdb=" C   ARG D  57 "
        pdb=" N   PHE D  58 "
        pdb=" CA  PHE D  58 "
      ideal   model   delta    sigma   weight residual
     121.14  117.09    4.05 1.75e+00 3.27e-01 5.35e+00
  ... (remaining 14531 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.97: 5826
       11.97 -    23.94: 526
       23.94 -    35.91: 153
       35.91 -    47.88: 34
       47.88 -    59.85: 5
  Dihedral angle restraints: 6544
    sinusoidal: 2596
      harmonic: 3948
  Sorted by residual:
  dihedral pdb=" CA  THR A 260 "
           pdb=" C   THR A 260 "
           pdb=" N   VAL A 261 "
           pdb=" CA  VAL A 261 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.23  -15.77     0      5.00e+00 4.00e-02 9.94e+00
  dihedral pdb=" CA  THR C 260 "
           pdb=" C   THR C 260 "
           pdb=" N   VAL C 261 "
           pdb=" CA  VAL C 261 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.32  -15.68     0      5.00e+00 4.00e-02 9.84e+00
  dihedral pdb=" CA  THR B 260 "
           pdb=" C   THR B 260 "
           pdb=" N   VAL B 261 "
           pdb=" CA  VAL B 261 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.32  -15.68     0      5.00e+00 4.00e-02 9.84e+00
  ... (remaining 6541 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 1108
       0.033 -    0.065: 338
       0.065 -    0.098: 141
       0.098 -    0.131: 53
       0.131 -    0.164: 4
  Chirality restraints: 1644
  Sorted by residual:
  chirality pdb=" CA  PHE C  58 "
            pdb=" N   PHE C  58 "
            pdb=" C   PHE C  58 "
            pdb=" CB  PHE C  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.69e-01
  chirality pdb=" CA  PHE B  58 "
            pdb=" N   PHE B  58 "
            pdb=" C   PHE B  58 "
            pdb=" CB  PHE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.67e-01
  chirality pdb=" CA  PHE A  58 "
            pdb=" N   PHE A  58 "
            pdb=" C   PHE A  58 "
            pdb=" CB  PHE A  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.27e-01
  ... (remaining 1641 not shown)

  Planarity restraints: 1892
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C  58 "   -0.017 2.00e-02 2.50e+03   1.49e-02 3.87e+00
        pdb=" CG  PHE C  58 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE C  58 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE C  58 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE C  58 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE C  58 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE C  58 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D  58 "    0.017 2.00e-02 2.50e+03   1.48e-02 3.83e+00
        pdb=" CG  PHE D  58 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE D  58 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE D  58 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE D  58 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE D  58 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE D  58 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  58 "   -0.016 2.00e-02 2.50e+03   1.47e-02 3.77e+00
        pdb=" CG  PHE B  58 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  58 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  58 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  58 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  58 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  58 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1889 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1480
        2.75 -     3.29: 10766
        3.29 -     3.83: 19952
        3.83 -     4.36: 23880
        4.36 -     4.90: 39095
  Nonbonded interactions: 95173
  Sorted by model distance:
  nonbonded pdb=" O   GLN B  61 "
            pdb=" OG1 THR B  65 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   GLN C  61 "
            pdb=" OG1 THR C  65 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" O   GLN A  61 "
            pdb=" OG1 THR A  65 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O   GLN D  61 "
            pdb=" OG1 THR D  65 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O   LYS C 289 "
            pdb=" O   HOH C 401 "
     model   vdw
     2.260 3.040
  ... (remaining 95168 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     10.870
  Find NCS groups from input model:        0.080
  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:             0.010
  Load rotamer database and sin/cos tables:9.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
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      :  0.004   0.038  10724  Z= 0.158
  Angle     :  0.543   5.247  14536  Z= 0.301
  Chirality :  0.041   0.164   1644
  Planarity :  0.005   0.039   1892
  Dihedral  : 10.541  59.847   4016
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  :  4.30 %
    Favored  : 93.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.22), residues: 1368
  helix:  1.07 (0.19), residues: 708
  sheet: -1.58 (0.35), residues: 192
  loop : -0.34 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 134 
 TYR   0.017   0.002   TYR D 214 
 PHE   0.034   0.003   PHE C  58 
