Starting phenix.real_space_refine
on Sun May  3 10:12:38 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/11nu_75871/05_2026/11nu_75871.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/11nu_75871/05_2026/11nu_75871.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=1.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/11nu_75871/05_2026/11nu_75871.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/11nu_75871/05_2026/11nu_75871.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/11nu_75871/05_2026/11nu_75871.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/11nu_75871/05_2026/11nu_75871.map"
  }
  resolution = 1.97
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
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      44      5.16       5
     C    6588      2.51       5
     N    1860      2.21       5
     O    3737      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12229
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
    Chain: "B"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
    Chain: "C"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
    Chain: "D"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
    Chain: "A"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 429, 429
          Classifications: {'water': 429}
          Link IDs: {None: 428}
    Chain: "B"
      Number of atoms: 430
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 430
          Classifications: {'water': 430}
          Link IDs: {None: 429}
    Chain: "C"
      Number of atoms: 457
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 457, 457
          Classifications: {'water': 457}
          Link IDs: {None: 456}
    Chain: "D"
      Number of atoms: 441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 441, 441
          Classifications: {'water': 441}
          Link IDs: {None: 440}
  Time building chain proxies: 3.44, per 1000 atoms: 0.28
  Number of scatterers: 12229
  At special positions: 0
  Unit cell: (99.225, 78.645, 109.515, 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      44     16.00
     O    3737      8.00
     N    1860      7.00
     C    6588      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: 1.21
  Conformation dependent library (CDL) restraints added in 450.5 milliseconds
  

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2520

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 8 sheets defined
      55.4% alpha, 13.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.59
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 23
    Processing helix  chain 'A' and resid 35 through 45
      removed outlier: 3.932A  pdb=" N   LYS A  41 " --> pdb=" O   GLY A  37 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ARG A  42 " --> pdb=" O   SER A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 64
    Processing helix  chain 'A' and resid 66 through 71
      Proline residue:  A  71  - end of helix
    Processing helix  chain 'A' and resid 79 through 84
      removed outlier: 3.727A  pdb=" N   TYR A  84 " --> pdb=" O   HIS A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 100
    Processing helix  chain 'A' and resid 129 through 140
    Processing helix  chain 'A' and resid 159 through 180
    Processing helix  chain 'A' and resid 197 through 219
    Processing helix  chain 'A' and resid 222 through 225
    Processing helix  chain 'A' and resid 244 through 260
    Processing helix  chain 'A' and resid 275 through 288
    Processing helix  chain 'A' and resid 302 through 314
      removed outlier: 5.383A  pdb=" N   SER A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 5.154A  pdb=" N   ALA A 309 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 318
      No H-bonds generated for 'chain 'A' and resid 316 through 318'
    Processing helix  chain 'A' and resid 319 through 338
    Processing helix  chain 'B' and resid 8 through 23
    Processing helix  chain 'B' and resid 35 through 45
      removed outlier: 3.913A  pdb=" N   LYS B  41 " --> pdb=" O   GLY B  37 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ARG B  42 " --> pdb=" O   SER B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 64
    Processing helix  chain 'B' and resid 66 through 70
    Processing helix  chain 'B' and resid 79 through 84
      removed outlier: 3.724A  pdb=" N   TYR B  84 " --> pdb=" O   HIS B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 100
    Processing helix  chain 'B' and resid 129 through 140
    Processing helix  chain 'B' and resid 159 through 180
    Processing helix  chain 'B' and resid 197 through 219
    Processing helix  chain 'B' and resid 222 through 225
    Processing helix  chain 'B' and resid 244 through 260
    Processing helix  chain 'B' and resid 275 through 288
    Processing helix  chain 'B' and resid 302 through 314
      removed outlier: 6.565A  pdb=" N   SER B 308 " --> pdb=" O   ALA B 304 " (cutoff:3.500A)
      removed outlier: 5.247A  pdb=" N   ALA B 309 " --> pdb=" O   LEU B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 318
      No H-bonds generated for 'chain 'B' and resid 316 through 318'
    Processing helix  chain 'B' and resid 319 through 338
    Processing helix  chain 'C' and resid 8 through 23
    Processing helix  chain 'C' and resid 35 through 45
      removed outlier: 3.908A  pdb=" N   LYS C  41 " --> pdb=" O   GLY C  37 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ARG C  42 " --> pdb=" O   SER C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 64
    Processing helix  chain 'C' and resid 66 through 71
      Proline residue:  C  71  - end of helix
    Processing helix  chain 'C' and resid 79 through 84
      removed outlier: 3.715A  pdb=" N   TYR C  84 " --> pdb=" O   HIS C  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 100
    Processing helix  chain 'C' and resid 129 through 141
    Processing helix  chain 'C' and resid 159 through 180
    Processing helix  chain 'C' and resid 197 through 219
    Processing helix  chain 'C' and resid 222 through 225
    Processing helix  chain 'C' and resid 244 through 260
    Processing helix  chain 'C' and resid 275 through 288
    Processing helix  chain 'C' and resid 302 through 314
      removed outlier: 6.584A  pdb=" N   SER C 308 " --> pdb=" O   ALA C 304 " (cutoff:3.500A)
      removed outlier: 5.231A  pdb=" N   ALA C 309 " --> pdb=" O   LEU C 305 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 316 through 318
      No H-bonds generated for 'chain 'C' and resid 316 through 318'
    Processing helix  chain 'C' and resid 319 through 338
    Processing helix  chain 'D' and resid 8 through 23
    Processing helix  chain 'D' and resid 35 through 45
      removed outlier: 3.927A  pdb=" N   LYS D  41 " --> pdb=" O   GLY D  37 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ARG D  42 " --> pdb=" O   SER D  38 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 51 through 64
    Processing helix  chain 'D' and resid 66 through 71
      Proline residue:  D  71  - end of helix
    Processing helix  chain 'D' and resid 79 through 84
      removed outlier: 3.731A  pdb=" N   TYR D  84 " --> pdb=" O   HIS D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 92 through 100
    Processing helix  chain 'D' and resid 129 through 140
    Processing helix  chain 'D' and resid 159 through 180
    Processing helix  chain 'D' and resid 197 through 219
    Processing helix  chain 'D' and resid 222 through 225
    Processing helix  chain 'D' and resid 244 through 260
    Processing helix  chain 'D' and resid 275 through 288
