Starting phenix.real_space_refine
on Sun May  3 09:35:19 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/11oc_75879/05_2026/11oc_75879.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/11oc_75879/05_2026/11oc_75879.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/11oc_75879/05_2026/11oc_75879.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/11oc_75879/05_2026/11oc_75879.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/11oc_75879/05_2026/11oc_75879.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/11oc_75879/05_2026/11oc_75879.map"
  }
  resolution = 2.18
  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    3529      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 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: 12021
  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: 376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 376, 376
          Classifications: {'water': 376}
          Link IDs: {None: 375}
    Chain: "B"
      Number of atoms: 391
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 391, 391
          Classifications: {'water': 391}
          Link IDs: {None: 390}
    Chain: "C"
      Number of atoms: 393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 393, 393
          Classifications: {'water': 393}
          Link IDs: {None: 392}
    Chain: "D"
      Number of atoms: 389
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 389, 389
          Classifications: {'water': 389}
          Link IDs: {None: 388}
  Time building chain proxies: 2.74, per 1000 atoms: 0.23
  Number of scatterers: 12021
  At special positions: 0
  Unit cell: (97.755, 80.115, 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    3529      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: 1.02
  Conformation dependent library (CDL) restraints added in 357.2 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
      53.4% alpha, 12.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 23
    Processing helix  chain 'A' and resid 35 through 45
      removed outlier: 3.841A  pdb=" N   LYS A  41 " --> pdb=" O   GLY A  37 " (cutoff:3.500A)
      removed outlier: 4.018A  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: 3.743A  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 258
    Processing helix  chain 'A' and resid 275 through 288
    Processing helix  chain 'A' and resid 306 through 314
    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: 3.847A  pdb=" N   LYS B  41 " --> pdb=" O   GLY B  37 " (cutoff:3.500A)
      removed outlier: 4.008A  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: 3.755A  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 258
    Processing helix  chain 'B' and resid 275 through 288
    Processing helix  chain 'B' and resid 306 through 314
    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: 3.834A  pdb=" N   LYS C  41 " --> pdb=" O   GLY C  37 " (cutoff:3.500A)
      removed outlier: 4.059A  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 79 through 84
      removed outlier: 3.793A  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 140
    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 258
    Processing helix  chain 'C' and resid 275 through 288
    Processing helix  chain 'C' and resid 306 through 314
    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: 3.844A  pdb=" N   LYS D  41 " --> pdb=" O   GLY D  37 " (cutoff:3.500A)
      removed outlier: 4.012A  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: 3.756A  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 258
    Processing helix  chain 'D' and resid 275 through 288
    Processing helix  chain 'D' and resid 306 through 314
    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: 6.643A  pdb=" N   GLY A  28 " --> pdb=" O   GLY A  74 " (cutoff:3.500A)
      removed outlier: 5.850A  pdb=" N   VAL A  76 " --> pdb=" O   GLY A  28 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   LEU A  30 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
      removed outlier: 5.779A  pdb=" N   LEU A  78 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   ALA A  32 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   VAL A 104 " --> pdb=" O   PHE A 144 " (cutoff:3.500A)
      removed outlier: 8.179A  pdb=" N   LYS A 146 " --> pdb=" O   VAL A 104 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   ILE A 106 " --> pdb=" O   LYS A 146 " (cutoff:3.500A)
      removed outlier: 8.554A  pdb=" N   ARG A 148 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   TRP A 147 " --> pdb=" O   ILE A 185 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   LEU A 228 " --> pdb=" O   THR A 268 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   VAL A 267 " --> pdb=" O   THR A 298 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   SER A 300 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
      removed outlier: 5.649A  pdb=" N   PHE A 269 " --> pdb=" O   SER A 300 " (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: 6.665A  pdb=" N   GLY B  28 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
      removed outlier: 5.857A  pdb=" N   VAL B  76 " --> pdb=" O   GLY B  28 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   LEU B  30 " --> pdb=" O   VAL B  76 " (cutoff:3.500A)
      removed outlier: 5.767A  pdb=" N   LEU B  78 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      removed outlier: 7.050A  pdb=" N   ALA B  32 " --> pdb=" O   LEU B  78 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   VAL B 104 " --> pdb=" O   PHE B 144 " (cutoff:3.500A)
      removed outlier: 8.190A  pdb=" N   LYS B 146 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ILE B 106 " --> pdb=" O   LYS B 146 " (cutoff:3.500A)
      removed outlier: 8.657A  pdb=" N   ARG B 148 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   TRP B 147 " --> pdb=" O   ILE B 185 " (cutoff:3.500A)
      removed outlier: 6.254A  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: 6.642A  pdb=" N   GLY C  28 " --> pdb=" O   GLY C  74 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   VAL C  76 " --> pdb=" O   GLY C  28 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   LEU C  30 " --> pdb=" O   VAL C  76 " (cutoff:3.500A)
      removed outlier: 5.761A  pdb=" N   LEU C  78 " --> pdb=" O   LEU C  30 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   ALA C  32 " --> pdb=" O   LEU C  78 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   VAL C 104 " --> pdb=" O   PHE C 144 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   LYS C 146 " --> pdb=" O   VAL C 104 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   ILE C 106 " --> pdb=" O   LYS C 146 " (cutoff:3.500A)
      removed outlier: 8.618A  pdb=" N   ARG C 148 " --> pdb=" O   ILE C 106 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   TRP C 147 " --> pdb=" O   ILE C 185 " (cutoff:3.500A)
      removed outlier: 6.286A  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: 6.662A  pdb=" N   GLY D  28 " --> pdb=" O   GLY D  74 " (cutoff:3.500A)
      removed outlier: 5.847A  pdb=" N   VAL D  76 " --> pdb=" O   GLY D  28 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   LEU D  30 " --> pdb=" O   VAL D  76 " (cutoff:3.500A)
      removed outlier: 5.775A  pdb=" N   LEU D  78 " --> pdb=" O   LEU D  30 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   ALA D  32 " --> pdb=" O   LEU D  78 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   GLY D  74 " --> pdb=" O   VAL D 103 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   GLY D 105 " --> pdb=" O   GLY D  74 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   VAL D  76 " --> pdb=" O   GLY D 105 " (cutoff:3.500A)
      removed outlier: 7.464A  pdb=" N   LYS D 107 " --> pdb=" O   VAL D  76 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   LEU D  78 " --> pdb=" O   LYS D 107 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   VAL D 104 " --> pdb=" O   PHE D 144 " (cutoff:3.500A)
      removed outlier: 8.175A  pdb=" N   LYS D 146 " --> pdb=" O   VAL D 104 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   ILE D 106 " --> pdb=" O   LYS D 146 " (cutoff:3.500A)
      removed outlier: 8.646A  pdb=" N   ARG D 148 " --> pdb=" O   ILE D 106 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   TRP D 147 " --> pdb=" O   ILE D 185 " (cutoff:3.500A)
      removed outlier: 6.298A  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