 TRP   0.011   0.002   TRP D 148 
 HIS   0.004   0.001   HIS D  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (10724)
  covalent geometry    : angle       0.54261 (14536)
  hydrogen bonds       : bond        0.14935 (  568)
  hydrogen bonds       : angle       5.78328 ( 1656)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 185
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 GLN cc_start: 0.7589 (mt0) cc_final: 0.7186 (mt0)
REVERT: A  174 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.8527 (t80)
REVERT: A  232 ASN cc_start: 0.8152 (p0) cc_final: 0.7818 (p0)
REVERT: A  251 MET cc_start: 0.7486 (mmm) cc_final: 0.6677 (mmp)
REVERT: B   11 GLU cc_start: 0.6814 (mm-30) cc_final: 0.6540 (mm-30)
REVERT: B   86 GLN cc_start: 0.7605 (mt0) cc_final: 0.7203 (mt0)
REVERT: B  174 TYR cc_start: 0.8728 (OUTLIER) cc_final: 0.8527 (t80)
REVERT: B  251 MET cc_start: 0.7541 (mmm) cc_final: 0.6715 (mmp)
REVERT: C   11 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6600 (mm-30)
REVERT: C   86 GLN cc_start: 0.7546 (mt0) cc_final: 0.7202 (mt0)
REVERT: C  251 MET cc_start: 0.7478 (mmm) cc_final: 0.7129 (mmp)
REVERT: D   11 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6583 (mm-30)
REVERT: D   86 GLN cc_start: 0.7636 (mt0) cc_final: 0.7265 (mt0)
REVERT: D  174 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.8522 (t80)
REVERT: D  251 MET cc_start: 0.7483 (mmm) cc_final: 0.7119 (mmp)
  outliers start: 24
  outliers final: 16
  residues processed: 205
  average time/residue: 0.5278
  time to fit residues: 117.0647
Evaluate side-chains
  174 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 155
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  296 TRP
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain C residue   62 LEU
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  174 TYR
Chi-restraints excluded: chain D residue  296 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  55 ASN
A 169 ASN
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS
B  55 ASN
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 HIS
C  55 ASN
C 169 ASN
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 220 HIS
D  55 ASN
D 169 ASN
** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 220 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.206156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.154950 restraints weight = 11631.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3664 rms_B_bonded: 2.25
r_work: 0.3542 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3393 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.1130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10724  Z= 0.162
  Angle     :  0.537   5.262  14536  Z= 0.287
  Chirality :  0.041   0.159   1644
  Planarity :  0.005   0.037   1892
  Dihedral  :  6.371  59.514   1510
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  :  9.59 %
    Favored  : 87.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.22), residues: 1368
  helix:  1.52 (0.19), residues: 720
  sheet: -2.01 (0.37), residues: 160
  loop : -0.18 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  60 
 TYR   0.013   0.002   TYR D 302 
 PHE   0.031   0.003   PHE C  58 
 TRP   0.010   0.002   TRP B 148 
 HIS   0.004   0.001   HIS A  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (10724)
  covalent geometry    : angle       0.53667 (14536)
  hydrogen bonds       : bond        0.04414 (  568)
  hydrogen bonds       : angle       4.61098 ( 1656)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 190
  time to evaluate  : 0.399 
Fit side-chains
REVERT: A   86 GLN cc_start: 0.7923 (mt0) cc_final: 0.7518 (mt0)
REVERT: A  232 ASN cc_start: 0.8402 (p0) cc_final: 0.8098 (p0)
REVERT: A  247 GLU cc_start: 0.7335 (mp0) cc_final: 0.6955 (mm-30)
REVERT: A  251 MET cc_start: 0.7676 (mmm) cc_final: 0.7363 (mmm)
REVERT: B   11 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6917 (mm-30)
REVERT: B   86 GLN cc_start: 0.8002 (mt0) cc_final: 0.7607 (mt0)
REVERT: B  247 GLU cc_start: 0.7302 (mp0) cc_final: 0.7030 (mm-30)
REVERT: B  251 MET cc_start: 0.7795 (mmm) cc_final: 0.7488 (tpt)
REVERT: C   11 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6881 (mm-30)
REVERT: D   11 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6926 (mm-30)
REVERT: D   86 GLN cc_start: 0.8015 (mt0) cc_final: 0.7580 (mt0)
REVERT: D  247 GLU cc_start: 0.7304 (mp0) cc_final: 0.6948 (mm-30)
REVERT: D  251 MET cc_start: 0.7699 (mmm) cc_final: 0.7390 (mmm)
  outliers start: 33
  outliers final: 22
  residues processed: 208
  average time/residue: 0.4576
  time to fit residues: 104.5610
Evaluate side-chains
  189 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 167
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  296 TRP
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  289 LYS
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain C residue   34 ASP
Chi-restraints excluded: chain C residue   62 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain D residue   34 ASP
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  174 TYR