    Processing helix  chain 'D' and resid 302 through 314
      removed outlier: 6.452A  pdb=" N   SER D 308 " --> pdb=" O   ALA D 304 " (cutoff:3.500A)
      removed outlier: 5.248A  pdb=" N   ALA D 309 " --> pdb=" O   LEU D 305 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 316 through 318
      No H-bonds generated for 'chain 'D' and resid 316 through 318'
    Processing helix  chain 'D' and resid 319 through 338
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32
      removed outlier: 6.859A  pdb=" N   GLY A  28 " --> pdb=" O   GLY A  74 " (cutoff:3.500A)
      removed outlier: 5.892A  pdb=" N   VAL A  76 " --> pdb=" O   GLY A  28 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   LEU A  30 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
      removed outlier: 5.789A  pdb=" N   LEU A  78 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   ALA A  32 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   VAL A 104 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
      removed outlier: 5.733A  pdb=" N   ALA A 145 " --> pdb=" O   VAL A 104 " (cutoff:3.500A)
      removed outlier: 5.849A  pdb=" N   ILE A 106 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
      removed outlier: 5.800A  pdb=" N   TRP A 147 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   TRP A 147 " --> pdb=" O   ILE A 185 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLU A 187 " --> pdb=" O   TRP A 147 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   LEU A 228 " --> pdb=" O   THR A 268 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 114
    Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 32
      removed outlier: 6.859A  pdb=" N   GLY B  28 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
      removed outlier: 5.894A  pdb=" N   VAL B  76 " --> pdb=" O   GLY B  28 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   LEU B  30 " --> pdb=" O   VAL B  76 " (cutoff:3.500A)
      removed outlier: 5.795A  pdb=" N   LEU B  78 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   ALA B  32 " --> pdb=" O   LEU B  78 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   VAL B 104 " --> pdb=" O   ASP B 143 " (cutoff:3.500A)
      removed outlier: 5.733A  pdb=" N   ALA B 145 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
      removed outlier: 5.848A  pdb=" N   ILE B 106 " --> pdb=" O   ALA B 145 " (cutoff:3.500A)
      removed outlier: 5.800A  pdb=" N   TRP B 147 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   TRP B 147 " --> pdb=" O   ILE B 185 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLU B 187 " --> pdb=" O   TRP B 147 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   LEU B 228 " --> pdb=" O   THR B 268 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 114
    Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 32
      removed outlier: 6.862A  pdb=" N   GLY C  28 " --> pdb=" O   GLY C  74 " (cutoff:3.500A)
      removed outlier: 5.897A  pdb=" N   VAL C  76 " --> pdb=" O   GLY C  28 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   LEU C  30 " --> pdb=" O   VAL C  76 " (cutoff:3.500A)
      removed outlier: 5.794A  pdb=" N   LEU C  78 " --> pdb=" O   LEU C  30 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   ALA C  32 " --> pdb=" O   LEU C  78 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   GLY C  74 " --> pdb=" O   VAL C 103 " (cutoff:3.500A)
      removed outlier: 7.782A  pdb=" N   GLY C 105 " --> pdb=" O   GLY C  74 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   VAL C  76 " --> pdb=" O   GLY C 105 " (cutoff:3.500A)
      removed outlier: 7.576A  pdb=" N   LYS C 107 " --> pdb=" O   VAL C  76 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   LEU C  78 " --> pdb=" O   LYS C 107 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   VAL C 104 " --> pdb=" O   PHE C 144 " (cutoff:3.500A)
      removed outlier: 8.414A  pdb=" N   LYS C 146 " --> pdb=" O   VAL C 104 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   ILE C 106 " --> pdb=" O   LYS C 146 " (cutoff:3.500A)
      removed outlier: 8.594A  pdb=" N   ARG C 148 " --> pdb=" O   ILE C 106 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   TRP C 147 " --> pdb=" O   ILE C 185 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLU C 187 " --> pdb=" O   TRP C 147 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   LEU C 228 " --> pdb=" O   THR C 268 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114
    Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 32
      removed outlier: 6.858A  pdb=" N   GLY D  28 " --> pdb=" O   GLY D  74 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   VAL D  76 " --> pdb=" O   GLY D  28 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   LEU D  30 " --> pdb=" O   VAL D  76 " (cutoff:3.500A)
      removed outlier: 5.796A  pdb=" N   LEU D  78 " --> pdb=" O   LEU D  30 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   ALA D  32 " --> pdb=" O   LEU D  78 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   VAL D 104 " --> pdb=" O   PHE D 144 " (cutoff:3.500A)
      removed outlier: 8.251A  pdb=" N   LYS D 146 " --> pdb=" O   VAL D 104 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   ILE D 106 " --> pdb=" O   LYS D 146 " (cutoff:3.500A)
      removed outlier: 8.613A  pdb=" N   ARG D 148 " --> pdb=" O   ILE D 106 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   TRP D 147 " --> pdb=" O   ILE D 185 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   LEU D 228 " --> pdb=" O   THR D 268 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114

    591 hydrogen bonds defined for protein.
    1710 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.30

  Time building geometry restraints manager: 1.55 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1782
        1.31 -     1.44: 2584
        1.44 -     1.56: 6250
        1.56 -     1.69: 0
        1.69 -     1.81: 56
  Bond restraints: 10672
  Sorted by residual:
  bond pdb=" N   THR A 234 "
       pdb=" CA  THR A 234 "
    ideal  model  delta    sigma   weight residual
    1.455  1.493 -0.038 9.60e-03 1.09e+04 1.61e+01
  bond pdb=" N   THR B 234 "
       pdb=" CA  THR B 234 "
    ideal  model  delta    sigma   weight residual
    1.455  1.493 -0.038 9.60e-03 1.09e+04 1.56e+01
  bond pdb=" N   THR C 234 "
       pdb=" CA  THR C 234 "
    ideal  model  delta    sigma   weight residual
    1.455  1.492 -0.038 9.60e-03 1.09e+04 1.54e+01
  bond pdb=" N   THR D 234 "
       pdb=" CA  THR D 234 "
    ideal  model  delta    sigma   weight residual
    1.455  1.492 -0.038 9.60e-03 1.09e+04 1.53e+01
  bond pdb=" C   PRO A   9 "
       pdb=" O   PRO A   9 "
    ideal  model  delta    sigma   weight residual
    1.237  1.190  0.047 1.26e-02 6.30e+03 1.42e+01
  ... (remaining 10667 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 13523
        1.83 -     3.66: 806
        3.66 -     5.49: 104
        5.49 -     7.33: 24
        7.33 -     9.16: 7
  Bond angle restraints: 14464
  Sorted by residual:
  angle pdb=" N   ALA A 307 "
        pdb=" CA  ALA A 307 "
        pdb=" C   ALA A 307 "
      ideal   model   delta    sigma   weight residual
     111.07  116.05   -4.98 1.07e+00 8.73e-01 2.17e+01
  angle pdb=" CA  PHE A 144 "
        pdb=" CB  PHE A 144 "
        pdb=" CG  PHE A 144 "
      ideal   model   delta    sigma   weight residual
     113.80  118.44   -4.64 1.00e+00 1.00e+00 2.15e+01
  angle pdb=" CA  PHE B 144 "
        pdb=" CB  PHE B 144 "
        pdb=" CG  PHE B 144 "