    571 hydrogen bonds defined for protein.
    1656 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.98

  Time building geometry restraints manager: 1.31 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1780
        1.31 -     1.43: 2579
        1.43 -     1.56: 6257
        1.56 -     1.69: 0
        1.69 -     1.81: 56
  Bond restraints: 10672
  Sorted by residual:
  bond pdb=" C   PRO A 294 "
       pdb=" O   PRO A 294 "
    ideal  model  delta    sigma   weight residual
    1.237  1.182  0.056 1.20e-02 6.94e+03 2.15e+01
  bond pdb=" C   VAL C 260 "
       pdb=" N   PRO C 261 "
    ideal  model  delta    sigma   weight residual
    1.329  1.372 -0.043 1.18e-02 7.18e+03 1.33e+01
  bond pdb=" C   VAL A 260 "
       pdb=" N   PRO A 261 "
    ideal  model  delta    sigma   weight residual
    1.329  1.372 -0.043 1.18e-02 7.18e+03 1.33e+01
  bond pdb=" C   VAL D 260 "
       pdb=" N   PRO D 261 "
    ideal  model  delta    sigma   weight residual
    1.329  1.372 -0.043 1.18e-02 7.18e+03 1.32e+01
  bond pdb=" C   VAL B 260 "
       pdb=" N   PRO B 261 "
    ideal  model  delta    sigma   weight residual
    1.329  1.372 -0.043 1.18e-02 7.18e+03 1.31e+01
  ... (remaining 10667 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.35: 13542
        1.35 -     2.70: 679
        2.70 -     4.05: 169
        4.05 -     5.41: 55
        5.41 -     6.76: 19
  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  118.79   -4.99 1.00e+00 1.00e+00 2.49e+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  118.79   -4.99 1.00e+00 1.00e+00 2.49e+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  118.77   -4.97 1.00e+00 1.00e+00 2.47e+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  118.65   -4.85 1.00e+00 1.00e+00 2.35e+01
  angle pdb=" N   PHE A  79 "
        pdb=" CA  PHE A  79 "
        pdb=" C   PHE A  79 "
      ideal   model   delta    sigma   weight residual
     110.53  104.77    5.76 1.29e+00 6.01e-01 1.99e+01
  ... (remaining 14459 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 6076
       18.00 -    36.00: 330
       36.00 -    53.99: 62
       53.99 -    71.99: 25
       71.99 -    89.99: 11
  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 -130.89    8.29     0      2.50e+00 1.60e-01 1.10e+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  163.79   16.21     0      5.00e+00 4.00e-02 1.05e+01
  dihedral pdb=" CA  PHE B 299 "
           pdb=" C   PHE B 299 "
           pdb=" N   SER B 300 "
           pdb=" CA  SER B 300 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.83   16.17     0      5.00e+00 4.00e-02 1.05e+01
  ... (remaining 6501 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1178
       0.042 -    0.085: 292
       0.085 -    0.127: 137
       0.127 -    0.170: 24
       0.170 -    0.212: 13
  Chirality restraints: 1644
  Sorted by residual:
  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    2.65   -0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  ILE D 190 "
            pdb=" N   ILE D 190 "
            pdb=" C   ILE D 190 "
            pdb=" CB  ILE D 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CA  PHE C 144 "
            pdb=" N   PHE C 144 "
            pdb=" C   PHE C 144 "
            pdb=" CB  PHE C 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.05e+00
  ... (remaining 1641 not shown)

