Starting phenix.real_space_refine
on Sun May  3 09:14:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/11nk_75863/05_2026/11nk_75863.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/11nk_75863/05_2026/11nk_75863.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/11nk_75863/05_2026/11nk_75863.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/11nk_75863/05_2026/11nk_75863.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/11nk_75863/05_2026/11nk_75863.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/11nk_75863/05_2026/11nk_75863.cif"
  }
  resolution = 2.17
  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=   0.009
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    3420      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 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: 11912
  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: 367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 367, 367
          Classifications: {'water': 367}
          Link IDs: {None: 366}
    Chain: "B"
      Number of atoms: 357
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 357, 357
          Classifications: {'water': 357}
          Link IDs: {None: 356}
    Chain: "C"
      Number of atoms: 357
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 357, 357
          Classifications: {'water': 357}
          Link IDs: {None: 356}
    Chain: "D"
      Number of atoms: 359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 359, 359
          Classifications: {'water': 359}
          Link IDs: {None: 358}
  Time building chain proxies: 2.96, per 1000 atoms: 0.25
  Number of scatterers: 11912
  At special positions: 0
  Unit cell: (97.755, 81.585, 106.575, 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    3420      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: 0.68
  Conformation dependent library (CDL) restraints added in 437.4 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
      55.0% alpha, 13.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 23
    Processing helix  chain 'A' and resid 35 through 45
      removed outlier: 4.255A  pdb=" N   LYS A  41 " --> pdb=" O   GLY A  37 " (cutoff:3.500A)
      removed outlier: 4.013A  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 70
    Processing helix  chain 'A' and resid 79 through 84
      removed outlier: 3.722A  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
      removed outlier: 3.530A  pdb=" N   ASN A 180 " --> pdb=" O   ILE A 176 " (cutoff:3.500A)
    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
      removed outlier: 3.606A  pdb=" N   THR A 259 " --> pdb=" O   ALA A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 288
    Processing helix  chain 'A' and resid 302 through 314
      removed outlier: 6.497A  pdb=" N   SER A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 5.163A  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: 4.308A  pdb=" N   LYS B  41 " --> pdb=" O   GLY B  37 " (cutoff:3.500A)
      removed outlier: 4.018A  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: 3.810A  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
      removed outlier: 3.528A  pdb=" N   ASN B 180 " --> pdb=" O   ILE B 176 " (cutoff:3.500A)
    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
      removed outlier: 3.607A  pdb=" N   THR B 259 " --> pdb=" O   ALA B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 288
    Processing helix  chain 'B' and resid 302 through 314
      removed outlier: 6.561A  pdb=" N   SER B 308 " --> pdb=" O   ALA B 304 " (cutoff:3.500A)
      removed outlier: 5.142A  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: 4.319A  pdb=" N   LYS C  41 " --> pdb=" O   GLY C  37 " (cutoff:3.500A)
      removed outlier: 4.005A  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 70
    Processing helix  chain 'C' and resid 81 through 85
    Processing helix  chain 'C' and resid 92 through 100
    Processing helix  chain 'C' and resid 129 through 140
    Processing helix  chain 'C' and resid 159 through 180
      removed outlier: 3.526A  pdb=" N   ASN C 180 " --> pdb=" O   ILE C 176 " (cutoff:3.500A)
    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
      removed outlier: 3.599A  pdb=" N   THR C 259 " --> pdb=" O   ALA C 255 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 275 through 288
    Processing helix  chain 'C' and resid 302 through 314
      removed outlier: 6.539A  pdb=" N   SER C 308 " --> pdb=" O   ALA C 304 " (cutoff:3.500A)
      removed outlier: 5.154A  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: 4.353A  pdb=" N   LYS D  41 " --> pdb=" O   GLY D  37 " (cutoff:3.500A)
      removed outlier: 4.005A  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 70
    Processing helix  chain 'D' and resid 79 through 84