      ideal   model   delta    sigma   weight residual
     113.80  118.41   -4.61 1.00e+00 1.00e+00 2.12e+01
  angle pdb=" CA  PHE D 144 "
        pdb=" CB  PHE D 144 "
        pdb=" CG  PHE D 144 "
      ideal   model   delta    sigma   weight residual
     113.80  118.40   -4.60 1.00e+00 1.00e+00 2.11e+01
  angle pdb=" C   THR C 157 "
        pdb=" CA  THR C 157 "
        pdb=" CB  THR C 157 "
      ideal   model   delta    sigma   weight residual
     108.63  115.57   -6.94 1.54e+00 4.22e-01 2.03e+01
  ... (remaining 14459 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 6066
       17.93 -    35.87: 342
       35.87 -    53.80: 59
       53.80 -    71.74: 21
       71.74 -    89.67: 16
  Dihedral angle restraints: 6504
    sinusoidal: 2572
      harmonic: 3932
  Sorted by residual:
  dihedral pdb=" CA  THR B 122 "
           pdb=" C   THR B 122 "
           pdb=" N   THR B 123 "
           pdb=" CA  THR B 123 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.40   17.60     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  THR D 122 "
           pdb=" C   THR D 122 "
           pdb=" N   THR D 123 "
           pdb=" CA  THR D 123 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.40   17.60     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  THR A 122 "
           pdb=" C   THR A 122 "
           pdb=" N   THR A 123 "
           pdb=" CA  THR A 123 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.46   17.54     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 6501 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1226
       0.060 -    0.119: 303
       0.119 -    0.178: 88
       0.178 -    0.238: 25
       0.238 -    0.297: 2
  Chirality restraints: 1644
  Sorted by residual:
  chirality pdb=" CA  HIS B   4 "
            pdb=" N   HIS B   4 "
            pdb=" C   HIS B   4 "
            pdb=" CB  HIS B   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.81   -0.30 2.00e-01 2.50e+01 2.21e+00
  chirality pdb=" CA  ILE A 190 "
            pdb=" N   ILE A 190 "
            pdb=" C   ILE A 190 "
            pdb=" CB  ILE A 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.71   -0.28 2.00e-01 2.50e+01 1.95e+00
  chirality pdb=" CA  HIS C   4 "
            pdb=" N   HIS C   4 "
            pdb=" C   HIS C   4 "
            pdb=" CB  HIS C   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.39e+00
  ... (remaining 1641 not shown)

  Planarity restraints: 1880
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 302 "    0.011 2.00e-02 2.50e+03   2.21e-02 4.89e+00
        pdb=" C   GLY A 302 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   GLY A 302 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ARG A 303 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY C 154 "    0.010 2.00e-02 2.50e+03   2.04e-02 4.18e+00
        pdb=" C   GLY C 154 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   GLY C 154 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLU C 155 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C  84 "    0.024 2.00e-02 2.50e+03   1.36e-02 3.73e+00
        pdb=" CG  TYR C  84 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR C  84 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR C  84 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 TYR C  84 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR C  84 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR C  84 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR C  84 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1877 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 4097
        2.82 -     3.34: 13187
        3.34 -     3.86: 24885
        3.86 -     4.38: 28769
        4.38 -     4.90: 45198
  Nonbonded interactions: 116136
  Sorted by model distance:
  nonbonded pdb=" O   HOH C 551 "
            pdb=" O   HOH C 767 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" O   ASP D 195 "
            pdb=" O   HOH D 401 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" O   ASP A 195 "
            pdb=" O   HOH A 401 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" O   ASP B 195 "
            pdb=" O   HOH B 401 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" O   HOH C 556 "
            pdb=" O   HOH C 769 "
     model   vdw
     2.305 3.040
  ... (remaining 116131 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

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:             4.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.440
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
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      :  0.006   0.047  10672  Z= 0.429
  Angle     :  0.923   9.157  14464  Z= 0.620
  Chirality :  0.062   0.297   1644
  Planarity :  0.005   0.035   1880
  Dihedral  : 13.023  89.673   3984
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 2.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  :  1.26 %
    Favored  : 97.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.03 (0.23), residues: 1364
  helix:  1.53 (0.19), residues: 684
  sheet: -1.54 (0.35), residues: 176
  loop :  0.55 (0.29), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 172 
 TYR   0.028   0.003   TYR C  84 
 PHE   0.025   0.003   PHE A 144 
 TRP   0.029   0.004   TRP A 147 
 HIS   0.006   0.001   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00597 (10672)
  covalent geometry    : angle       0.92252 (14464)
  hydrogen bonds       : bond        0.14002 (  591)
  hydrogen bonds       : angle       5.88612 ( 1710)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 155
  time to evaluate  : 0.491 
Fit side-chains
REVERT: A   67 ASP cc_start: 0.6582 (t0) cc_final: 0.5986 (p0)
REVERT: A  199 LYS cc_start: 0.8581 (ttpp) cc_final: 0.8296 (tptp)
REVERT: A  242 LYS cc_start: 0.7961 (mmtm) cc_final: 0.7422 (tmmt)
REVERT: A  288 LYS cc_start: 0.8469 (mtpp) cc_final: 0.8260 (mtpt)
REVERT: A  303 ARG cc_start: 0.7218 (ttm110) cc_final: 0.6594 (ttp-170)
REVERT: A  310 LEU cc_start: 0.8002 (tp) cc_final: 0.7633 (tp)
REVERT: A  341 LYS cc_start: 0.8345 (mttt) cc_final: 0.7961 (mtpt)
REVERT: B   67 ASP cc_start: 0.6250 (t70) cc_final: 0.5874 (p0)
REVERT: B  199 LYS cc_start: 0.8558 (ttpp) cc_final: 0.8194 (tptp)
REVERT: B  242 LYS cc_start: 0.7927 (mmtm) cc_final: 0.7411 (tmmt)
REVERT: B  288 LYS cc_start: 0.8495 (mtpp) cc_final: 0.8283 (mtpt)
REVERT: B  310 LEU cc_start: 0.8167 (tp) cc_final: 0.7921 (tt)
REVERT: B  341 LYS cc_start: 0.8381 (mttt) cc_final: 0.7979 (mtpt)
REVERT: C   67 ASP cc_start: 0.6780 (t0) cc_final: 0.5976 (p0)
REVERT: C  199 LYS cc_start: 0.8588 (ttpp) cc_final: 0.8242 (tptp)
REVERT: C  242 LYS cc_start: 0.7982 (mmtm) cc_final: 0.7444 (tmmt)
REVERT: C  310 LEU cc_start: 0.8211 (tp) cc_final: 0.7978 (tt)
REVERT: C  341 LYS cc_start: 0.8387 (mttt) cc_final: 0.7989 (mtpt)
REVERT: D   67 ASP cc_start: 0.6835 (t0) cc_final: 0.6008 (p0)
REVERT: D  199 LYS cc_start: 0.8547 (ttpp) cc_final: 0.8269 (tptp)
REVERT: D  242 LYS cc_start: 0.7916 (mmtm) cc_final: 0.7382 (tmmt)
REVERT: D  310 LEU cc_start: 0.8143 (tp) cc_final: 0.7881 (tt)
REVERT: D  341 LYS cc_start: 0.8343 (mttt) cc_final: 0.7930 (mtpt)
  outliers start: 18
  outliers final: 7
  residues processed: 170
  average time/residue: 1.0452
  time to fit residues: 187.1022
Evaluate side-chains
  108 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue    3 SER
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  330 ARG
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  330 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    7.9990