  Planarity restraints: 1880
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C 292 "   -0.010 2.00e-02 2.50e+03   2.04e-02 4.16e+00
        pdb=" C   LEU C 292 "    0.035 2.00e-02 2.50e+03
        pdb=" O   LEU C 292 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   LYS C 293 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D 292 "    0.010 2.00e-02 2.50e+03   2.00e-02 4.00e+00
        pdb=" C   LEU D 292 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   LEU D 292 "    0.013 2.00e-02 2.50e+03
        pdb=" N   LYS D 293 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU C 326 "    0.009 2.00e-02 2.50e+03   1.81e-02 3.28e+00
        pdb=" C   GLU C 326 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   GLU C 326 "    0.012 2.00e-02 2.50e+03
        pdb=" N   TYR C 327 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1877 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 3910
        2.82 -     3.34: 12625
        3.34 -     3.86: 24576
        3.86 -     4.38: 28352
        4.38 -     4.90: 43846
  Nonbonded interactions: 113309
  Sorted by model distance:
  nonbonded pdb=" O   PRO B 114 "
            pdb=" O   HOH B 401 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" OD2 ASP B 195 "
            pdb=" O   HOH B 402 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   PRO C 114 "
            pdb=" O   HOH C 401 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   HOH A 456 "
            pdb=" O   HOH B 462 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" OD2 ASP A 195 "
            pdb=" O   HOH A 401 "
     model   vdw
     2.302 3.040
  ... (remaining 113304 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:             3.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.620
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  10672  Z= 0.320
  Angle     :  0.753   6.757  14464  Z= 0.494
  Chirality :  0.050   0.212   1644
  Planarity :  0.005   0.039   1880
  Dihedral  : 12.715  89.990   3984
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 1.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  0.99 %
    Favored  : 98.29 %
  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:  0.95 (0.22), residues: 1364
  helix:  1.51 (0.20), residues: 712
  sheet: -1.27 (0.40), residues: 144
  loop :  0.10 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 330 
 TYR   0.018   0.002   TYR C 213 
 PHE   0.026   0.003   PHE D 144 
 TRP   0.016   0.003   TRP B 295 
 HIS   0.003   0.001   HIS C   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 (10672)
  covalent geometry    : angle       0.75333 (14464)
  hydrogen bonds       : bond        0.14511 (  571)
  hydrogen bonds       : angle       6.10261 ( 1656)

*********************** 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: 8
    poor density    : 165
  time to evaluate  : 0.447 
Fit side-chains
REVERT: A   86 LYS cc_start: 0.8395 (mtpp) cc_final: 0.8101 (mttp)
REVERT: A  199 LYS cc_start: 0.8144 (mmtp) cc_final: 0.7835 (mtpm)
REVERT: A  292 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7710 (tt)
REVERT: A  295 TRP cc_start: 0.8159 (OUTLIER) cc_final: 0.5462 (m-90)
REVERT: B   86 LYS cc_start: 0.8419 (mtpp) cc_final: 0.8153 (mttp)
REVERT: B  173 TYR cc_start: 0.9097 (OUTLIER) cc_final: 0.8837 (t80)
REVERT: B  199 LYS cc_start: 0.8252 (ttpt) cc_final: 0.7785 (mptp)
REVERT: B  246 GLU cc_start: 0.8164 (mp0) cc_final: 0.7934 (mp0)
REVERT: C   86 LYS cc_start: 0.8489 (mtpp) cc_final: 0.8258 (mttp)
REVERT: C  199 LYS cc_start: 0.8279 (ttpt) cc_final: 0.7936 (mptp)
REVERT: D  139 LYS cc_start: 0.8529 (mttp) cc_final: 0.8114 (mtmt)
REVERT: D  173 TYR cc_start: 0.9121 (OUTLIER) cc_final: 0.8845 (t80)
REVERT: D  199 LYS cc_start: 0.8354 (ttpt) cc_final: 0.8068 (mptp)
REVERT: D  237 HIS cc_start: 0.7751 (t-90) cc_final: 0.6588 (p-80)
  outliers start: 8
  outliers final: 3
  residues processed: 172
  average time/residue: 0.9304
  time to fit residues: 168.5864
Evaluate side-chains
  104 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue  173 TYR
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:    6.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    0.5980
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
B  85 GLN
C 119 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.149920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.111496 restraints weight = 9359.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 1.16
r_work: 0.3085 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2964 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.1458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10672  Z= 0.159
  Angle     :  0.593   5.872  14464  Z= 0.315
  Chirality :  0.044   0.152   1644
  Planarity :  0.004   0.025   1880
  Dihedral  :  5.745  54.769   1486
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  5.58 %
    Favored  : 93.26 %
  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:  2.23 (0.19), residues: 708
  sheet: -0.88 (0.36), residues: 176
  loop :  0.16 (0.27), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 200 
 TYR   0.027   0.002   TYR B 213 
 PHE   0.013   0.002   PHE D 144 
 TRP   0.012   0.002   TRP A 147 
 HIS   0.006   0.001   HIS C   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (10672)
  covalent geometry    : angle       0.59261 (14464)
  hydrogen bonds       : bond        0.06506 (  571)
  hydrogen bonds       : angle       4.77046 ( 1656)

*********************** 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
  109 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.332 
Fit side-chains
REVERT: A   52 GLU cc_start: 0.7698 (tt0) cc_final: 0.7324 (tt0)
REVERT: A   86 LYS cc_start: 0.8404 (mtpp) cc_final: 0.8117 (mttp)
REVERT: A  199 LYS cc_start: 0.8364 (mmtp) cc_final: 0.7916 (mmpt)
REVERT: A  292 LEU cc_start: 0.8216 (tt) cc_final: 0.7996 (tt)
REVERT: B   52 GLU cc_start: 0.7736 (tt0) cc_final: 0.7378 (tt0)
REVERT: B   86 LYS cc_start: 0.8419 (mtpp) cc_final: 0.8158 (mttp)
REVERT: B  199 LYS cc_start: 0.8360 (ttpt) cc_final: 0.7783 (mptp)
REVERT: B  242 LYS cc_start: 0.7616 (mptt) cc_final: 0.7363 (mmpt)
REVERT: B  246 GLU cc_start: 0.8088 (mp0) cc_final: 0.7786 (mp0)
REVERT: C   86 LYS cc_start: 0.8394 (mtpp) cc_final: 0.8123 (mttp)
REVERT: C  173 TYR cc_start: 0.9204 (OUTLIER) cc_final: 0.8863 (t80)
REVERT: C  199 LYS cc_start: 0.8362 (ttpt) cc_final: 0.7774 (mptp)
REVERT: C  242 LYS cc_start: 0.7631 (mptt) cc_final: 0.7381 (mmpt)
REVERT: D   52 GLU cc_start: 0.7700 (tt0) cc_final: 0.7325 (tt0)
REVERT: D  199 LYS cc_start: 0.8379 (ttpt) cc_final: 0.7756 (mptp)
REVERT: D  237 HIS cc_start: 0.7705 (t-90) cc_final: 0.6436 (p-80)
REVERT: D  242 LYS cc_start: 0.7538 (mmtm) cc_final: 0.7227 (mmpt)
  outliers start: 13
  outliers final: 6
  residues processed: 105
  average time/residue: 0.8438
  time to fit residues: 93.9317
Evaluate side-chains
  97 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 114 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 96 optimal weight:    2.9990
   chunk 123 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 124 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 108 optimal weight:   10.0000
   chunk 80 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.5586