      removed outlier: 3.816A  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
      removed outlier: 3.529A  pdb=" N   ASN D 180 " --> pdb=" O   ILE D 176 " (cutoff:3.500A)
    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
      removed outlier: 3.605A  pdb=" N   THR D 259 " --> pdb=" O   ALA D 255 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 275 through 288
    Processing helix  chain 'D' and resid 302 through 314
      removed outlier: 6.542A  pdb=" N   SER D 308 " --> pdb=" O   ALA D 304 " (cutoff:3.500A)
      removed outlier: 5.186A  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: 6.792A  pdb=" N   GLY A  28 " --> pdb=" O   GLY A  74 " (cutoff:3.500A)
      removed outlier: 5.909A  pdb=" N   VAL A  76 " --> pdb=" O   GLY A  28 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   LEU A  30 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
      removed outlier: 5.825A  pdb=" N   LEU A  78 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 7.088A  pdb=" N   ALA A  32 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   GLY A  74 " --> pdb=" O   VAL A 103 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   GLY A 105 " --> pdb=" O   GLY A  74 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   VAL A  76 " --> pdb=" O   GLY A 105 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   LYS A 107 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   LEU A  78 " --> pdb=" O   LYS A 107 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   VAL A 104 " --> pdb=" O   PHE A 144 " (cutoff:3.500A)
      removed outlier: 8.147A  pdb=" N   LYS A 146 " --> pdb=" O   VAL A 104 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   ILE A 106 " --> pdb=" O   LYS A 146 " (cutoff:3.500A)
      removed outlier: 8.701A  pdb=" N   ARG A 148 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 6.323A  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: 6.782A  pdb=" N   GLY B  28 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
      removed outlier: 5.897A  pdb=" N   VAL B  76 " --> pdb=" O   GLY B  28 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   LEU B  30 " --> pdb=" O   VAL B  76 " (cutoff:3.500A)
      removed outlier: 5.819A  pdb=" N   LEU B  78 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      removed outlier: 7.086A  pdb=" N   ALA B  32 " --> pdb=" O   LEU B  78 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   VAL B 104 " --> pdb=" O   PHE B 144 " (cutoff:3.500A)
      removed outlier: 8.234A  pdb=" N   LYS B 146 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   ILE B 106 " --> pdb=" O   LYS B 146 " (cutoff:3.500A)
      removed outlier: 8.581A  pdb=" N   ARG B 148 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   TRP B 147 " --> pdb=" O   ILE B 185 " (cutoff:3.500A)
      removed outlier: 6.331A  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: 6.783A  pdb=" N   GLY C  28 " --> pdb=" O   GLY C  74 " (cutoff:3.500A)
      removed outlier: 5.889A  pdb=" N   VAL C  76 " --> pdb=" O   GLY C  28 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   LEU C  30 " --> pdb=" O   VAL C  76 " (cutoff:3.500A)
      removed outlier: 5.819A  pdb=" N   LEU C  78 " --> pdb=" O   LEU C  30 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   ALA C  32 " --> pdb=" O   LEU C  78 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   VAL C 104 " --> pdb=" O   PHE C 144 " (cutoff:3.500A)
      removed outlier: 8.235A  pdb=" N   LYS C 146 " --> pdb=" O   VAL C 104 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ILE C 106 " --> pdb=" O   LYS C 146 " (cutoff:3.500A)
      removed outlier: 8.580A  pdb=" N   ARG C 148 " --> pdb=" O   ILE C 106 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   TRP C 147 " --> pdb=" O   ILE C 185 " (cutoff:3.500A)
      removed outlier: 6.346A  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: 6.787A  pdb=" N   GLY D  28 " --> pdb=" O   GLY D  74 " (cutoff:3.500A)
      removed outlier: 5.902A  pdb=" N   VAL D  76 " --> pdb=" O   GLY D  28 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   LEU D  30 " --> pdb=" O   VAL D  76 " (cutoff:3.500A)
      removed outlier: 5.822A  pdb=" N   LEU D  78 " --> pdb=" O   LEU D  30 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   ALA D  32 " --> pdb=" O   LEU D  78 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   VAL D 104 " --> pdb=" O   PHE D 144 " (cutoff:3.500A)
      removed outlier: 8.234A  pdb=" N   LYS D 146 " --> pdb=" O   VAL D 104 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   ILE D 106 " --> pdb=" O   LYS D 146 " (cutoff:3.500A)
      removed outlier: 8.585A  pdb=" N   ARG D 148 " --> pdb=" O   ILE D 106 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   TRP D 147 " --> pdb=" O   ILE D 185 " (cutoff:3.500A)
      removed outlier: 6.346A  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