   chunk 130 optimal weight:    0.0470
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    0.1980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.6280

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.165206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.126381 restraints weight = 9215.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 1.08
r_work: 0.3282 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 2.50 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.1289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10672  Z= 0.130
  Angle     :  0.542   5.555  14464  Z= 0.291
  Chirality :  0.041   0.152   1644
  Planarity :  0.004   0.045   1880
  Dihedral  :  6.193  57.484   1489
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  7.37 %
    Favored  : 91.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.62 (0.22), residues: 1364
  helix:  2.16 (0.19), residues: 712
  sheet: -1.52 (0.35), residues: 176
  loop :  0.61 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  42 
 TYR   0.020   0.002   TYR A 213 
 PHE   0.012   0.002   PHE A 144 
 TRP   0.016   0.002   TRP A 147 
 HIS   0.003   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (10672)
  covalent geometry    : angle       0.54194 (14464)
  hydrogen bonds       : bond        0.05467 (  591)
  hydrogen bonds       : angle       4.64860 ( 1710)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 0.446 
Fit side-chains
REVERT: A   10 GLU cc_start: 0.8210 (mp0) cc_final: 0.7909 (mp0)
REVERT: A   67 ASP cc_start: 0.6603 (t0) cc_final: 0.5921 (p0)
REVERT: A  199 LYS cc_start: 0.8520 (ttpp) cc_final: 0.8306 (pptt)
REVERT: A  242 LYS cc_start: 0.7915 (mmtm) cc_final: 0.7395 (tmmt)
REVERT: A  288 LYS cc_start: 0.8413 (mtpp) cc_final: 0.8181 (mtpt)
REVERT: A  303 ARG cc_start: 0.7505 (ttm110) cc_final: 0.6675 (ttt-90)
REVERT: A  310 LEU cc_start: 0.7986 (tp) cc_final: 0.7694 (tp)
REVERT: A  330 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7465 (mmm160)
REVERT: A  341 LYS cc_start: 0.8427 (mttt) cc_final: 0.8058 (mtpt)
REVERT: B   10 GLU cc_start: 0.8249 (mp0) cc_final: 0.7999 (mp0)
REVERT: B   67 ASP cc_start: 0.6158 (t70) cc_final: 0.5638 (p0)
REVERT: B   81 GLU cc_start: 0.8110 (tt0) cc_final: 0.7738 (tt0)
REVERT: B  199 LYS cc_start: 0.8530 (ttpp) cc_final: 0.8188 (tptp)
REVERT: B  242 LYS cc_start: 0.7899 (mmtm) cc_final: 0.7336 (tmmt)
REVERT: B  310 LEU cc_start: 0.8087 (tp) cc_final: 0.7841 (tp)
REVERT: B  325 GLU cc_start: 0.7530 (tp30) cc_final: 0.7291 (tp30)
REVERT: B  341 LYS cc_start: 0.8405 (mttt) cc_final: 0.8062 (mtpt)
REVERT: C   10 GLU cc_start: 0.8233 (mp0) cc_final: 0.7967 (mp0)
REVERT: C   42 ARG cc_start: 0.6246 (OUTLIER) cc_final: 0.5866 (mpt180)
REVERT: C   67 ASP cc_start: 0.6525 (t0) cc_final: 0.5988 (p0)
REVERT: C   81 GLU cc_start: 0.8055 (pt0) cc_final: 0.7649 (tt0)
REVERT: C  199 LYS cc_start: 0.8543 (ttpp) cc_final: 0.8166 (tptp)
REVERT: C  242 LYS cc_start: 0.7895 (mmtm) cc_final: 0.7324 (tmmt)
REVERT: C  277 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8260 (tp30)
REVERT: C  288 LYS cc_start: 0.8462 (mtpp) cc_final: 0.8234 (mtpt)
REVERT: C  310 LEU cc_start: 0.8078 (tp) cc_final: 0.7863 (tp)
REVERT: C  341 LYS cc_start: 0.8449 (mttt) cc_final: 0.8073 (mtpt)
REVERT: D   10 GLU cc_start: 0.8238 (mp0) cc_final: 0.7936 (mp0)
REVERT: D   67 ASP cc_start: 0.6568 (t0) cc_final: 0.6015 (p0)
REVERT: D   81 GLU cc_start: 0.8119 (pt0) cc_final: 0.7764 (tt0)
REVERT: D  199 LYS cc_start: 0.8508 (ttpp) cc_final: 0.8141 (tptp)
REVERT: D  242 LYS cc_start: 0.7929 (mmtm) cc_final: 0.7363 (tmmt)
REVERT: D  310 LEU cc_start: 0.8046 (tp) cc_final: 0.7811 (tp)
REVERT: D  341 LYS cc_start: 0.8395 (mttt) cc_final: 0.8046 (mtpt)
  outliers start: 10
  outliers final: 7
  residues processed: 118
  average time/residue: 1.0322
  time to fit residues: 128.5836
Evaluate side-chains
  115 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  330 ARG
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  330 ARG
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue  271 SER
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  330 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 103 optimal weight:    4.9990
   chunk 28 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 129 optimal weight:    4.9990
   chunk 58 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
A 324 GLN
B 324 GLN
D 339 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.159739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.119692 restraints weight = 9163.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 1.00
r_work: 0.3199 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.3077 rms_B_bonded: 2.54 restraints_weight: 0.2500
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.1329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10672  Z= 0.173
  Angle     :  0.599   5.868  14464  Z= 0.326
  Chirality :  0.045   0.155   1644
  Planarity :  0.004   0.036   1880
  Dihedral  :  6.218  55.608   1488
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  :  6.47 %
    Favored  : 91.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.60 (0.22), residues: 1364
  helix:  2.16 (0.18), residues: 712
  sheet: -1.49 (0.36), residues: 176
  loop :  0.55 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 172 
 TYR   0.031   0.003   TYR D 213 
 PHE   0.014   0.003   PHE C 144 
 TRP   0.016   0.003   TRP D 147 
 HIS   0.006   0.001   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (10672)
  covalent geometry    : angle       0.59910 (14464)
  hydrogen bonds       : bond        0.06801 (  591)
  hydrogen bonds       : angle       4.78853 ( 1710)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.511 
Fit side-chains
REVERT: A   67 ASP cc_start: 0.6812 (t0) cc_final: 0.6006 (p0)
REVERT: A  199 LYS cc_start: 0.8681 (ttpp) cc_final: 0.8345 (tptp)
REVERT: A  242 LYS cc_start: 0.8032 (mmtm) cc_final: 0.7533 (tmmt)
REVERT: A  288 LYS cc_start: 0.8522 (mtpp) cc_final: 0.8310 (mtpt)
REVERT: A  303 ARG cc_start: 0.7575 (ttm110) cc_final: 0.6900 (ttp-170)
REVERT: A  310 LEU cc_start: 0.8234 (tp) cc_final: 0.7921 (tp)
REVERT: A  330 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.7078 (mmm160)
REVERT: A  341 LYS cc_start: 0.8506 (mttt) cc_final: 0.8166 (mtpt)
REVERT: B   67 ASP cc_start: 0.6402 (t70) cc_final: 0.5896 (p0)
REVERT: B  199 LYS cc_start: 0.8651 (ttpp) cc_final: 0.8354 (tptp)
REVERT: B  242 LYS cc_start: 0.8002 (mmtm) cc_final: 0.7461 (tmmt)
REVERT: B  303 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7391 (ttp-170)
REVERT: B  310 LEU cc_start: 0.8298 (tp) cc_final: 0.8064 (tp)
REVERT: B  325 GLU cc_start: 0.7751 (tp30) cc_final: 0.7541 (tp30)
REVERT: B  341 LYS cc_start: 0.8489 (mttt) cc_final: 0.8158 (mtpt)
REVERT: C   67 ASP cc_start: 0.6798 (t0) cc_final: 0.6175 (p0)
REVERT: C  173 TYR cc_start: 0.9291 (OUTLIER) cc_final: 0.8893 (t80)
REVERT: C  199 LYS cc_start: 0.8669 (ttpp) cc_final: 0.8359 (tptp)
REVERT: C  242 LYS cc_start: 0.8010 (mmtm) cc_final: 0.7456 (tmmt)
REVERT: C  288 LYS cc_start: 0.8570 (mtpp) cc_final: 0.8340 (mtpt)
REVERT: C  310 LEU cc_start: 0.8291 (tp) cc_final: 0.8047 (tp)
REVERT: C  325 GLU cc_start: 0.7616 (tp30) cc_final: 0.7411 (tp30)
REVERT: C  341 LYS cc_start: 0.8506 (mttt) cc_final: 0.8158 (mtpt)
REVERT: D   67 ASP cc_start: 0.6738 (t0) cc_final: 0.6119 (p0)
REVERT: D  199 LYS cc_start: 0.8689 (ttpp) cc_final: 0.8350 (tptp)
REVERT: D  242 LYS cc_start: 0.8014 (mmtm) cc_final: 0.7476 (tmmt)
REVERT: D  303 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7278 (ttp-170)