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.149103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.110550 restraints weight = 9431.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 1.16
r_work: 0.3072 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.1605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10672  Z= 0.156
  Angle     :  0.583   5.833  14464  Z= 0.309
  Chirality :  0.044   0.153   1644
  Planarity :  0.004   0.025   1880
  Dihedral  :  5.764  55.338   1484
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  5.85 %
    Favored  : 92.72 %
  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:  1.57 (0.23), residues: 1364
  helix:  2.53 (0.18), residues: 684
  sheet: -1.91 (0.33), residues: 204
  loop :  0.33 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 148 
 TYR   0.027   0.002   TYR D 213 
 PHE   0.017   0.002   PHE D 144 
 TRP   0.010   0.002   TRP A 147 
 HIS   0.005   0.001   HIS C   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (10672)
  covalent geometry    : angle       0.58304 (14464)
  hydrogen bonds       : bond        0.06527 (  571)
  hydrogen bonds       : angle       4.72365 ( 1656)

*********************** 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
  105 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.455 
Fit side-chains
REVERT: A   52 GLU cc_start: 0.7758 (tt0) cc_final: 0.7376 (tt0)
REVERT: A   86 LYS cc_start: 0.8413 (mtpp) cc_final: 0.8127 (mttp)
REVERT: A  173 TYR cc_start: 0.9197 (OUTLIER) cc_final: 0.8919 (t80)
REVERT: A  199 LYS cc_start: 0.8365 (mmtp) cc_final: 0.7905 (mmpt)
REVERT: A  242 LYS cc_start: 0.7636 (mptt) cc_final: 0.7343 (mmpt)
REVERT: B   52 GLU cc_start: 0.7757 (tt0) cc_final: 0.7376 (tt0)
REVERT: B   86 LYS cc_start: 0.8430 (mtpp) cc_final: 0.8180 (mttp)
REVERT: B  107 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8424 (tmmm)
REVERT: B  199 LYS cc_start: 0.8344 (ttpt) cc_final: 0.7709 (mptp)
REVERT: B  246 GLU cc_start: 0.8117 (mp0) cc_final: 0.7814 (mp0)
REVERT: C   86 LYS cc_start: 0.8406 (mtpp) cc_final: 0.8150 (mttp)
REVERT: C  173 TYR cc_start: 0.9197 (OUTLIER) cc_final: 0.8856 (t80)
REVERT: C  199 LYS cc_start: 0.8349 (ttpt) cc_final: 0.7690 (mptp)
REVERT: D   52 GLU cc_start: 0.7727 (tt0) cc_final: 0.7356 (tt0)
REVERT: D  107 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8415 (tmmm)
REVERT: D  199 LYS cc_start: 0.8350 (ttpt) cc_final: 0.7664 (mptp)
REVERT: D  237 HIS cc_start: 0.7697 (t-90) cc_final: 0.6435 (p-80)
REVERT: D  242 LYS cc_start: 0.7517 (mmtm) cc_final: 0.7178 (mmpt)
  outliers start: 16
  outliers final: 6
  residues processed: 103
  average time/residue: 0.8998
  time to fit residues: 98.2955
Evaluate side-chains
  94 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue  107 LYS
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 105 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 123 optimal weight:    2.9990
   chunk 37 optimal weight:    6.9990
   chunk 91 optimal weight:    0.0470
   chunk 128 optimal weight:    0.9990
   chunk 95 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9990
   chunk 81 optimal weight:    0.6980
   chunk 130 optimal weight:    3.9990
   chunk 110 optimal weight:    4.9990
   overall best weight:    0.6680

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

Flipped N/Q/H residues before XYZ refinement:
D  95 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.153090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.115311 restraints weight = 9443.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 1.16
r_work: 0.3138 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.1683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  10672  Z= 0.110
  Angle     :  0.496   5.282  14464  Z= 0.258
  Chirality :  0.040   0.141   1644
  Planarity :  0.003   0.027   1880
  Dihedral  :  5.463  55.812   1484
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  6.92 %
    Favored  : 92.09 %
  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:  2.54 (0.19), residues: 736
  sheet: -1.26 (0.30), residues: 248
  loop :  0.42 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  55 
 TYR   0.018   0.002   TYR C 213 
 PHE   0.015   0.001   PHE A 144 
 TRP   0.007   0.001   TRP A 147 
 HIS   0.002   0.001   HIS C 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 (10672)
  covalent geometry    : angle       0.49579 (14464)
  hydrogen bonds       : bond        0.04992 (  571)
  hydrogen bonds       : angle       4.37274 ( 1656)