Chi-restraints excluded: chain D residue  296 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 57 optimal weight:    0.7980
   chunk 59 optimal weight:    0.5980
   chunk 119 optimal weight:    0.9990
   chunk 1 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 101 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 127 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0000
   overall best weight:    0.5384

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  71 ASN
B  81 HIS
B 169 ASN
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  71 ASN
C  81 HIS
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  71 ASN
D  81 HIS
** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 246 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.209437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.157583 restraints weight = 11651.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 2.24
r_work: 0.3586 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.1508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10724  Z= 0.125
  Angle     :  0.503   6.093  14536  Z= 0.263
  Chirality :  0.040   0.158   1644
  Planarity :  0.005   0.034   1892
  Dihedral  :  6.084  58.675   1508
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  :  9.77 %
    Favored  : 87.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.94 (0.22), residues: 1368
  helix:  1.81 (0.18), residues: 720
  sheet: -2.10 (0.36), residues: 160
  loop : -0.07 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  22 
 TYR   0.010   0.002   TYR D 302 
 PHE   0.028   0.003   PHE C  58 
 TRP   0.008   0.001   TRP D 148 
 HIS   0.006   0.001   HIS D 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (10724)
  covalent geometry    : angle       0.50298 (14536)
  hydrogen bonds       : bond        0.03724 (  568)
  hydrogen bonds       : angle       4.22791 ( 1656)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 190
  time to evaluate  : 0.396 
Fit side-chains
REVERT: A   86 GLN cc_start: 0.8016 (mt0) cc_final: 0.7734 (mt0)
REVERT: A   99 LYS cc_start: 0.8132 (mmtp) cc_final: 0.7901 (mmtp)
REVERT: A  174 TYR cc_start: 0.8867 (OUTLIER) cc_final: 0.8608 (t80)
REVERT: A  232 ASN cc_start: 0.8194 (p0) cc_final: 0.7911 (p0)
REVERT: A  251 MET cc_start: 0.7624 (mmm) cc_final: 0.7249 (mmp)
REVERT: B   11 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6881 (mm-30)
REVERT: B   86 GLN cc_start: 0.7949 (mt0) cc_final: 0.7576 (mt0)
REVERT: B  174 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.8614 (t80)
REVERT: B  251 MET cc_start: 0.7687 (mmm) cc_final: 0.7324 (tpt)
REVERT: C   11 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6879 (mm-30)
REVERT: C   71 ASN cc_start: 0.7309 (m-40) cc_final: 0.7075 (m-40)
REVERT: C   99 LYS cc_start: 0.8152 (mmtp) cc_final: 0.7948 (mmtp)
REVERT: C  251 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7242 (tpp)
REVERT: D   11 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6897 (mm-30)
REVERT: D   86 GLN cc_start: 0.8072 (mt0) cc_final: 0.7629 (mt0)
REVERT: D  174 TYR cc_start: 0.8865 (OUTLIER) cc_final: 0.8610 (t80)
REVERT: D  251 MET cc_start: 0.7613 (mmm) cc_final: 0.7264 (mmp)
  outliers start: 32
  outliers final: 21
  residues processed: 212
  average time/residue: 0.4259
  time to fit residues: 99.3131
Evaluate side-chains
  198 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 173
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  296 TRP
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  289 LYS
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain C residue   34 ASP
Chi-restraints excluded: chain C residue   62 LEU
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain D residue   34 ASP
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  174 TYR
Chi-restraints excluded: chain D residue  296 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 71 optimal weight:    6.9990
   chunk 102 optimal weight:    3.9990
   chunk 22 optimal weight:    0.5980
   chunk 67 optimal weight:    4.9990
   chunk 96 optimal weight:    0.0870
   chunk 122 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0170
   chunk 20 optimal weight:    0.5980
   chunk 90 optimal weight:    0.8980
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
A  81 HIS
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  81 HIS
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 169 ASN
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  81 HIS
** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  81 HIS
** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 307 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.210288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.158712 restraints weight = 11775.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3711 rms_B_bonded: 2.23
r_work: 0.3588 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10724  Z= 0.117
  Angle     :  0.500   5.995  14536  Z= 0.261
  Chirality :  0.040   0.159   1644
  Planarity :  0.004   0.032   1892
  Dihedral  :  5.967  58.728   1508
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 10.93 %
    Favored  : 85.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  1.09 (0.22), residues: 1368