REVERT: D  310 LEU cc_start: 0.8281 (tp) cc_final: 0.8046 (tp)
REVERT: D  341 LYS cc_start: 0.8484 (mttt) cc_final: 0.8149 (mtpt)
  outliers start: 20
  outliers final: 5
  residues processed: 125
  average time/residue: 0.9469
  time to fit residues: 125.3936
Evaluate side-chains
  105 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  330 ARG
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  303 ARG
Chi-restraints excluded: chain B residue  330 ARG
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  303 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 84 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 74 optimal weight:    6.9990
   chunk 101 optimal weight:    3.9990
   chunk 111 optimal weight:    5.9990
   chunk 29 optimal weight:    0.4980
   chunk 75 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 127 optimal weight:    1.9990
   chunk 112 optimal weight:    2.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
B   4 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.160561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.119954 restraints weight = 9167.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 1.01
r_work: 0.3210 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 2.50 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.1451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10672  Z= 0.152
  Angle     :  0.569   5.556  14464  Z= 0.308
  Chirality :  0.043   0.150   1644
  Planarity :  0.004   0.031   1880
  Dihedral  :  5.986  55.457   1484
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  6.83 %
    Favored  : 91.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.71 (0.22), residues: 1364
  helix:  2.29 (0.18), residues: 712
  sheet: -1.47 (0.36), residues: 176
  loop :  0.53 (0.27), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 172 
 TYR   0.028   0.002   TYR C 213 
 PHE   0.013   0.002   PHE C 144 
 TRP   0.013   0.002   TRP D 147 
 HIS   0.004   0.001   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (10672)
  covalent geometry    : angle       0.56852 (14464)
  hydrogen bonds       : bond        0.06259 (  591)
  hydrogen bonds       : angle       4.65878 ( 1710)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.486 
Fit side-chains
REVERT: A   67 ASP cc_start: 0.6752 (t0) cc_final: 0.5873 (p0)
REVERT: A  173 TYR cc_start: 0.9300 (OUTLIER) cc_final: 0.8908 (t80)
REVERT: A  199 LYS cc_start: 0.8672 (ttpp) cc_final: 0.8270 (tptp)
REVERT: A  242 LYS cc_start: 0.7983 (mmtm) cc_final: 0.7461 (tmmt)
REVERT: A  288 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8235 (mtpt)
REVERT: A  303 ARG cc_start: 0.7519 (ttm110) cc_final: 0.6818 (ttp-170)
REVERT: A  310 LEU cc_start: 0.8153 (tp) cc_final: 0.7880 (tp)
REVERT: A  330 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7050 (mmm160)
REVERT: A  341 LYS cc_start: 0.8462 (mttt) cc_final: 0.8106 (mtpt)
REVERT: B   67 ASP cc_start: 0.6338 (t70) cc_final: 0.5822 (p0)
REVERT: B  173 TYR cc_start: 0.9305 (OUTLIER) cc_final: 0.8912 (t80)
REVERT: B  199 LYS cc_start: 0.8638 (ttpp) cc_final: 0.8288 (tptp)
REVERT: B  242 LYS cc_start: 0.7950 (mmtm) cc_final: 0.7398 (tmmt)
REVERT: B  303 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7234 (ttp-170)
REVERT: B  310 LEU cc_start: 0.8213 (tp) cc_final: 0.7959 (tp)
REVERT: B  341 LYS cc_start: 0.8442 (mttt) cc_final: 0.8090 (mtpt)
REVERT: C   67 ASP cc_start: 0.6736 (t0) cc_final: 0.6097 (p0)
REVERT: C  173 TYR cc_start: 0.9299 (OUTLIER) cc_final: 0.8807 (t80)
REVERT: C  199 LYS cc_start: 0.8666 (ttpp) cc_final: 0.8314 (tptp)
REVERT: C  242 LYS cc_start: 0.7953 (mmtm) cc_final: 0.7383 (tmmt)
REVERT: C  288 LYS cc_start: 0.8513 (mtpp) cc_final: 0.8283 (mtpt)
REVERT: C  310 LEU cc_start: 0.8185 (tp) cc_final: 0.7945 (tp)
REVERT: C  325 GLU cc_start: 0.7559 (tp30) cc_final: 0.7273 (tp30)
REVERT: C  341 LYS cc_start: 0.8446 (mttt) cc_final: 0.8086 (mtpt)
REVERT: D   67 ASP cc_start: 0.6703 (t0) cc_final: 0.6056 (p0)
REVERT: D  173 TYR cc_start: 0.9296 (OUTLIER) cc_final: 0.8836 (t80)
REVERT: D  199 LYS cc_start: 0.8648 (ttpp) cc_final: 0.8264 (tptp)
REVERT: D  242 LYS cc_start: 0.7972 (mmtm) cc_final: 0.7426 (tmmt)
REVERT: D  303 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7148 (ttp-170)
REVERT: D  310 LEU cc_start: 0.8204 (tp) cc_final: 0.7936 (tp)
REVERT: D  341 LYS cc_start: 0.8438 (mttt) cc_final: 0.8077 (mtpt)
  outliers start: 19
  outliers final: 8
  residues processed: 114
  average time/residue: 0.9467
  time to fit residues: 114.0968
Evaluate side-chains
  112 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  330 ARG
Chi-restraints excluded: chain B residue   86 LYS
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  303 ARG
Chi-restraints excluded: chain B residue  330 ARG
Chi-restraints excluded: chain C residue   86 LYS
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue   86 LYS
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  303 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 81 optimal weight:    4.9990
   chunk 23 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 133 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 129 optimal weight:    0.9990
   chunk 100 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 86 optimal weight:    6.9990
   chunk 111 optimal weight:    2.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 319 ASN
B 319 ASN
C 319 ASN
D 319 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.158736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.117940 restraints weight = 9152.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 1.01
r_work: 0.3187 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 2.48 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.1502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10672  Z= 0.188
  Angle     :  0.625   6.206  14464  Z= 0.341
  Chirality :  0.045   0.159   1644
  Planarity :  0.004   0.030   1880
  Dihedral  :  5.987  55.065   1484
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  6.29 %
    Favored  : 92.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.55 (0.22), residues: 1364
  helix:  2.32 (0.18), residues: 688
  sheet: -1.55 (0.36), residues: 176
  loop :  0.29 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 172 
 TYR   0.035   0.003   TYR A 213 
 PHE   0.014   0.003   PHE C 144 
 TRP   0.013   0.003   TRP D 147 
 HIS   0.005   0.001   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 (10672)
  covalent geometry    : angle       0.62549 (14464)
  hydrogen bonds       : bond        0.07102 (  591)
  hydrogen bonds       : angle       4.87446 ( 1710)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.477 
Fit side-chains
REVERT: A   10 GLU cc_start: 0.8315 (mp0) cc_final: 0.8074 (mp0)
REVERT: A   67 ASP cc_start: 0.6885 (t0) cc_final: 0.5913 (p0)
REVERT: A  173 TYR cc_start: 0.9308 (OUTLIER) cc_final: 0.8906 (t80)
REVERT: A  199 LYS cc_start: 0.8673 (ttpp) cc_final: 0.8271 (tptp)
REVERT: A  242 LYS cc_start: 0.7965 (mmtm) cc_final: 0.7453 (tmmt)
REVERT: A  288 LYS cc_start: 0.8495 (mtpp) cc_final: 0.8242 (mtpt)
REVERT: A  303 ARG cc_start: 0.7544 (ttm110) cc_final: 0.6819 (ttp-170)
REVERT: A  310 LEU cc_start: 0.8230 (tp) cc_final: 0.7963 (tp)
REVERT: A  321 LYS cc_start: 0.7282 (tptt) cc_final: 0.6971 (mppt)
REVERT: A  330 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.7092 (mmm160)
REVERT: A  341 LYS cc_start: 0.8471 (mttt) cc_final: 0.8093 (mtpt)
REVERT: B   10 GLU cc_start: 0.8333 (mp0) cc_final: 0.8099 (mp0)