*********************** 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
  98 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.471 
Fit side-chains
REVERT: A   52 GLU cc_start: 0.7714 (tt0) cc_final: 0.7348 (tt0)
REVERT: A   86 LYS cc_start: 0.8367 (mtpp) cc_final: 0.8076 (mttp)
REVERT: A  199 LYS cc_start: 0.8287 (mmtp) cc_final: 0.7510 (mptp)
REVERT: A  242 LYS cc_start: 0.7562 (mptt) cc_final: 0.7281 (mmpt)
REVERT: B   52 GLU cc_start: 0.7730 (tt0) cc_final: 0.7372 (tt0)
REVERT: B   86 LYS cc_start: 0.8413 (mtpp) cc_final: 0.8154 (mttp)
REVERT: B  107 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8388 (tmmm)
REVERT: B  173 TYR cc_start: 0.9138 (OUTLIER) cc_final: 0.8765 (t80)
REVERT: B  199 LYS cc_start: 0.8239 (ttpt) cc_final: 0.7684 (mptp)
REVERT: B  246 GLU cc_start: 0.8076 (mp0) cc_final: 0.7780 (mp0)
REVERT: C   86 LYS cc_start: 0.8383 (mtpp) cc_final: 0.8114 (mttp)
REVERT: C  199 LYS cc_start: 0.8248 (ttpt) cc_final: 0.7663 (mptp)
REVERT: D   52 GLU cc_start: 0.7671 (tt0) cc_final: 0.7328 (tt0)
REVERT: D  107 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8340 (tmmm)
REVERT: D  173 TYR cc_start: 0.9137 (OUTLIER) cc_final: 0.8768 (t80)
REVERT: D  199 LYS cc_start: 0.8253 (ttpt) cc_final: 0.7619 (mptp)
REVERT: D  237 HIS cc_start: 0.7650 (t-90) cc_final: 0.6390 (p-80)
REVERT: D  242 LYS cc_start: 0.7453 (mmtm) cc_final: 0.7249 (mptt)
  outliers start: 11
  outliers final: 4
  residues processed: 98
  average time/residue: 0.8988
  time to fit residues: 93.3905
Evaluate side-chains
  94 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue  107 LYS
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 31 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0770
   chunk 114 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 97 optimal weight:    0.6980
   chunk 47 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   chunk 128 optimal weight:    4.9990
   overall best weight:    0.5938

-------------------------------------------------------------------------------
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 = 0.3713 r_free = 0.3713 target = 0.154041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.116507 restraints weight = 9478.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 1.16
r_work: 0.3152 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3034 rms_B_bonded: 2.97 restraints_weight: 0.2500
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
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      :  0.002   0.022  10672  Z= 0.105
  Angle     :  0.480   5.275  14464  Z= 0.249
  Chirality :  0.040   0.143   1644
  Planarity :  0.003   0.026   1880
  Dihedral  :  5.361  55.623   1484
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  7.55 %
    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:  2.00 (0.23), residues: 1364
  helix:  2.74 (0.19), residues: 732
  sheet: -1.20 (0.31), residues: 248
  loop :  0.40 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 303 
 TYR   0.018   0.001   TYR C 213 
 PHE   0.014   0.001   PHE D 144 
 TRP   0.008   0.001   TRP A 147 
 HIS   0.002   0.001   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 (10672)
  covalent geometry    : angle       0.48042 (14464)
  hydrogen bonds       : bond        0.04764 (  571)
  hydrogen bonds       : angle       4.24316 ( 1656)

*********************** 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
  98 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.415 
Fit side-chains
REVERT: A   52 GLU cc_start: 0.7709 (tt0) cc_final: 0.7358 (tt0)
REVERT: A   86 LYS cc_start: 0.8371 (mtpp) cc_final: 0.8088 (mttp)
REVERT: A  199 LYS cc_start: 0.8256 (mmtp) cc_final: 0.7489 (mptp)
REVERT: B   52 GLU cc_start: 0.7730 (tt0) cc_final: 0.7393 (tt0)
REVERT: B   86 LYS cc_start: 0.8427 (mtpp) cc_final: 0.8171 (mttp)
REVERT: B  107 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8564 (ttmm)
REVERT: B  173 TYR cc_start: 0.9123 (OUTLIER) cc_final: 0.8757 (t80)
REVERT: B  199 LYS cc_start: 0.8233 (ttpt) cc_final: 0.7722 (mptp)
REVERT: B  242 LYS cc_start: 0.7510 (mmtt) cc_final: 0.7303 (mmtt)
REVERT: B  246 GLU cc_start: 0.8110 (mp0) cc_final: 0.7888 (mp0)
REVERT: C   86 LYS cc_start: 0.8394 (mtpp) cc_final: 0.8134 (mttp)
REVERT: C  199 LYS cc_start: 0.8241 (ttpt) cc_final: 0.7700 (mptp)
REVERT: C  242 LYS cc_start: 0.7522 (mmtt) cc_final: 0.7319 (mmtt)
REVERT: D   52 GLU cc_start: 0.7689 (tt0) cc_final: 0.7348 (tt0)
REVERT: D  107 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8297 (tmmm)
REVERT: D  139 LYS cc_start: 0.8423 (mttp) cc_final: 0.7831 (mtmt)
REVERT: D  173 TYR cc_start: 0.9119 (OUTLIER) cc_final: 0.8761 (t80)
REVERT: D  199 LYS cc_start: 0.8250 (ttpt) cc_final: 0.7655 (mptp)
REVERT: D  237 HIS cc_start: 0.7674 (t-90) cc_final: 0.6399 (p-80)
  outliers start: 10
  outliers final: 4
  residues processed: 98
  average time/residue: 0.8969
  time to fit residues: 93.3347
Evaluate side-chains
  97 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue  107 LYS
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 120 optimal weight:    0.2980
   chunk 37 optimal weight:    7.9990
   chunk 126 optimal weight:    4.9990
   chunk 129 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 122 optimal weight:    4.9990
   chunk 115 optimal weight:    0.6980
   chunk 110 optimal weight:    4.9990
   chunk 4 optimal weight:    7.9990
   chunk 75 optimal weight:    0.3980
   chunk 108 optimal weight:    0.6980
   overall best weight:    0.6182