  helix:  1.93 (0.18), residues: 724
  sheet: -2.12 (0.36), residues: 160
  loop :  0.01 (0.29), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  22 
 TYR   0.011   0.001   TYR D 302 
 PHE   0.028   0.003   PHE C  58 
 TRP   0.007   0.001   TRP A 148 
 HIS   0.004   0.001   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (10724)
  covalent geometry    : angle       0.49973 (14536)
  hydrogen bonds       : bond        0.03546 (  568)
  hydrogen bonds       : angle       4.10947 ( 1656)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 179
  time to evaluate  : 0.422 
Fit side-chains
REVERT: A  174 TYR cc_start: 0.8810 (OUTLIER) cc_final: 0.8602 (t80)
REVERT: A  232 ASN cc_start: 0.8080 (p0) cc_final: 0.7765 (p0)
REVERT: A  247 GLU cc_start: 0.7241 (mp0) cc_final: 0.7007 (mm-30)
REVERT: A  251 MET cc_start: 0.7638 (mmm) cc_final: 0.7287 (tpt)
REVERT: B   11 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6903 (mm-30)
REVERT: B   86 GLN cc_start: 0.7899 (mt0) cc_final: 0.7474 (mt0)
REVERT: B  174 TYR cc_start: 0.8818 (OUTLIER) cc_final: 0.8541 (t80)
REVERT: B  247 GLU cc_start: 0.7212 (mp0) cc_final: 0.6988 (mm-30)
REVERT: B  251 MET cc_start: 0.7751 (mmm) cc_final: 0.7402 (tpt)
REVERT: C   11 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6900 (mm-30)
REVERT: C  247 GLU cc_start: 0.7095 (mp0) cc_final: 0.6866 (mm-30)
REVERT: D   11 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6892 (mm-30)
REVERT: D   86 GLN cc_start: 0.8008 (mt0) cc_final: 0.7595 (mt0)
REVERT: D  174 TYR cc_start: 0.8804 (OUTLIER) cc_final: 0.8593 (t80)
REVERT: D  247 GLU cc_start: 0.7208 (mp0) cc_final: 0.6954 (mm-30)
REVERT: D  251 MET cc_start: 0.7709 (mmm) cc_final: 0.7357 (mmp)
  outliers start: 36
  outliers final: 24
  residues processed: 205
  average time/residue: 0.4750
  time to fit residues: 106.7750
Evaluate side-chains
  192 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 165
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  296 TRP
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain C residue   34 ASP
Chi-restraints excluded: chain C residue   62 LEU
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain D residue   34 ASP
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  174 TYR
Chi-restraints excluded: chain D residue  296 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 37 optimal weight:    6.9990
   chunk 111 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 121 optimal weight:    0.5980
   chunk 60 optimal weight:    0.6980
   chunk 31 optimal weight:    9.9990
   chunk 123 optimal weight:    0.8980
   chunk 68 optimal weight:    0.8980
   chunk 134 optimal weight:    3.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A  71 ASN
A  81 HIS
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 307 GLN
B  81 HIS
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  81 HIS
** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  81 HIS
** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.207890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.156696 restraints weight = 11738.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 2.43
r_work: 0.3539 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.1744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10724  Z= 0.153
  Angle     :  0.526   6.429  14536  Z= 0.275
  Chirality :  0.041   0.159   1644
  Planarity :  0.005   0.036   1892
  Dihedral  :  6.096  58.556   1508
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 12.46 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.22), residues: 1368
  helix:  1.91 (0.18), residues: 720
  sheet: -2.25 (0.37), residues: 160
  loop : -0.16 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D  22 
 TYR   0.018   0.002   TYR B 138 
 PHE   0.028   0.003   PHE B  58 
 TRP   0.009   0.001   TRP C 148 
 HIS   0.004   0.001   HIS A  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (10724)
  covalent geometry    : angle       0.52571 (14536)
  hydrogen bonds       : bond        0.03868 (  568)
  hydrogen bonds       : angle       4.18825 ( 1656)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 177
  time to evaluate  : 0.395 
Fit side-chains
REVERT: A  101 LYS cc_start: 0.7994 (tptm) cc_final: 0.7785 (tptp)
REVERT: A  174 TYR cc_start: 0.8890 (OUTLIER) cc_final: 0.8638 (t80)
REVERT: A  232 ASN cc_start: 0.8284 (p0) cc_final: 0.8018 (p0)
REVERT: A  247 GLU cc_start: 0.7274 (mp0) cc_final: 0.6989 (mm-30)
REVERT: A  251 MET cc_start: 0.7652 (mmm) cc_final: 0.7284 (mmp)
REVERT: B   11 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7060 (mm-30)
REVERT: B   86 GLN cc_start: 0.8053 (mt0) cc_final: 0.7635 (mt0)
REVERT: B  174 TYR cc_start: 0.8891 (OUTLIER) cc_final: 0.8642 (t80)
REVERT: B  251 MET cc_start: 0.7696 (mmm) cc_final: 0.7365 (tpt)
REVERT: C   11 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7054 (mm-30)
REVERT: C   81 HIS cc_start: 0.7014 (t-170) cc_final: 0.6795 (t70)
REVERT: D   11 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7012 (mm-30)
REVERT: D   86 GLN cc_start: 0.8064 (mt0) cc_final: 0.7709 (mt0)