    589 hydrogen bonds defined for protein.
    1704 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: 2.34

  Time building geometry restraints manager: 0.94 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 1780
        1.30 -     1.43: 2488
        1.43 -     1.56: 6348
        1.56 -     1.68: 0
        1.68 -     1.81: 56
  Bond restraints: 10672
  Sorted by residual:
  bond pdb=" C   PRO B 294 "
       pdb=" O   PRO B 294 "
    ideal  model  delta    sigma   weight residual
    1.237  1.178  0.059 1.28e-02 6.10e+03 2.14e+01
  bond pdb=" N   ILE C  46 "
       pdb=" CA  ILE C  46 "
    ideal  model  delta    sigma   weight residual
    1.459  1.500 -0.041 1.25e-02 6.40e+03 1.08e+01
  bond pdb=" N   ILE D  46 "
       pdb=" CA  ILE D  46 "
    ideal  model  delta    sigma   weight residual
    1.459  1.500 -0.041 1.25e-02 6.40e+03 1.06e+01
  bond pdb=" N   PHE A 144 "
       pdb=" CA  PHE A 144 "
    ideal  model  delta    sigma   weight residual
    1.454  1.496 -0.042 1.29e-02 6.01e+03 1.05e+01
  bond pdb=" N   TYR C  84 "
       pdb=" CA  TYR C  84 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.16e-02 7.43e+03 1.00e+01
  ... (remaining 10667 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 13547
        1.42 -     2.84: 735
        2.84 -     4.26: 133
        4.26 -     5.67: 33
        5.67 -     7.09: 16
  Bond angle restraints: 14464
  Sorted by residual:
  angle pdb=" CA  PHE C 144 "
        pdb=" CB  PHE C 144 "
        pdb=" CG  PHE C 144 "
      ideal   model   delta    sigma   weight residual
     113.80  118.61   -4.81 1.00e+00 1.00e+00 2.31e+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  118.55   -4.75 1.00e+00 1.00e+00 2.26e+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  118.52   -4.72 1.00e+00 1.00e+00 2.23e+01
  angle pdb=" C   PRO B 262 "
        pdb=" CA  PRO B 262 "
        pdb=" CB  PRO B 262 "
      ideal   model   delta    sigma   weight residual
     111.85  105.32    6.53 1.42e+00 4.96e-01 2.11e+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  118.22   -4.42 1.00e+00 1.00e+00 1.96e+01
  ... (remaining 14459 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.97: 5998
       15.97 -    31.94: 357
       31.94 -    47.90: 100
       47.90 -    63.87: 40
       63.87 -    79.84: 9
  Dihedral angle restraints: 6504
    sinusoidal: 2572
      harmonic: 3932
  Sorted by residual:
  dihedral pdb=" C   PHE C 144 "
           pdb=" N   PHE C 144 "
           pdb=" CA  PHE C 144 "
           pdb=" CB  PHE C 144 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.78    8.18     0      2.50e+00 1.60e-01 1.07e+01
  dihedral pdb=" CA  PHE A 299 "
           pdb=" C   PHE A 299 "
           pdb=" N   SER A 300 "
           pdb=" CA  SER A 300 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.65   16.35     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CA  PHE D 299 "
           pdb=" C   PHE D 299 "
           pdb=" N   SER D 300 "
           pdb=" CA  SER D 300 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.69   16.31     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 6501 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1247
       0.047 -    0.094: 253
       0.094 -    0.142: 115
       0.142 -    0.189: 21
       0.189 -    0.236: 8
  Chirality restraints: 1644
  Sorted by residual:
  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    2.67   -0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CA  ILE C 190 "
            pdb=" N   ILE C 190 "
            pdb=" C   ILE C 190 "
            pdb=" CB  ILE C 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" CA  ILE B 190 "
            pdb=" N   ILE B 190 "
            pdb=" C   ILE B 190 "
            pdb=" CB  ILE B 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.23 2.00e-01 2.50e+01 1.34e+00
  ... (remaining 1641 not shown)

  Planarity restraints: 1880
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 292 "    0.012 2.00e-02 2.50e+03   2.35e-02 5.50e+00
        pdb=" C   LEU A 292 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   LEU A 292 "    0.015 2.00e-02 2.50e+03
        pdb=" N   LYS A 293 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 147 "   -0.026 2.00e-02 2.50e+03   1.39e-02 4.84e+00
        pdb=" CG  TRP A 147 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 147 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 147 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 147 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 147 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 147 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 147 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 147 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 147 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 292 "   -0.011 2.00e-02 2.50e+03   2.16e-02 4.65e+00
        pdb=" C   LEU B 292 "    0.037 2.00e-02 2.50e+03
        pdb=" O   LEU B 292 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   LYS B 293 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1877 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2588
        2.77 -     3.30: 12223
        3.30 -     3.84: 23166
        3.84 -     4.37: 28200
        4.37 -     4.90: 44190
  Nonbonded interactions: 110367
  Sorted by model distance:
  nonbonded pdb=" O   GLN B  60 "
            pdb=" OG1 THR B  64 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   GLN C  60 "
            pdb=" OG1 THR C  64 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   GLN A  60 "
            pdb=" OG1 THR A  64 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" O   HOH A 481 "
            pdb=" O   HOH A 748 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" O   HOH C 505 "
            pdb=" O   HOH C 744 "
     model   vdw
     2.305 3.040
  ... (remaining 110362 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:             4.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.710
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:7.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
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      :  0.005   0.059  10672  Z= 0.342
  Angle     :  0.760   7.093  14464  Z= 0.505
  Chirality :  0.051   0.236   1644
  Planarity :  0.005   0.033   1880
  Dihedral  : 12.631  79.840   3984
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 1.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  :  1.44 %
    Favored  : 96.49 %
  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:  1.63 (0.20), residues: 688
  sheet: -0.99 (0.32), residues: 212
  loop :  0.25 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 133 
 TYR   0.024   0.003   TYR C  84 
 PHE   0.026   0.002   PHE C 144 
 TRP   0.026   0.004   TRP A 147 
 HIS   0.007   0.001   HIS C   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 (10672)
  covalent geometry    : angle       0.76015 (14464)
  hydrogen bonds       : bond        0.15022 (  589)
  hydrogen bonds       : angle       6.12149 ( 1704)