REVERT: B   67 ASP cc_start: 0.6416 (t70) cc_final: 0.5886 (p0)
REVERT: B  173 TYR cc_start: 0.9309 (OUTLIER) cc_final: 0.8906 (t80)
REVERT: B  199 LYS cc_start: 0.8642 (ttpp) cc_final: 0.8262 (tptp)
REVERT: B  242 LYS cc_start: 0.7928 (mmtm) cc_final: 0.7396 (tmmt)
REVERT: B  303 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7200 (ttp-170)
REVERT: B  310 LEU cc_start: 0.8242 (tp) cc_final: 0.7994 (tp)
REVERT: B  321 LYS cc_start: 0.7270 (tptt) cc_final: 0.6929 (mppt)
REVERT: B  341 LYS cc_start: 0.8435 (mttt) cc_final: 0.8070 (mtpt)
REVERT: C   10 GLU cc_start: 0.8311 (mp0) cc_final: 0.8068 (mp0)
REVERT: C   67 ASP cc_start: 0.6854 (t0) cc_final: 0.6129 (p0)
REVERT: C  173 TYR cc_start: 0.9306 (OUTLIER) cc_final: 0.8892 (t80)
REVERT: C  199 LYS cc_start: 0.8682 (ttpp) cc_final: 0.8289 (tptp)
REVERT: C  242 LYS cc_start: 0.7939 (mmtm) cc_final: 0.7376 (tmmt)
REVERT: C  288 LYS cc_start: 0.8541 (mtpp) cc_final: 0.8291 (mtpt)
REVERT: C  303 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7211 (ttp-170)
REVERT: C  310 LEU cc_start: 0.8222 (tp) cc_final: 0.7965 (tp)
REVERT: C  325 GLU cc_start: 0.7702 (tp30) cc_final: 0.7449 (tp30)
REVERT: C  341 LYS cc_start: 0.8447 (mttt) cc_final: 0.8069 (mtpt)
REVERT: D   10 GLU cc_start: 0.8328 (mp0) cc_final: 0.8083 (mp0)
REVERT: D   67 ASP cc_start: 0.6794 (t0) cc_final: 0.6063 (p0)
REVERT: D  173 TYR cc_start: 0.9308 (OUTLIER) cc_final: 0.8926 (t80)
REVERT: D  199 LYS cc_start: 0.8675 (ttpp) cc_final: 0.8269 (tptp)
REVERT: D  242 LYS cc_start: 0.7951 (mmtm) cc_final: 0.7417 (tmmt)
REVERT: D  303 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7131 (ttp-170)
REVERT: D  310 LEU cc_start: 0.8219 (tp) cc_final: 0.7959 (tp)
REVERT: D  341 LYS cc_start: 0.8449 (mttt) cc_final: 0.8079 (mtpt)
  outliers start: 19
  outliers final: 7
  residues processed: 116
  average time/residue: 0.9958
  time to fit residues: 121.9783
Evaluate side-chains
  113 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  330 ARG
Chi-restraints excluded: chain B residue   86 LYS
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  303 ARG
Chi-restraints excluded: chain C residue   86 LYS
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain C residue  303 ARG
Chi-restraints excluded: chain D residue   86 LYS
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  303 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 57 optimal weight:    4.9990
   chunk 92 optimal weight:    0.0970
   chunk 130 optimal weight:    0.7980
   chunk 82 optimal weight:    6.9990
   chunk 13 optimal weight:    0.5980
   chunk 108 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0050
   chunk 96 optimal weight:    0.9990
   chunk 135 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.4592

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

Flipped N/Q/H residues before XYZ refinement:
C 306 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.164342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.125287 restraints weight = 9336.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 1.00
r_work: 0.3275 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3155 rms_B_bonded: 2.57 restraints_weight: 0.2500
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  10672  Z= 0.110
  Angle     :  0.492   5.663  14464  Z= 0.261
  Chirality :  0.040   0.132   1644
  Planarity :  0.003   0.025   1880
  Dihedral  :  5.342  55.945   1480
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 2.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  :  6.47 %
    Favored  : 92.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.94 (0.23), residues: 1364
  helix:  2.59 (0.19), residues: 712
  sheet: -1.65 (0.34), residues: 204
  loop :  0.73 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  59 
 TYR   0.017   0.001   TYR A 213 
 PHE   0.014   0.002   PHE D 144 
 TRP   0.008   0.001   TRP A 147 
 HIS   0.002   0.000   HIS A 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (10672)
  covalent geometry    : angle       0.49195 (14464)
  hydrogen bonds       : bond        0.04686 (  591)
  hydrogen bonds       : angle       4.33762 ( 1710)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.478 
Fit side-chains
REVERT: A   67 ASP cc_start: 0.6821 (t0) cc_final: 0.5904 (p0)
REVERT: A  199 LYS cc_start: 0.8641 (ttpp) cc_final: 0.8347 (pptt)
REVERT: A  242 LYS cc_start: 0.7944 (mmtm) cc_final: 0.7475 (tmmt)
REVERT: A  303 ARG cc_start: 0.7646 (ttm110) cc_final: 0.6920 (ttp-170)
REVERT: A  310 LEU cc_start: 0.8179 (tp) cc_final: 0.7945 (tp)
REVERT: A  341 LYS cc_start: 0.8489 (mttt) cc_final: 0.8150 (mtpt)
REVERT: B   67 ASP cc_start: 0.6362 (t70) cc_final: 0.5882 (p0)
REVERT: B  242 LYS cc_start: 0.7944 (mmtm) cc_final: 0.7466 (tmmt)
REVERT: B  303 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7318 (ttp-170)
REVERT: B  310 LEU cc_start: 0.8189 (tp) cc_final: 0.7945 (tp)
REVERT: B  341 LYS cc_start: 0.8478 (mttt) cc_final: 0.8140 (mtpt)
REVERT: C   67 ASP cc_start: 0.6757 (t0) cc_final: 0.6159 (p0)
REVERT: C  107 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8481 (tmmm)
REVERT: C  199 LYS cc_start: 0.8656 (ttpp) cc_final: 0.8348 (pptt)
REVERT: C  242 LYS cc_start: 0.7947 (mmtm) cc_final: 0.7449 (tmmt)
REVERT: C  303 ARG cc_start: 0.7601 (ttt-90) cc_final: 0.7249 (ttp-170)
REVERT: C  310 LEU cc_start: 0.8182 (tp) cc_final: 0.7923 (tp)
REVERT: C  330 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.6964 (mmm160)
REVERT: C  341 LYS cc_start: 0.8494 (mttt) cc_final: 0.8138 (mtpt)
REVERT: D   67 ASP cc_start: 0.6735 (t0) cc_final: 0.6139 (p0)
REVERT: D  199 LYS cc_start: 0.8646 (ttpp) cc_final: 0.8300 (tptp)
REVERT: D  242 LYS cc_start: 0.7949 (mmtm) cc_final: 0.7464 (tmmt)
REVERT: D  303 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7252 (ttp-170)
REVERT: D  310 LEU cc_start: 0.8171 (tp) cc_final: 0.7914 (tp)
  outliers start: 14
  outliers final: 4
  residues processed: 116
  average time/residue: 0.9290
  time to fit residues: 114.1153
Evaluate side-chains
  106 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  303 ARG
Chi-restraints excluded: chain C residue  107 LYS
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain C residue  330 ARG
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  303 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 126 optimal weight:    6.9990
   chunk 75 optimal weight:    4.9990
   chunk 134 optimal weight:    6.9990
   chunk 49 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 106 optimal weight:    4.9990
   chunk 133 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 29 optimal weight:    0.4980
   chunk 115 optimal weight:    0.3980
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.163895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.123944 restraints weight = 9223.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 1.01
r_work: 0.3264 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3144 rms_B_bonded: 2.51 restraints_weight: 0.2500
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.1791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  10672  Z= 0.113
  Angle     :  0.499   5.420  14464  Z= 0.265
  Chirality :  0.040   0.143   1644
  Planarity :  0.003   0.026   1880
  Dihedral  :  5.312  56.031   1480
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  7.64 %
    Favored  : 91.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  2.05 (0.23), residues: 1364
  helix:  2.67 (0.19), residues: 712
  sheet: -1.44 (0.36), residues: 184
  loop :  0.61 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 172 