REVERT: D  174 TYR cc_start: 0.8893 (OUTLIER) cc_final: 0.8640 (t80)
REVERT: D  251 MET cc_start: 0.7676 (mmm) cc_final: 0.7318 (mmp)
  outliers start: 36
  outliers final: 25
  residues processed: 204
  average time/residue: 0.4077
  time to fit residues: 92.0426
Evaluate side-chains
  199 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 171
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  296 TRP
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain C residue   34 ASP
Chi-restraints excluded: chain C residue   62 LEU
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain D residue   34 ASP
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  174 TYR
Chi-restraints excluded: chain D residue  296 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 3 optimal weight:    6.9990
   chunk 111 optimal weight:    0.8980
   chunk 94 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 60 optimal weight:    0.6980
   chunk 98 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 90 optimal weight:    0.4980
   chunk 76 optimal weight:    2.9990
   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  81 HIS
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 179 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 = 0.4225 r_free = 0.4225 target = 0.208110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.156830 restraints weight = 11841.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3691 rms_B_bonded: 2.48
r_work: 0.3543 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10724  Z= 0.146
  Angle     :  0.531   6.913  14536  Z= 0.279
  Chirality :  0.041   0.160   1644
  Planarity :  0.005   0.041   1892
  Dihedral  :  6.118  59.170   1508
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 12.63 %
    Favored  : 84.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  1.10 (0.22), residues: 1368
  helix:  1.98 (0.18), residues: 720
  sheet: -2.05 (0.51), residues: 96
  loop : -0.39 (0.26), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D  22 
 TYR   0.031   0.002   TYR C 138 
 PHE   0.028   0.003   PHE C  58 
 TRP   0.009   0.001   TRP C 148 
 HIS   0.007   0.001   HIS C  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (10724)
  covalent geometry    : angle       0.53148 (14536)
  hydrogen bonds       : bond        0.03857 (  568)
  hydrogen bonds       : angle       4.21569 ( 1656)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 178
  time to evaluate  : 0.400 
Fit side-chains
REVERT: A   31 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7190 (tp)
REVERT: A  174 TYR cc_start: 0.8915 (OUTLIER) cc_final: 0.8667 (t80)
REVERT: A  232 ASN cc_start: 0.8184 (p0) cc_final: 0.7872 (p0)
REVERT: A  247 GLU cc_start: 0.7207 (mp0) cc_final: 0.6971 (mm-30)
REVERT: A  251 MET cc_start: 0.7648 (mmm) cc_final: 0.7284 (mmp)
REVERT: B   11 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6978 (mm-30)
REVERT: B   86 GLN cc_start: 0.8045 (mt0) cc_final: 0.7612 (mt0)
REVERT: B  174 TYR cc_start: 0.8905 (OUTLIER) cc_final: 0.8654 (t80)
REVERT: B  247 GLU cc_start: 0.7225 (mp0) cc_final: 0.6987 (mm-30)
REVERT: B  251 MET cc_start: 0.7688 (mmm) cc_final: 0.7314 (mmp)
REVERT: C   11 GLU cc_start: 0.7248 (mm-30) cc_final: 0.6907 (mm-30)
REVERT: C   31 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7148 (tp)
REVERT: C  174 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.8622 (t80)
REVERT: C  247 GLU cc_start: 0.7246 (mp0) cc_final: 0.6967 (mm-30)
REVERT: D   11 GLU cc_start: 0.7367 (mm-30) cc_final: 0.7012 (mm-30)
REVERT: D   31 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7154 (tp)
REVERT: D   86 GLN cc_start: 0.8030 (mt0) cc_final: 0.7704 (mt0)
REVERT: D  174 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.8661 (t80)
REVERT: D  247 GLU cc_start: 0.7205 (mp0) cc_final: 0.6950 (mm-30)
REVERT: D  251 MET cc_start: 0.7648 (mmm) cc_final: 0.7303 (mmp)
  outliers start: 37
  outliers final: 25
  residues processed: 205
  average time/residue: 0.4497
  time to fit residues: 101.7471
Evaluate side-chains
  203 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 171
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  296 TRP
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   34 ASP
Chi-restraints excluded: chain C residue   62 LEU
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue  105 VAL
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  174 TYR
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   34 ASP
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  174 TYR
Chi-restraints excluded: chain D residue  296 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 122 optimal weight:    0.9990
   chunk 72 optimal weight:    9.9990
   chunk 86 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 98 optimal weight:    3.9990
   chunk 50 optimal weight:    0.5980
   chunk 107 optimal weight:    0.9990
   chunk 126 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 77 optimal weight:    0.6980
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 246 HIS
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 275 GLN
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 275 GLN
** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 275 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.207498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.157850 restraints weight = 11749.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 2.41
r_work: 0.3554 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.1921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10724  Z= 0.159
  Angle     :  0.548   7.186  14536  Z= 0.288
  Chirality :  0.041   0.164   1644
  Planarity :  0.005   0.049   1892
  Dihedral  :  6.142  59.279   1507
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 13.26 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  1.01 (0.22), residues: 1368
  helix:  1.94 (0.18), residues: 720
  sheet: -2.08 (0.50), residues: 96
  loop : -0.48 (0.26), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  22 
 TYR   0.036   0.002   TYR C 138 
 PHE   0.028   0.003   PHE C  58 
 TRP   0.009   0.001   TRP C 148 
 HIS   0.005   0.001   HIS A 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 (10724)
  covalent geometry    : angle       0.54760 (14536)
  hydrogen bonds       : bond        0.03960 (  568)
  hydrogen bonds       : angle       4.27478 ( 1656)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 178
  time to evaluate  : 0.431 
Fit side-chains
REVERT: A   31 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7118 (tp)
REVERT: A  174 TYR cc_start: 0.8949 (OUTLIER) cc_final: 0.8657 (t80)
REVERT: A  232 ASN cc_start: 0.8215 (p0) cc_final: 0.7907 (p0)
REVERT: A  247 GLU cc_start: 0.7154 (mp0) cc_final: 0.6933 (mp0)
REVERT: A  251 MET cc_start: 0.7582 (mmm) cc_final: 0.6891 (mmp)
REVERT: B   11 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6979 (mm-30)
REVERT: B   86 GLN cc_start: 0.7836 (mt0) cc_final: 0.7424 (mt0)
REVERT: B  174 TYR cc_start: 0.8937 (OUTLIER) cc_final: 0.8634 (t80)
REVERT: B  247 GLU cc_start: 0.7152 (mp0) cc_final: 0.6933 (mm-30)
REVERT: B  251 MET cc_start: 0.7656 (mmm) cc_final: 0.7337 (tpt)
REVERT: C   11 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6988 (mm-30)
REVERT: C   31 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7119 (tp)
REVERT: C   85 TYR cc_start: 0.5630 (m-80) cc_final: 0.5421 (m-80)
REVERT: C  174 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.8675 (t80)
REVERT: C  247 GLU cc_start: 0.7213 (mp0) cc_final: 0.6907 (mm-30)
REVERT: D   11 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6987 (mm-30)
REVERT: D   31 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7093 (tp)
REVERT: D   86 GLN cc_start: 0.8041 (mt0) cc_final: 0.7695 (mt0)
REVERT: D  174 TYR cc_start: 0.8949 (OUTLIER) cc_final: 0.8653 (t80)
REVERT: D  247 GLU cc_start: 0.7111 (mp0) cc_final: 0.6780 (mm-30)
  outliers start: 37
  outliers final: 22
  residues processed: 204
  average time/residue: 0.4524
  time to fit residues: 101.8110
Evaluate side-chains
  200 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 171
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  296 TRP
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   34 ASP
Chi-restraints excluded: chain C residue   62 LEU
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  174 TYR
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   34 ASP
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  174 TYR
Chi-restraints excluded: chain D residue  296 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 59 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 94 optimal weight:    0.4980
   chunk 44 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 134 optimal weight:    6.9990
   chunk 88 optimal weight:    1.9990
   chunk 115 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.207606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.155784 restraints weight = 11716.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 2.25
r_work: 0.3562 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3414 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10724  Z= 0.149
  Angle     :  0.549   7.471  14536  Z= 0.286
  Chirality :  0.041   0.161   1644
  Planarity :  0.005   0.049   1892
  Dihedral  :  6.072  59.667   1506
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 13.62 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  1.02 (0.22), residues: 1368
  helix:  1.91 (0.18), residues: 724
  sheet: -2.07 (0.50), residues: 96
  loop : -0.43 (0.26), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG D  22 
 TYR   0.028   0.002   TYR C 138 
 PHE   0.028   0.003   PHE C  58 
 TRP   0.009   0.001   TRP C 148 
 HIS   0.004   0.001   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (10724)
  covalent geometry    : angle       0.54859 (14536)
  hydrogen bonds       : bond        0.03860 (  568)
  hydrogen bonds       : angle       4.23081 ( 1656)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 174
  time to evaluate  : 0.436 
Fit side-chains
REVERT: A   31 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7252 (tp)
REVERT: A  174 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.8755 (t80)
REVERT: A  232 ASN cc_start: 0.8297 (p0) cc_final: 0.7995 (p0)