*********************** 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
  171 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 148
  time to evaluate  : 0.455 
Fit side-chains
REVERT: A  246 GLU cc_start: 0.8299 (mp0) cc_final: 0.8095 (mp0)
REVERT: A  303 ARG cc_start: 0.8237 (mtp85) cc_final: 0.7287 (ttt-90)
REVERT: B  303 ARG cc_start: 0.8199 (mtp85) cc_final: 0.7287 (ttt-90)
REVERT: C  303 ARG cc_start: 0.8199 (mtp85) cc_final: 0.7381 (ttt-90)
REVERT: D  303 ARG cc_start: 0.8237 (mtp85) cc_final: 0.7301 (ttt-90)
  outliers start: 23
  outliers final: 4
  residues processed: 167
  average time/residue: 0.9848
  time to fit residues: 173.0112
Evaluate side-chains
  105 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 101
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:    0.5980
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A   4 HIS
A  95 GLN
A 168 ASN
A 237 HIS
A 241 GLN
A 319 ASN
B   4 HIS
B  95 GLN
B 219 HIS
B 237 HIS
B 241 GLN
C   4 HIS
C  95 GLN
C 168 ASN
C 219 HIS
C 237 HIS
C 241 GLN
C 319 ASN
D   4 HIS
D  85 GLN
D  95 GLN
D 219 HIS
D 237 HIS
D 241 GLN
D 319 ASN

Total number of N/Q/H flips: 25

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.143183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.103407 restraints weight = 9796.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 1.35
r_work: 0.3001 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 3.04 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.1484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10672  Z= 0.142
  Angle     :  0.556   5.143  14464  Z= 0.298
  Chirality :  0.043   0.150   1644
  Planarity :  0.004   0.032   1880
  Dihedral  :  5.437  57.747   1480
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 2.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  :  7.28 %
    Favored  : 90.11 %
  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:  1.66 (0.23), residues: 1364
  helix:  2.49 (0.19), residues: 688
  sheet: -1.15 (0.31), residues: 224
  loop :  0.24 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 257 
 TYR   0.020   0.002   TYR A 213 
 PHE   0.015   0.002   PHE C 144 
 TRP   0.017   0.002   TRP A 147 
 HIS   0.007   0.002   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (10672)
  covalent geometry    : angle       0.55574 (14464)
  hydrogen bonds       : bond        0.05737 (  589)
  hydrogen bonds       : angle       4.70649 ( 1704)

*********************** 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
  139 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 110
  time to evaluate  : 0.462 
Fit side-chains
REVERT: A  199 LYS cc_start: 0.8594 (mtpt) cc_final: 0.8317 (mtmm)
REVERT: A  246 GLU cc_start: 0.8068 (mp0) cc_final: 0.7829 (mp0)
REVERT: A  303 ARG cc_start: 0.8087 (mtp85) cc_final: 0.6925 (ttt-90)
REVERT: B  303 ARG cc_start: 0.8104 (mtp85) cc_final: 0.7020 (ttt-90)
REVERT: C  303 ARG cc_start: 0.8121 (mtp85) cc_final: 0.7011 (ttt-90)
REVERT: D  303 ARG cc_start: 0.8079 (mtp85) cc_final: 0.6925 (ttt-90)
  outliers start: 29
  outliers final: 8
  residues processed: 132
  average time/residue: 0.9362
  time to fit residues: 130.2558
Evaluate side-chains
  108 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
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  295 TRP
Chi-restraints excluded: chain C residue  330 ARG
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 99 optimal weight:    0.8980
   chunk 50 optimal weight:    0.7980
   chunk 112 optimal weight:    4.9990
   chunk 122 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 14 optimal weight:    8.9990
   chunk 108 optimal weight:    6.9990
   chunk 70 optimal weight:    4.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 237 HIS
A 241 GLN
A 319 ASN
B 237 HIS
B 241 GLN
C 319 ASN
D 237 HIS
D 319 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.141383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.101811 restraints weight = 9837.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3100 rms_B_bonded: 1.36
r_work: 0.2980 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.2853 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.1626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10672  Z= 0.143
  Angle     :  0.534   5.293  14464  Z= 0.286
  Chirality :  0.043   0.150   1644
  Planarity :  0.004   0.033   1880
  Dihedral  :  5.467  57.399   1480
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  8.63 %
    Favored  : 89.66 %
  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:  1.80 (0.23), residues: 1364
  helix:  2.67 (0.19), residues: 688
  sheet: -1.13 (0.32), residues: 224
  loop :  0.20 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  59 
 TYR   0.022   0.002   TYR C 213 
 PHE   0.015   0.002   PHE D 144 
 TRP   0.013   0.002   TRP A 147 
 HIS   0.004   0.001   HIS C 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (10672)
  covalent geometry    : angle       0.53371 (14464)
  hydrogen bonds       : bond        0.05690 (  589)
  hydrogen bonds       : angle       4.58839 ( 1704)