 TYR   0.022   0.002   TYR A 213 
 PHE   0.013   0.002   PHE B 144 
 TRP   0.010   0.002   TRP C 147 
 HIS   0.002   0.001   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (10672)
  covalent geometry    : angle       0.49892 (14464)
  hydrogen bonds       : bond        0.04967 (  591)
  hydrogen bonds       : angle       4.30371 ( 1710)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.471 
Fit side-chains
REVERT: A   67 ASP cc_start: 0.6786 (t0) cc_final: 0.5834 (p0)
REVERT: A  199 LYS cc_start: 0.8611 (ttpp) cc_final: 0.8174 (tptp)
REVERT: A  242 LYS cc_start: 0.7917 (mmtm) cc_final: 0.7415 (tmmt)
REVERT: A  303 ARG cc_start: 0.7560 (ttm110) cc_final: 0.6811 (ttp-170)
REVERT: A  310 LEU cc_start: 0.8123 (tp) cc_final: 0.7897 (tp)
REVERT: A  341 LYS cc_start: 0.8446 (mttt) cc_final: 0.8085 (mtpt)
REVERT: B   67 ASP cc_start: 0.6283 (t70) cc_final: 0.5802 (p0)
REVERT: B  242 LYS cc_start: 0.7909 (mmtm) cc_final: 0.7391 (tmmt)
REVERT: B  303 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7232 (ttp-170)
REVERT: B  310 LEU cc_start: 0.8152 (tp) cc_final: 0.7894 (tt)
REVERT: B  341 LYS cc_start: 0.8452 (mttt) cc_final: 0.8099 (mtpt)
REVERT: C   67 ASP cc_start: 0.6715 (t0) cc_final: 0.6073 (p0)
REVERT: C  242 LYS cc_start: 0.7911 (mmtm) cc_final: 0.7377 (tmmt)
REVERT: C  303 ARG cc_start: 0.7545 (ttt-90) cc_final: 0.7215 (ttp-170)
REVERT: C  310 LEU cc_start: 0.8105 (tp) cc_final: 0.7856 (tp)
REVERT: C  330 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.6879 (mmm160)
REVERT: C  341 LYS cc_start: 0.8436 (mttt) cc_final: 0.8067 (mtpt)
REVERT: D   67 ASP cc_start: 0.6684 (t0) cc_final: 0.6060 (p0)
REVERT: D  199 LYS cc_start: 0.8603 (ttpp) cc_final: 0.8212 (tptp)
REVERT: D  242 LYS cc_start: 0.7920 (mmtm) cc_final: 0.7412 (tmmt)
REVERT: D  303 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7177 (ttp-170)
REVERT: D  310 LEU cc_start: 0.8116 (tp) cc_final: 0.7871 (tp)
  outliers start: 9
  outliers final: 4
  residues processed: 108
  average time/residue: 0.9483
  time to fit residues: 108.5294
Evaluate side-chains
  107 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  303 ARG
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain C residue  330 ARG
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  303 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 62 optimal weight:    0.7980
   chunk 60 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 15 optimal weight:    7.9990
   chunk 72 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 57 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   overall best weight:    1.9588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.159156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.118929 restraints weight = 9185.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 1.01
r_work: 0.3192 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3069 rms_B_bonded: 2.56 restraints_weight: 0.2500
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.1617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10672  Z= 0.173
  Angle     :  0.599   5.945  14464  Z= 0.324
  Chirality :  0.044   0.154   1644
  Planarity :  0.004   0.025   1880
  Dihedral  :  5.702  55.232   1480
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 2.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  :  7.01 %
    Favored  : 91.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.75 (0.22), residues: 1364
  helix:  2.39 (0.18), residues: 712
  sheet: -1.60 (0.36), residues: 184
  loop :  0.54 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 172 
 TYR   0.035   0.003   TYR B 213 
 PHE   0.014   0.003   PHE D  57 
 TRP   0.013   0.002   TRP D 147 
 HIS   0.004   0.001   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (10672)
  covalent geometry    : angle       0.59881 (14464)
  hydrogen bonds       : bond        0.06726 (  591)
  hydrogen bonds       : angle       4.71578 ( 1710)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.532 
Fit side-chains
REVERT: A   67 ASP cc_start: 0.6912 (t0) cc_final: 0.5984 (p0)
REVERT: A  199 LYS cc_start: 0.8706 (ttpp) cc_final: 0.8330 (tptp)
REVERT: A  242 LYS cc_start: 0.7993 (mmtm) cc_final: 0.7530 (tmmt)
REVERT: A  303 ARG cc_start: 0.7606 (ttm110) cc_final: 0.6924 (ttp-170)
REVERT: A  310 LEU cc_start: 0.8263 (tp) cc_final: 0.8041 (tp)
REVERT: A  330 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.7185 (mmm160)
REVERT: A  341 LYS cc_start: 0.8483 (mttt) cc_final: 0.8150 (mtpt)
REVERT: B   67 ASP cc_start: 0.6496 (t70) cc_final: 0.5989 (p0)
REVERT: B  242 LYS cc_start: 0.7964 (mmtm) cc_final: 0.7463 (tmmt)
REVERT: B  303 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7262 (ttp-170)
REVERT: B  310 LEU cc_start: 0.8336 (tp) cc_final: 0.8094 (tp)
REVERT: B  341 LYS cc_start: 0.8484 (mttt) cc_final: 0.8156 (mtpt)
REVERT: C   67 ASP cc_start: 0.6885 (t0) cc_final: 0.6229 (p0)
REVERT: C  242 LYS cc_start: 0.7954 (mmtm) cc_final: 0.7454 (tmmt)
REVERT: C  303 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7269 (ttp-170)
REVERT: C  310 LEU cc_start: 0.8272 (tp) cc_final: 0.8015 (tp)
REVERT: C  330 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.7276 (mmm160)
REVERT: C  341 LYS cc_start: 0.8476 (mttt) cc_final: 0.8134 (mtpt)
REVERT: D   67 ASP cc_start: 0.6865 (t0) cc_final: 0.6215 (p0)
REVERT: D  199 LYS cc_start: 0.8701 (ttpp) cc_final: 0.8326 (tptp)
REVERT: D  242 LYS cc_start: 0.7980 (mmtm) cc_final: 0.7499 (tmmt)
REVERT: D  303 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7230 (ttp-170)
REVERT: D  310 LEU cc_start: 0.8276 (tp) cc_final: 0.8023 (tp)
  outliers start: 14
  outliers final: 5
  residues processed: 113
  average time/residue: 0.9494
  time to fit residues: 113.4715
Evaluate side-chains
  109 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  330 ARG
Chi-restraints excluded: chain B residue  278 GLU
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  303 ARG
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain C residue  303 ARG
Chi-restraints excluded: chain C residue  330 ARG
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  303 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 62 optimal weight:    0.8980
   chunk 115 optimal weight:    0.6980
   chunk 101 optimal weight:    3.9990
   chunk 111 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9990
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.161997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.121984 restraints weight = 9153.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 1.01
r_work: 0.3237 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3117 rms_B_bonded: 2.49 restraints_weight: 0.2500
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.1776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10672  Z= 0.125
  Angle     :  0.528   5.567  14464  Z= 0.282
  Chirality :  0.041   0.142   1644
  Planarity :  0.003   0.024   1880
  Dihedral  :  5.479  55.738   1480
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  7.55 %
    Favored  : 91.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.89 (0.22), residues: 1364
  helix:  2.55 (0.19), residues: 712
  sheet: -1.57 (0.36), residues: 184
  loop :  0.55 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 172 
 TYR   0.023   0.002   TYR C 213 
 PHE   0.014   0.002   PHE A 144 
 TRP   0.011   0.002   TRP D 147 
 HIS   0.002   0.001   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (10672)
  covalent geometry    : angle       0.52813 (14464)
  hydrogen bonds       : bond        0.05436 (  591)