-------------------------------------------------------------------------------
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 = 0.3712 r_free = 0.3712 target = 0.153999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.116441 restraints weight = 9430.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 1.16
r_work: 0.3153 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3034 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.1756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  10672  Z= 0.105
  Angle     :  0.480   5.589  14464  Z= 0.248
  Chirality :  0.040   0.143   1644
  Planarity :  0.003   0.026   1880
  Dihedral  :  5.332  55.586   1484
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  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:  2.06 (0.23), residues: 1364
  helix:  2.80 (0.19), residues: 732
  sheet: -1.18 (0.31), residues: 248
  loop :  0.42 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 330 
 TYR   0.019   0.001   TYR C 213 
 PHE   0.014   0.001   PHE D 144 
 TRP   0.008   0.001   TRP A 147 
 HIS   0.002   0.001   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 (10672)
  covalent geometry    : angle       0.48016 (14464)
  hydrogen bonds       : bond        0.04769 (  571)
  hydrogen bonds       : angle       4.20774 ( 1656)

*********************** 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
  103 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.458 
Fit side-chains
REVERT: A   52 GLU cc_start: 0.7703 (tt0) cc_final: 0.7357 (tt0)
REVERT: A   86 LYS cc_start: 0.8369 (mtpp) cc_final: 0.8088 (mttp)
REVERT: A  107 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8389 (tmmm)
REVERT: A  199 LYS cc_start: 0.8249 (mmtp) cc_final: 0.7470 (mptp)
REVERT: B   52 GLU cc_start: 0.7712 (tt0) cc_final: 0.7384 (tt0)
REVERT: B   86 LYS cc_start: 0.8415 (mtpp) cc_final: 0.8163 (mttp)
REVERT: B  107 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8391 (tmmm)
REVERT: B  173 TYR cc_start: 0.9129 (OUTLIER) cc_final: 0.8761 (t80)
REVERT: B  199 LYS cc_start: 0.8210 (ttpt) cc_final: 0.7712 (mptp)
REVERT: B  242 LYS cc_start: 0.7546 (mmtt) cc_final: 0.7330 (mmtt)
REVERT: B  246 GLU cc_start: 0.8109 (mp0) cc_final: 0.7902 (mp0)
REVERT: C   86 LYS cc_start: 0.8393 (mtpp) cc_final: 0.8135 (mttp)
REVERT: C  199 LYS cc_start: 0.8217 (ttpt) cc_final: 0.7675 (mptp)
REVERT: C  242 LYS cc_start: 0.7561 (mmtt) cc_final: 0.7349 (mmtt)
REVERT: D   52 GLU cc_start: 0.7693 (tt0) cc_final: 0.7361 (tt0)
REVERT: D  139 LYS cc_start: 0.8411 (mttp) cc_final: 0.7815 (mtmt)
REVERT: D  173 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.8760 (t80)
REVERT: D  199 LYS cc_start: 0.8221 (ttpt) cc_final: 0.7647 (mptp)
REVERT: D  237 HIS cc_start: 0.7652 (t-90) cc_final: 0.6403 (p-80)
  outliers start: 10
  outliers final: 4
  residues processed: 103
  average time/residue: 0.8927
  time to fit residues: 97.5560
Evaluate side-chains
  97 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue  173 TYR
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 24 optimal weight:    0.5980
   chunk 64 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 15 optimal weight:    5.9990
   chunk 3 optimal weight:    6.9990
   chunk 53 optimal weight:    0.8980
   chunk 123 optimal weight:    0.7980
   chunk 74 optimal weight:    3.9990
   chunk 81 optimal weight:    0.6980
   chunk 55 optimal weight:    7.9990
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3705 r_free = 0.3705 target = 0.153341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.115626 restraints weight = 9410.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 1.16
r_work: 0.3141 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3023 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  10672  Z= 0.109
  Angle     :  0.489   6.228  14464  Z= 0.252
  Chirality :  0.040   0.146   1644
  Planarity :  0.003   0.026   1880
  Dihedral  :  5.371  55.474   1484
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  7.01 %
    Favored  : 91.82 %
  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:  2.06 (0.23), residues: 1364
  helix:  2.79 (0.19), residues: 732
  sheet: -1.20 (0.31), residues: 248
  loop :  0.44 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  59 
 TYR   0.021   0.002   TYR D 213 
 PHE   0.015   0.001   PHE D 144 
 TRP   0.008   0.001   TRP B 147 
 HIS   0.002   0.001   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (10672)
  covalent geometry    : angle       0.48894 (14464)
  hydrogen bonds       : bond        0.04944 (  571)
  hydrogen bonds       : angle       4.23125 ( 1656)