*********************** 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
  128 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.487 
Fit side-chains
REVERT: A  246 GLU cc_start: 0.8139 (mp0) cc_final: 0.7842 (mp0)
REVERT: A  303 ARG cc_start: 0.8094 (mtp85) cc_final: 0.6958 (ttt-90)
REVERT: A  316 LYS cc_start: 0.7125 (mtpt) cc_final: 0.6911 (mtmm)
REVERT: B  303 ARG cc_start: 0.8117 (mtp85) cc_final: 0.7019 (ttt-90)
REVERT: C  303 ARG cc_start: 0.8006 (mtp85) cc_final: 0.6947 (ttt-90)
REVERT: C  316 LYS cc_start: 0.7122 (mtpt) cc_final: 0.6908 (mtmm)
REVERT: D  303 ARG cc_start: 0.8050 (mtp85) cc_final: 0.6902 (ttt-90)
REVERT: D  316 LYS cc_start: 0.7138 (mtpt) cc_final: 0.6917 (mtmm)
  outliers start: 19
  outliers final: 8
  residues processed: 126
  average time/residue: 0.9537
  time to fit residues: 126.7856
Evaluate side-chains
  115 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
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  295 TRP
Chi-restraints excluded: chain C residue  330 ARG
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  330 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 135 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 26 optimal weight:    8.9990
   chunk 25 optimal weight:    0.7980
   chunk 128 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 123 optimal weight:    0.8980
   chunk 3 optimal weight:   10.0000
   chunk 107 optimal weight:    8.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 237 HIS
A 241 GLN
B 241 GLN
B 319 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.141384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.102707 restraints weight = 10004.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 1.36
r_work: 0.2996 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.2871 rms_B_bonded: 3.04 restraints_weight: 0.2500
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  10672  Z= 0.124
  Angle     :  0.496   4.677  14464  Z= 0.265
  Chirality :  0.041   0.143   1644
  Planarity :  0.004   0.034   1880
  Dihedral  :  5.346  57.306   1480
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  :  8.27 %
    Favored  : 89.48 %
  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:  1.97 (0.23), residues: 1364
  helix:  2.87 (0.19), residues: 688
  sheet: -1.14 (0.32), residues: 224
  loop :  0.23 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  59 
 TYR   0.020   0.002   TYR A 213 
 PHE   0.014   0.001   PHE C 144 
 TRP   0.012   0.001   TRP A 147 
 HIS   0.004   0.001   HIS D 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (10672)
  covalent geometry    : angle       0.49566 (14464)
  hydrogen bonds       : bond        0.05103 (  589)
  hydrogen bonds       : angle       4.39246 ( 1704)

*********************** 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
  130 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 0.462 
Fit side-chains
REVERT: A   66 ASP cc_start: 0.7005 (OUTLIER) cc_final: 0.6405 (m-30)
REVERT: A  246 GLU cc_start: 0.8126 (mp0) cc_final: 0.7824 (mp0)
REVERT: A  303 ARG cc_start: 0.7969 (mtp85) cc_final: 0.6864 (ttt-90)
REVERT: B   67 ASP cc_start: 0.6672 (OUTLIER) cc_final: 0.6471 (t70)
REVERT: B  303 ARG cc_start: 0.8004 (mtp85) cc_final: 0.6964 (ttt-90)
REVERT: C  303 ARG cc_start: 0.7981 (mtp85) cc_final: 0.6937 (ttt-90)
REVERT: D  303 ARG cc_start: 0.7933 (mtp85) cc_final: 0.6843 (ttt-90)
  outliers start: 25
  outliers final: 11
  residues processed: 123
  average time/residue: 0.9476
  time to fit residues: 123.0374
Evaluate side-chains
  114 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  330 ARG
Chi-restraints excluded: chain B residue   67 ASP
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 C residue  330 ARG
Chi-restraints excluded: chain D residue   66 ASP
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  330 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 123 optimal weight:    0.8980
   chunk 119 optimal weight:    0.6980
   chunk 57 optimal weight:    6.9990
   chunk 2 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 122 optimal weight:    0.9990
   chunk 103 optimal weight:    0.9980
   chunk 18 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 241 GLN
A 319 ASN
B  95 GLN
B 241 GLN
C  95 GLN
C 319 ASN
D  95 GLN
D 237 HIS
D 319 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.142734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.103498 restraints weight = 9923.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 1.36
r_work: 0.3003 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.2879 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021  10672  Z= 0.117
  Angle     :  0.483   4.672  14464  Z= 0.258
  Chirality :  0.041   0.143   1644
  Planarity :  0.004   0.033   1880
  Dihedral  :  5.297  57.573   1480
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  :  7.82 %
    Favored  : 89.75 %
  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:  2.02 (0.23), residues: 1364
  helix:  2.92 (0.19), residues: 688
  sheet: -1.10 (0.32), residues: 224
  loop :  0.22 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  59 
 TYR   0.020   0.002   TYR C 213 
 PHE   0.014   0.001   PHE B 144 
 TRP   0.010   0.001   TRP A 147 
 HIS   0.003   0.001   HIS D 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (10672)
  covalent geometry    : angle       0.48281 (14464)
  hydrogen bonds       : bond        0.04940 (  589)
  hydrogen bonds       : angle       4.35373 ( 1704)