  hydrogen bonds       : angle       4.46757 ( 1710)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.506 
Fit side-chains
REVERT: A   67 ASP cc_start: 0.6812 (t0) cc_final: 0.5874 (p0)
REVERT: A  199 LYS cc_start: 0.8627 (ttpp) cc_final: 0.8221 (tptp)
REVERT: A  242 LYS cc_start: 0.7937 (mmtm) cc_final: 0.7449 (tmmt)
REVERT: A  303 ARG cc_start: 0.7579 (ttm110) cc_final: 0.6849 (ttp-170)
REVERT: A  310 LEU cc_start: 0.8126 (tp) cc_final: 0.7899 (tp)
REVERT: A  330 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.6833 (mmm160)
REVERT: A  341 LYS cc_start: 0.8445 (mttt) cc_final: 0.8089 (mtpt)
REVERT: B   67 ASP cc_start: 0.6396 (t70) cc_final: 0.5891 (p0)
REVERT: B  242 LYS cc_start: 0.7921 (mmtm) cc_final: 0.7409 (tmmt)
REVERT: B  303 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7218 (ttp-170)
REVERT: B  310 LEU cc_start: 0.8171 (tp) cc_final: 0.7925 (tp)
REVERT: B  341 LYS cc_start: 0.8441 (mttt) cc_final: 0.8088 (mtpt)
REVERT: C   67 ASP cc_start: 0.6705 (t0) cc_final: 0.6071 (p0)
REVERT: C  242 LYS cc_start: 0.7911 (mmtm) cc_final: 0.7386 (tmmt)
REVERT: C  303 ARG cc_start: 0.7532 (ttt-90) cc_final: 0.7202 (ttp-170)
REVERT: C  310 LEU cc_start: 0.8134 (tp) cc_final: 0.7868 (tp)
REVERT: C  330 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.6995 (mmm160)
REVERT: C  341 LYS cc_start: 0.8428 (mttt) cc_final: 0.8065 (mtpt)
REVERT: D   67 ASP cc_start: 0.6678 (t0) cc_final: 0.6054 (p0)
REVERT: D  199 LYS cc_start: 0.8643 (ttpp) cc_final: 0.8232 (tptp)
REVERT: D  242 LYS cc_start: 0.7930 (mmtm) cc_final: 0.7431 (tmmt)
REVERT: D  303 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7184 (ttp-170)
REVERT: D  310 LEU cc_start: 0.8148 (tp) cc_final: 0.7885 (tp)
  outliers start: 12
  outliers final: 5
  residues processed: 102
  average time/residue: 0.9490
  time to fit residues: 102.6062
Evaluate side-chains
  101 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  330 ARG
Chi-restraints excluded: chain B residue  278 GLU
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  303 ARG
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain C residue  330 ARG
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  303 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 67 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 5 optimal weight:    8.9990
   chunk 93 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 118 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   overall best weight:    0.8382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.162415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.122481 restraints weight = 9266.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 1.01
r_work: 0.3239 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3119 rms_B_bonded: 2.57 restraints_weight: 0.2500
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.1798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10672  Z= 0.123
  Angle     :  0.525   5.870  14464  Z= 0.279
  Chirality :  0.041   0.144   1644
  Planarity :  0.003   0.024   1880
  Dihedral  :  5.424  55.799   1480
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  8.00 %
    Favored  : 91.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.95 (0.23), residues: 1364
  helix:  2.61 (0.19), residues: 712
  sheet: -1.55 (0.36), residues: 184
  loop :  0.55 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 172 
 TYR   0.024   0.002   TYR A 213 
 PHE   0.013   0.002   PHE A 144 
 TRP   0.010   0.002   TRP B 147 
 HIS   0.002   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (10672)
  covalent geometry    : angle       0.52497 (14464)
  hydrogen bonds       : bond        0.05305 (  591)
  hydrogen bonds       : angle       4.40468 ( 1710)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.480 
Fit side-chains
REVERT: A   67 ASP cc_start: 0.6889 (t0) cc_final: 0.5960 (p0)
REVERT: A  199 LYS cc_start: 0.8665 (ttpp) cc_final: 0.8299 (tptp)
REVERT: A  242 LYS cc_start: 0.7953 (mmtm) cc_final: 0.7486 (tmmt)
REVERT: A  303 ARG cc_start: 0.7640 (ttm110) cc_final: 0.6932 (ttp-170)
REVERT: A  310 LEU cc_start: 0.8212 (tp) cc_final: 0.7980 (tp)
REVERT: A  330 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.6904 (mmm160)
REVERT: A  341 LYS cc_start: 0.8464 (mttt) cc_final: 0.8132 (mtpt)
REVERT: B   67 ASP cc_start: 0.6441 (t70) cc_final: 0.5950 (p0)
REVERT: B  242 LYS cc_start: 0.7937 (mmtm) cc_final: 0.7451 (tmmt)
REVERT: B  303 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7258 (ttp-170)
REVERT: B  310 LEU cc_start: 0.8224 (tp) cc_final: 0.7994 (tp)
REVERT: B  341 LYS cc_start: 0.8481 (mttt) cc_final: 0.8145 (mtpt)
REVERT: C   67 ASP cc_start: 0.6780 (t0) cc_final: 0.6146 (p0)
REVERT: C  242 LYS cc_start: 0.7924 (mmtm) cc_final: 0.7433 (tmmt)
REVERT: C  303 ARG cc_start: 0.7572 (ttt-90) cc_final: 0.7249 (ttp-170)
REVERT: C  310 LEU cc_start: 0.8201 (tp) cc_final: 0.7950 (tp)
REVERT: C  330 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7060 (mmm160)
REVERT: C  341 LYS cc_start: 0.8464 (mttt) cc_final: 0.8118 (mtpt)
REVERT: D   67 ASP cc_start: 0.6748 (t0) cc_final: 0.6143 (p0)
REVERT: D  199 LYS cc_start: 0.8674 (ttpp) cc_final: 0.8304 (tptp)
REVERT: D  242 LYS cc_start: 0.7934 (mmtm) cc_final: 0.7465 (tmmt)
REVERT: D  303 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7219 (ttp-170)
REVERT: D  310 LEU cc_start: 0.8212 (tp) cc_final: 0.7972 (tp)
  outliers start: 9
  outliers final: 4
  residues processed: 102
  average time/residue: 0.9663
  time to fit residues: 104.3267
Evaluate side-chains
  102 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  330 ARG
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  303 ARG
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain C residue  330 ARG
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  303 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 73 optimal weight:    8.9990
   chunk 25 optimal weight:    0.8980
   chunk 89 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 95 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 86 optimal weight:    5.9990
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.162796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.122796 restraints weight = 9204.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 1.01
r_work: 0.3249 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3128 rms_B_bonded: 2.50 restraints_weight: 0.2500
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.1840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10672  Z= 0.121
  Angle     :  0.519   5.740  14464  Z= 0.276
  Chirality :  0.040   0.143   1644
  Planarity :  0.003   0.024   1880
  Dihedral  :  5.385  55.997   1480
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 2.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  7.82 %
    Favored  : 91.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.96 (0.23), residues: 1364
  helix:  2.62 (0.19), residues: 712
  sheet: -1.54 (0.36), residues: 184
  loop :  0.56 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 172 
 TYR   0.023   0.002   TYR A 213 
 PHE   0.015   0.002   PHE C  57 
 TRP   0.010   0.002   TRP C 147 
 HIS   0.002   0.001   HIS B 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (10672)
  covalent geometry    : angle       0.51937 (14464)
  hydrogen bonds       : bond        0.05213 (  591)
  hydrogen bonds       : angle       4.38350 ( 1710)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5693.93 seconds
wall clock time: 97 minutes 53.59 seconds (5873.59 seconds total)