*********************** 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
  103 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.493 
Fit side-chains
REVERT: A   52 GLU cc_start: 0.7700 (tt0) cc_final: 0.7354 (tt0)
REVERT: A   86 LYS cc_start: 0.8360 (mtpp) cc_final: 0.8080 (mttp)
REVERT: A  107 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8387 (tmmm)
REVERT: A  199 LYS cc_start: 0.8274 (mmtp) cc_final: 0.7500 (mptp)
REVERT: A  330 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.6312 (mmm160)
REVERT: B   52 GLU cc_start: 0.7687 (tt0) cc_final: 0.7358 (tt0)
REVERT: B   86 LYS cc_start: 0.8410 (mtpp) cc_final: 0.8156 (mttp)
REVERT: B  107 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8423 (tmmm)
REVERT: B  173 TYR cc_start: 0.9138 (OUTLIER) cc_final: 0.8755 (t80)
REVERT: B  199 LYS cc_start: 0.8236 (ttpt) cc_final: 0.7712 (mptp)
REVERT: B  242 LYS cc_start: 0.7564 (mmtt) cc_final: 0.7348 (mmtt)
REVERT: B  246 GLU cc_start: 0.8075 (mp0) cc_final: 0.7865 (mp0)
REVERT: B  330 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.6342 (mmm160)
REVERT: C   86 LYS cc_start: 0.8388 (mtpp) cc_final: 0.8129 (mttp)
REVERT: C  173 TYR cc_start: 0.9126 (OUTLIER) cc_final: 0.8870 (t80)
REVERT: C  199 LYS cc_start: 0.8239 (ttpt) cc_final: 0.7678 (mptp)
REVERT: C  242 LYS cc_start: 0.7581 (mmtt) cc_final: 0.7369 (mmtt)
REVERT: D   52 GLU cc_start: 0.7676 (tt0) cc_final: 0.7338 (tt0)
REVERT: D  107 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8335 (tmmm)
REVERT: D  139 LYS cc_start: 0.8406 (mttp) cc_final: 0.7794 (mtmt)
REVERT: D  173 TYR cc_start: 0.9136 (OUTLIER) cc_final: 0.8753 (t80)
REVERT: D  199 LYS cc_start: 0.8247 (ttpt) cc_final: 0.7652 (mptp)
REVERT: D  237 HIS cc_start: 0.7645 (t-90) cc_final: 0.6390 (p-80)
  outliers start: 13
  outliers final: 4
  residues processed: 103
  average time/residue: 0.9182
  time to fit residues: 100.2019
Evaluate side-chains
  99 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  330 ARG
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  295 TRP
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  107 LYS
Chi-restraints excluded: chain D residue  173 TYR
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 118 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0870
   chunk 49 optimal weight:    3.9990
   chunk 99 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9990
   chunk 115 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 82 optimal weight:    7.9990
   chunk 120 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.6558

-------------------------------------------------------------------------------
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 = 0.3709 r_free = 0.3709 target = 0.153766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.116699 restraints weight = 9413.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 1.15
r_work: 0.3152 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3034 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  10672  Z= 0.106
  Angle     :  0.483   6.851  14464  Z= 0.248
  Chirality :  0.040   0.143   1644
  Planarity :  0.003   0.026   1880
  Dihedral  :  5.334  55.452   1484
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  7.37 %
    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:  2.09 (0.23), residues: 1364
  helix:  2.81 (0.19), residues: 732
  sheet: -1.19 (0.30), residues: 248
  loop :  0.47 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  59 
 TYR   0.019   0.002   TYR D 213 
 PHE   0.015   0.001   PHE D 144 
 TRP   0.008   0.001   TRP A 147 
 HIS   0.002   0.001   HIS B  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 (10672)
  covalent geometry    : angle       0.48270 (14464)
  hydrogen bonds       : bond        0.04792 (  571)
  hydrogen bonds       : angle       4.19464 ( 1656)

*********************** 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
  103 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.442 
Fit side-chains
REVERT: A   52 GLU cc_start: 0.7702 (tt0) cc_final: 0.7358 (tt0)
REVERT: A   86 LYS cc_start: 0.8365 (mtpp) cc_final: 0.8084 (mttp)
REVERT: A  107 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8387 (tmmm)
REVERT: A  199 LYS cc_start: 0.8252 (mmtp) cc_final: 0.7483 (mptp)
REVERT: A  330 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.6319 (mmm160)
REVERT: B   52 GLU cc_start: 0.7693 (tt0) cc_final: 0.7368 (tt0)
REVERT: B   86 LYS cc_start: 0.8412 (mtpp) cc_final: 0.8162 (mttp)
REVERT: B  107 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8409 (tmmm)
REVERT: B  173 TYR cc_start: 0.9131 (OUTLIER) cc_final: 0.8762 (t80)
REVERT: B  199 LYS cc_start: 0.8224 (ttpt) cc_final: 0.7720 (mptp)
REVERT: B  242 LYS cc_start: 0.7580 (mmtt) cc_final: 0.7372 (mmtt)
REVERT: B  246 GLU cc_start: 0.8110 (mp0) cc_final: 0.7885 (mp0)
REVERT: B  330 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.6340 (mmm160)
REVERT: C   86 LYS cc_start: 0.8392 (mtpp) cc_final: 0.8134 (mttp)
REVERT: C  199 LYS cc_start: 0.8223 (ttpt) cc_final: 0.7678 (mptp)
REVERT: C  242 LYS cc_start: 0.7598 (mmtt) cc_final: 0.7393 (mmtt)
REVERT: D   52 GLU cc_start: 0.7683 (tt0) cc_final: 0.7345 (tt0)
REVERT: D  107 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8335 (tmmm)
REVERT: D  139 LYS cc_start: 0.8420 (mttp) cc_final: 0.7812 (mtmt)
REVERT: D  173 TYR cc_start: 0.9127 (OUTLIER) cc_final: 0.8755 (t80)
REVERT: D  199 LYS cc_start: 0.8262 (ttpt) cc_final: 0.7673 (mptp)
  outliers start: 13
  outliers final: 4
  residues processed: 103
  average time/residue: 0.9045
  time to fit residues: 98.8004
Evaluate side-chains
  98 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  330 ARG
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain B residue  173 TYR
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  107 LYS
Chi-restraints excluded: chain D residue  173 TYR
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 71 optimal weight:    4.9990
   chunk 64 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 110 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0980
   chunk 97 optimal weight:    1.9990
   chunk 131 optimal weight:    0.5980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3708 r_free = 0.3708 target = 0.153688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.116098 restraints weight = 9384.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 1.16
r_work: 0.3147 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3028 rms_B_bonded: 2.97 restraints_weight: 0.2500
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
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      :  0.002   0.021  10672  Z= 0.107
  Angle     :  0.489   7.430  14464  Z= 0.251
  Chirality :  0.040   0.144   1644
  Planarity :  0.003   0.026   1880
  Dihedral  :  5.348  55.478   1484
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  7.73 %
    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:  2.07 (0.23), residues: 1364
  helix:  2.75 (0.19), residues: 736
  sheet: -1.20 (0.30), residues: 248
  loop :  0.54 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  59 
 TYR   0.020   0.002   TYR D 213 
 PHE   0.015   0.001   PHE D 144 
 TRP   0.008   0.001   TRP D 147 
 HIS   0.002   0.001   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 (10672)
  covalent geometry    : angle       0.48878 (14464)
  hydrogen bonds       : bond        0.04852 (  571)
  hydrogen bonds       : angle       4.20260 ( 1656)