*********************** 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
  128 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 101
  time to evaluate  : 0.451 
Fit side-chains
REVERT: A  246 GLU cc_start: 0.8118 (mp0) cc_final: 0.7810 (mp0)
REVERT: A  303 ARG cc_start: 0.7924 (mtp85) cc_final: 0.6865 (ttt-90)
REVERT: A  330 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8441 (tpm170)
REVERT: B  107 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8710 (ttmm)
REVERT: B  303 ARG cc_start: 0.7954 (mtp85) cc_final: 0.6933 (ttt-90)
REVERT: B  330 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8434 (tpm170)
REVERT: C  303 ARG cc_start: 0.7999 (mtp85) cc_final: 0.6949 (ttt-90)
REVERT: C  330 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8412 (tpm170)
REVERT: D  303 ARG cc_start: 0.7947 (mtp85) cc_final: 0.6889 (ttt-90)
  outliers start: 27
  outliers final: 14
  residues processed: 121
  average time/residue: 0.9309
  time to fit residues: 119.0775
Evaluate side-chains
  117 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  330 ARG
Chi-restraints excluded: chain B residue    2 HIS
Chi-restraints excluded: chain B residue   14 GLU
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  330 ARG
Chi-restraints excluded: chain C residue   14 GLU
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain C residue  330 ARG
Chi-restraints excluded: chain D residue   14 GLU
Chi-restraints excluded: chain D residue   66 ASP
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  330 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 101 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 86 optimal weight:    0.4980
   chunk 45 optimal weight:    0.8980
   chunk 19 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 122 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
A 241 GLN
B 241 GLN
C  95 GLN
D  95 GLN
D 237 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.143276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.104126 restraints weight = 9945.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 1.36
r_work: 0.3016 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2893 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020  10672  Z= 0.112
  Angle     :  0.472   4.624  14464  Z= 0.252
  Chirality :  0.040   0.142   1644
  Planarity :  0.004   0.033   1880
  Dihedral  :  5.244  57.669   1480
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  :  8.36 %
    Favored  : 89.30 %
  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:  2.11 (0.23), residues: 1364
  helix:  2.99 (0.19), residues: 688
  sheet: -0.97 (0.34), residues: 204
  loop :  0.15 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  59 
 TYR   0.019   0.002   TYR A 213 
 PHE   0.014   0.001   PHE D 144 
 TRP   0.009   0.001   TRP A 147 
 HIS   0.003   0.001   HIS C 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (10672)
  covalent geometry    : angle       0.47222 (14464)
  hydrogen bonds       : bond        0.04759 (  589)
  hydrogen bonds       : angle       4.30162 ( 1704)

*********************** 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
  129 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 103
  time to evaluate  : 0.468 
Fit side-chains
REVERT: A  246 GLU cc_start: 0.8108 (mp0) cc_final: 0.7794 (mp0)
REVERT: A  303 ARG cc_start: 0.7925 (mtp85) cc_final: 0.6863 (ttt-90)
REVERT: B  303 ARG cc_start: 0.7962 (mtp85) cc_final: 0.6933 (ttt-90)
REVERT: C  303 ARG cc_start: 0.7987 (mtp85) cc_final: 0.6949 (ttt-90)
REVERT: D  303 ARG cc_start: 0.7938 (mtp85) cc_final: 0.6885 (ttt-90)
  outliers start: 26
  outliers final: 13
  residues processed: 122
  average time/residue: 0.9407
  time to fit residues: 121.2022
Evaluate side-chains
  115 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue    2 HIS
Chi-restraints excluded: chain B residue   14 GLU
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue   14 GLU
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue   14 GLU
Chi-restraints excluded: chain D residue   66 ASP
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 118 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 78 optimal weight:    7.9990
   chunk 91 optimal weight:    5.9990
   chunk 106 optimal weight:    3.9990
   chunk 127 optimal weight:    0.7980
   chunk 30 optimal weight:    5.9990
   chunk 95 optimal weight:    0.9980
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
A 237 HIS
A 241 GLN
B 237 HIS
B 241 GLN
D 237 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.140106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.100559 restraints weight = 9853.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 1.37
r_work: 0.2975 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2849 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
moved from start:          0.1843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  10672  Z= 0.171
  Angle     :  0.558   5.157  14464  Z= 0.301
  Chirality :  0.044   0.157   1644
  Planarity :  0.005   0.041   1880
  Dihedral  :  5.518  56.587   1480
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  :  9.08 %
    Favored  : 88.76 %
  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:  1.82 (0.23), residues: 1364
  helix:  2.73 (0.19), residues: 688
  sheet: -1.18 (0.32), residues: 224
  loop :  0.16 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 172 
 TYR   0.027   0.003   TYR A 213 
 PHE   0.016   0.002   PHE C 144 
 TRP   0.013   0.002   TRP A 147 
 HIS   0.005   0.001   HIS D 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (10672)
  covalent geometry    : angle       0.55759 (14464)
  hydrogen bonds       : bond        0.06159 (  589)
  hydrogen bonds       : angle       4.57274 ( 1704)