REVERT: B   11 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7122 (mm-30)
REVERT: B   86 GLN cc_start: 0.7900 (mt0) cc_final: 0.7661 (mt0)
REVERT: B  174 TYR cc_start: 0.8940 (OUTLIER) cc_final: 0.8657 (t80)
REVERT: B  251 MET cc_start: 0.7734 (mmm) cc_final: 0.7440 (tpt)
REVERT: C   11 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7141 (mm-30)
REVERT: C   31 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7275 (tp)
REVERT: D   11 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7113 (mm-30)
REVERT: D   31 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7230 (tp)
REVERT: D   86 GLN cc_start: 0.8104 (mt0) cc_final: 0.7659 (mt0)
REVERT: D  174 TYR cc_start: 0.8956 (OUTLIER) cc_final: 0.8751 (t80)
  outliers start: 35
  outliers final: 26
  residues processed: 200
  average time/residue: 0.4521
  time to fit residues: 99.7313
Evaluate side-chains
  200 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 168
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  156 GLU
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  296 TRP
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   34 ASP
Chi-restraints excluded: chain C residue   62 LEU
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   34 ASP
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  174 TYR
Chi-restraints excluded: chain D residue  296 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 133 optimal weight:    0.9980
   chunk 105 optimal weight:    7.9990
   chunk 70 optimal weight:    0.5980
   chunk 128 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0010
   overall best weight:    0.6986

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 307 GLN
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 179 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 = 0.4223 r_free = 0.4223 target = 0.208047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.156543 restraints weight = 11706.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3703 rms_B_bonded: 2.25
r_work: 0.3577 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3428 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10724  Z= 0.144
  Angle     :  0.558   7.741  14536  Z= 0.290
  Chirality :  0.041   0.161   1644
  Planarity :  0.005   0.054   1892
  Dihedral  :  6.051  59.999   1506
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 14.16 %
    Favored  : 82.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.93 (0.22), residues: 1368
  helix:  1.96 (0.18), residues: 724
  sheet: -2.68 (0.38), residues: 148
  loop : -0.24 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG D  22 
 TYR   0.026   0.002   TYR D 302 
 PHE   0.028   0.003   PHE C  58 
 TRP   0.008   0.001   TRP A 148 
 HIS   0.004   0.001   HIS C  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (10724)
  covalent geometry    : angle       0.55802 (14536)
  hydrogen bonds       : bond        0.03840 (  568)
  hydrogen bonds       : angle       4.23851 ( 1656)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 168
  time to evaluate  : 0.396 
Fit side-chains
REVERT: A   31 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7235 (tp)
REVERT: A   86 GLN cc_start: 0.8087 (mt0) cc_final: 0.7792 (mt0)
REVERT: A  174 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.8738 (t80)
REVERT: A  232 ASN cc_start: 0.8293 (p0) cc_final: 0.7999 (p0)
REVERT: A  247 GLU cc_start: 0.7298 (mp0) cc_final: 0.7008 (mm-30)
REVERT: A  307 GLN cc_start: 0.6780 (OUTLIER) cc_final: 0.6554 (pm20)
REVERT: B   11 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7212 (mm-30)
REVERT: B   86 GLN cc_start: 0.7899 (mt0) cc_final: 0.7659 (mt0)
REVERT: B  174 TYR cc_start: 0.8930 (OUTLIER) cc_final: 0.8708 (t80)
REVERT: B  251 MET cc_start: 0.7735 (mmm) cc_final: 0.7368 (mmp)
REVERT: C   11 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7227 (mm-30)
REVERT: C   31 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7284 (tp)
REVERT: C  247 GLU cc_start: 0.7434 (mp0) cc_final: 0.7111 (mm-30)
REVERT: D   11 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7201 (mm-30)
REVERT: D   31 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7227 (tp)
REVERT: D   86 GLN cc_start: 0.8094 (mt0) cc_final: 0.7667 (mt0)
REVERT: D  174 TYR cc_start: 0.8937 (OUTLIER) cc_final: 0.8727 (t80)
REVERT: D  247 GLU cc_start: 0.7331 (mp0) cc_final: 0.7007 (mm-30)
  outliers start: 36
  outliers final: 25
  residues processed: 195
  average time/residue: 0.4747
  time to fit residues: 101.7393
Evaluate side-chains
  199 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 167
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  156 GLU
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  296 TRP
Chi-restraints excluded: chain A residue  307 GLN
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   34 ASP
Chi-restraints excluded: chain C residue   62 LEU
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   34 ASP
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  174 TYR
Chi-restraints excluded: chain D residue  296 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 80 optimal weight:    0.2980