*********************** 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
  127 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.466 
Fit side-chains
REVERT: A  246 GLU cc_start: 0.8130 (mp0) cc_final: 0.7808 (mp0)
REVERT: A  303 ARG cc_start: 0.8007 (mtp85) cc_final: 0.6930 (ttt-90)
REVERT: B  303 ARG cc_start: 0.8008 (mtp85) cc_final: 0.6962 (ttt-90)
REVERT: C  303 ARG cc_start: 0.8035 (mtp85) cc_final: 0.6993 (ttt-90)
REVERT: C  316 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6237 (mtmm)
REVERT: D  303 ARG cc_start: 0.7998 (mtp85) cc_final: 0.6902 (ttt-90)
  outliers start: 24
  outliers final: 12
  residues processed: 120
  average time/residue: 0.9650
  time to fit residues: 122.2235
Evaluate side-chains
  114 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue    2 HIS
Chi-restraints excluded: chain B residue   14 GLU
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue   14 GLU
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain C residue  316 LYS
Chi-restraints excluded: chain D residue   14 GLU
Chi-restraints excluded: chain D residue   66 ASP
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 38 optimal weight:    0.3980
   chunk 107 optimal weight:    8.9990
   chunk 99 optimal weight:   10.0000
   chunk 3 optimal weight:    9.9990
   chunk 16 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 95 optimal weight:    0.9990
   chunk 78 optimal weight:    7.9990
   chunk 97 optimal weight:    0.5980
   chunk 28 optimal weight:    0.3980
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
A 241 GLN
B 241 GLN
C  95 GLN
D  95 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.144109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.105126 restraints weight = 9874.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 1.35
r_work: 0.3051 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2927 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.1912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019  10672  Z= 0.105
  Angle     :  0.463   4.541  14464  Z= 0.246
  Chirality :  0.040   0.134   1644
  Planarity :  0.004   0.033   1880
  Dihedral  :  5.207  57.425   1480
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  9.80 %
    Favored  : 88.76 %
  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:  2.18 (0.23), residues: 1364
  helix:  3.06 (0.19), residues: 688
  sheet: -1.01 (0.34), residues: 204
  loop :  0.19 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  59 
 TYR   0.017   0.002   TYR C 213 
 PHE   0.015   0.001   PHE D 144 
 TRP   0.008   0.001   TRP A 147 
 HIS   0.002   0.001   HIS D 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 (10672)
  covalent geometry    : angle       0.46253 (14464)
  hydrogen bonds       : bond        0.04474 (  589)
  hydrogen bonds       : angle       4.27005 ( 1704)

*********************** 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
  120 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.516 
Fit side-chains
REVERT: A  246 GLU cc_start: 0.8101 (mp0) cc_final: 0.7790 (mp0)
REVERT: A  303 ARG cc_start: 0.7882 (mtp85) cc_final: 0.6799 (ttt-90)
REVERT: B  303 ARG cc_start: 0.7918 (mtp85) cc_final: 0.6879 (ttt-90)
REVERT: C  303 ARG cc_start: 0.7953 (mtp85) cc_final: 0.6870 (ttt-90)
REVERT: C  316 LYS cc_start: 0.7000 (OUTLIER) cc_final: 0.6223 (mtmm)
REVERT: D  303 ARG cc_start: 0.7900 (mtp85) cc_final: 0.6822 (ttt-90)
  outliers start: 16
  outliers final: 11
  residues processed: 113
  average time/residue: 0.9561
  time to fit residues: 113.9694
Evaluate side-chains
  114 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue    2 HIS
Chi-restraints excluded: chain B residue   14 GLU
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue   14 GLU
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain C residue  316 LYS
Chi-restraints excluded: chain D residue   14 GLU
Chi-restraints excluded: chain D residue   66 ASP
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 83 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 86 optimal weight:    4.9990
   chunk 1 optimal weight:    0.6980
   chunk 95 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 125 optimal weight:    5.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 241 GLN
A 339 GLN
B 241 GLN
C 241 GLN
C 339 GLN
D 237 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.143382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.105366 restraints weight = 9881.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 1.34
r_work: 0.3020 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2897 rms_B_bonded: 3.01 restraints_weight: 0.2500
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.1930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020  10672  Z= 0.108
  Angle     :  0.466   4.543  14464  Z= 0.248
  Chirality :  0.040   0.142   1644
  Planarity :  0.004   0.033   1880
  Dihedral  :  5.204  57.614   1480
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 10.16 %
    Favored  : 88.76 %
  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:  2.19 (0.23), residues: 1364
  helix:  3.07 (0.19), residues: 688
  sheet: -0.97 (0.34), residues: 204
  loop :  0.18 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  59 
 TYR   0.019   0.002   TYR B 213 
 PHE   0.013   0.001   PHE B 144 
 TRP   0.009   0.001   TRP A 147 
 HIS   0.002   0.001   HIS D 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (10672)
  covalent geometry    : angle       0.46593 (14464)
  hydrogen bonds       : bond        0.04617 (  589)
  hydrogen bonds       : angle       4.26873 ( 1704)

*********************** 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
  116 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.465 
Fit side-chains
REVERT: A  246 GLU cc_start: 0.8116 (mp0) cc_final: 0.7801 (mp0)
REVERT: A  303 ARG cc_start: 0.7893 (mtp85) cc_final: 0.6835 (ttt-90)
REVERT: B  303 ARG cc_start: 0.7916 (mtp85) cc_final: 0.6908 (ttt-90)
REVERT: B  316 LYS cc_start: 0.7026 (mtmm) cc_final: 0.6264 (mmtm)
REVERT: C  303 ARG cc_start: 0.7941 (mtp85) cc_final: 0.6873 (ttt-90)
REVERT: C  316 LYS cc_start: 0.6978 (OUTLIER) cc_final: 0.6267 (mtmm)
REVERT: D  303 ARG cc_start: 0.7890 (mtp85) cc_final: 0.6805 (ttt-90)
  outliers start: 12
  outliers final: 11
  residues processed: 112
  average time/residue: 0.9700
  time to fit residues: 114.7295
Evaluate side-chains
  113 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue    2 HIS
Chi-restraints excluded: chain B residue   14 GLU
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue   14 GLU
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain C residue  316 LYS
Chi-restraints excluded: chain D residue   14 GLU
Chi-restraints excluded: chain D residue   66 ASP
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 105 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 118 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 120 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9980
   chunk 129 optimal weight:    2.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A 237 HIS
A 241 GLN
B 241 GLN
C  95 GLN
C 241 GLN
D  95 GLN
D 237 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.140040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.100495 restraints weight = 9855.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 1.36
r_work: 0.2975 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2848 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8593
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10672  Z= 0.163
  Angle     :  0.549   5.046  14464  Z= 0.295
  Chirality :  0.044   0.157   1644
  Planarity :  0.004   0.034   1880
  Dihedral  :  5.499  56.508   1480
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 10.16 %
    Favored  : 88.58 %
  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:  1.92 (0.23), residues: 1364
  helix:  2.83 (0.19), residues: 688
  sheet: -1.19 (0.32), residues: 224
  loop :  0.21 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG C  59 
 TYR   0.026   0.003   TYR C 213 
 PHE   0.015   0.002   PHE C 144 
 TRP   0.013   0.002   TRP A 147 
 HIS   0.004   0.001   HIS D 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (10672)
  covalent geometry    : angle       0.54886 (14464)
  hydrogen bonds       : bond        0.06043 (  589)
  hydrogen bonds       : angle       4.55313 ( 1704)

********************** 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
  118 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.459 
Fit side-chains
REVERT: A  246 GLU cc_start: 0.8130 (mp0) cc_final: 0.7802 (mp0)
REVERT: A  303 ARG cc_start: 0.7944 (mtp85) cc_final: 0.6862 (ttt-90)
REVERT: B  303 ARG cc_start: 0.7971 (mtp85) cc_final: 0.6903 (ttt-90)
REVERT: B  316 LYS cc_start: 0.7027 (mtmm) cc_final: 0.6271 (mmtm)
REVERT: C  303 ARG cc_start: 0.8000 (mtp85) cc_final: 0.6925 (ttt-90)
REVERT: C  316 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6250 (mtmm)
REVERT: D  303 ARG cc_start: 0.7910 (mtp85) cc_final: 0.6837 (ttt-90)
  outliers start: 14
  outliers final: 11
  residues processed: 112
  average time/residue: 0.9405
  time to fit residues: 111.3609
Evaluate side-chains
  114 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue    2 HIS
Chi-restraints excluded: chain B residue   14 GLU
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue   14 GLU
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain C residue  316 LYS
Chi-restraints excluded: chain D residue   14 GLU
Chi-restraints excluded: chain D residue   66 ASP
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 96 optimal weight:    0.5980
   chunk 49 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9990
   chunk 119 optimal weight:    0.3980
   chunk 28 optimal weight:    0.6980
   chunk 109 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 114 optimal weight:    0.6980
   chunk 83 optimal weight:    2.9990
   chunk 79 optimal weight:    0.6980
   chunk 117 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
A 241 GLN
B 241 GLN
C  95 GLN
C 241 GLN
D  95 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.144330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.105473 restraints weight = 9881.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 1.35
r_work: 0.3044 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 3.04 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019  10672  Z= 0.103
  Angle     :  0.459   4.533  14464  Z= 0.244
  Chirality :  0.040   0.135   1644
  Planarity :  0.004   0.033   1880
  Dihedral  :  5.190  57.438   1480
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  9.89 %
    Favored  : 88.76 %
  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:  2.24 (0.23), residues: 1364
  helix:  3.12 (0.19), residues: 688
  sheet: -1.00 (0.34), residues: 204
  loop :  0.22 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  59 
 TYR   0.017   0.002   TYR C 213 
 PHE   0.015   0.001   PHE D 144 
 TRP   0.007   0.001   TRP A 147 
 HIS   0.002   0.001   HIS D 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 (10672)
  covalent geometry    : angle       0.45909 (14464)
  hydrogen bonds       : bond        0.04386 (  589)
  hydrogen bonds       : angle       4.25368 ( 1704)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5012.96 seconds
wall clock time: 86 minutes 13.76 seconds (5173.76 seconds total)