   chunk 97 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 109 optimal weight:    4.9990
   chunk 40 optimal weight:    0.1980
   chunk 65 optimal weight:    0.8980
   chunk 34 optimal weight:    0.3980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 307 GLN
** D 179 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 = 0.4232 r_free = 0.4232 target = 0.209082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.157815 restraints weight = 11712.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 2.25
r_work: 0.3583 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10724  Z= 0.129
  Angle     :  0.559   8.165  14536  Z= 0.288
  Chirality :  0.040   0.161   1644
  Planarity :  0.005   0.059   1892
  Dihedral  :  6.016  59.820   1506
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 14.34 %
    Favored  : 82.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.97 (0.22), residues: 1368
  helix:  2.00 (0.18), residues: 724
  sheet: -2.70 (0.38), residues: 148
  loop : -0.20 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG C  22 
 TYR   0.032   0.002   TYR C 302 
 PHE   0.028   0.002   PHE C  58 
 TRP   0.007   0.001   TRP A 148 
 HIS   0.004   0.001   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (10724)
  covalent geometry    : angle       0.55918 (14536)
  hydrogen bonds       : bond        0.03721 (  568)
  hydrogen bonds       : angle       4.24525 ( 1656)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 169
  time to evaluate  : 0.404 
Fit side-chains
REVERT: A   31 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7159 (tp)
REVERT: A   86 GLN cc_start: 0.8022 (mt0) cc_final: 0.7789 (mt0)
REVERT: A  174 TYR cc_start: 0.8902 (OUTLIER) cc_final: 0.8657 (t80)
REVERT: A  232 ASN cc_start: 0.8189 (p0) cc_final: 0.7882 (p0)
REVERT: A  247 GLU cc_start: 0.7268 (mp0) cc_final: 0.6959 (mm-30)
REVERT: B   11 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7117 (mm-30)
REVERT: B   81 HIS cc_start: 0.7102 (t70) cc_final: 0.6706 (t-90)
REVERT: B  174 TYR cc_start: 0.8885 (OUTLIER) cc_final: 0.8629 (t80)
REVERT: B  251 MET cc_start: 0.7690 (mmm) cc_final: 0.7302 (tpt)
REVERT: C   11 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7138 (mm-30)
REVERT: C   31 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7153 (tp)
REVERT: C  247 GLU cc_start: 0.7328 (mp0) cc_final: 0.7000 (mm-30)
REVERT: D   11 GLU cc_start: 0.7313 (mm-30) cc_final: 0.7093 (mm-30)
REVERT: D   31 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7143 (tp)
REVERT: D   86 GLN cc_start: 0.8071 (mt0) cc_final: 0.7661 (mt0)
REVERT: D  174 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.8654 (t80)
REVERT: D  247 GLU cc_start: 0.7271 (mp0) cc_final: 0.6933 (mm-30)
  outliers start: 34
  outliers final: 25
  residues processed: 195
  average time/residue: 0.4719
  time to fit residues: 100.9314
Evaluate side-chains
  195 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 164
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  156 GLU
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  296 TRP
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   34 ASP
Chi-restraints excluded: chain C residue   62 LEU
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   34 ASP
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  174 TYR
Chi-restraints excluded: chain D residue  296 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 89 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 93 optimal weight:    0.9980
   chunk 127 optimal weight:    0.6980
   chunk 121 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 130 optimal weight:    0.0980
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 307 GLN
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 179 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 = 0.4228 r_free = 0.4228 target = 0.208562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.157234 restraints weight = 11735.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 2.24
r_work: 0.3573 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3427 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.2186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10724  Z= 0.141
  Angle     :  0.565   8.058  14536  Z= 0.290
  Chirality :  0.041   0.161   1644
  Planarity :  0.005   0.054   1892
  Dihedral  :  5.995  59.661   1506
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 14.78 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.22), residues: 1368
  helix:  1.98 (0.18), residues: 724
  sheet: -2.70 (0.38), residues: 148
  loop : -0.22 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG C  22 
 TYR   0.033   0.002   TYR C 302 
 PHE   0.028   0.003   PHE C  58 
 TRP   0.007   0.001   TRP A 148 
 HIS   0.004   0.001   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (10724)
  covalent geometry    : angle       0.56472 (14536)
  hydrogen bonds       : bond        0.03772 (  568)
  hydrogen bonds       : angle       4.28671 ( 1656)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3689.06 seconds
wall clock time: 63 minutes 50.48 seconds (3830.48 seconds total)