*********************** 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
  101 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.464 
Fit side-chains
REVERT: A   52 GLU cc_start: 0.7707 (tt0) cc_final: 0.7365 (tt0)
REVERT: A   86 LYS cc_start: 0.8355 (mtpp) cc_final: 0.8079 (mttp)
REVERT: A  107 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8395 (tmmm)
REVERT: A  199 LYS cc_start: 0.8261 (mmtp) cc_final: 0.7488 (mptp)
REVERT: A  330 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.6265 (mmm160)
REVERT: B   52 GLU cc_start: 0.7697 (tt0) cc_final: 0.7372 (tt0)
REVERT: B   86 LYS cc_start: 0.8414 (mtpp) cc_final: 0.8166 (mttp)
REVERT: B  107 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8422 (tmmm)
REVERT: B  173 TYR cc_start: 0.9140 (OUTLIER) cc_final: 0.8764 (t80)
REVERT: B  199 LYS cc_start: 0.8238 (ttpt) cc_final: 0.7729 (mptp)
REVERT: B  242 LYS cc_start: 0.7597 (mmtt) cc_final: 0.7390 (mmtt)
REVERT: B  246 GLU cc_start: 0.8125 (mp0) cc_final: 0.7919 (mp0)
REVERT: B  330 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.6324 (mmm160)
REVERT: C   86 LYS cc_start: 0.8382 (mtpp) cc_final: 0.8126 (mttp)
REVERT: C  199 LYS cc_start: 0.8236 (ttpt) cc_final: 0.7693 (mptp)
REVERT: C  242 LYS cc_start: 0.7612 (mmtt) cc_final: 0.7408 (mmtt)
REVERT: D   52 GLU cc_start: 0.7678 (tt0) cc_final: 0.7346 (tt0)
REVERT: D  107 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8340 (tmmm)
REVERT: D  139 LYS cc_start: 0.8419 (mttp) cc_final: 0.7808 (mtmt)
REVERT: D  173 TYR cc_start: 0.9135 (OUTLIER) cc_final: 0.8759 (t80)
REVERT: D  199 LYS cc_start: 0.8278 (ttpt) cc_final: 0.7684 (mptp)
  outliers start: 11
  outliers final: 4
  residues processed: 101
  average time/residue: 0.9075
  time to fit residues: 96.8881
Evaluate side-chains
  98 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  330 ARG
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain B residue  173 TYR
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  107 LYS
Chi-restraints excluded: chain D residue  173 TYR
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 19 optimal weight:    0.6980
   chunk 134 optimal weight:    0.9990
   chunk 11 optimal weight:    0.4980
   chunk 97 optimal weight:    6.9990
   chunk 81 optimal weight:    0.7980
   chunk 4 optimal weight:    8.9990
   chunk 56 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 102 optimal weight:    7.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3693 r_free = 0.3693 target = 0.152406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.114971 restraints weight = 9460.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 1.15
r_work: 0.3133 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3015 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  10672  Z= 0.114
  Angle     :  0.505   7.952  14464  Z= 0.260
  Chirality :  0.040   0.147   1644
  Planarity :  0.003   0.026   1880
  Dihedral  :  5.405  55.164   1484
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  7.91 %
    Favored  : 91.10 %
  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:  2.70 (0.19), residues: 736
  sheet: -1.24 (0.30), residues: 248
  loop :  0.54 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  59 
 TYR   0.022   0.002   TYR D 213 
 PHE   0.015   0.002   PHE D 144 
 TRP   0.009   0.001   TRP D 147 
 HIS   0.002   0.001   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 (10672)
  covalent geometry    : angle       0.50508 (14464)
  hydrogen bonds       : bond        0.05120 (  571)
  hydrogen bonds       : angle       4.27539 ( 1656)

********************** 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
  101 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.483 
Fit side-chains
REVERT: A   52 GLU cc_start: 0.7696 (tt0) cc_final: 0.7353 (tt0)
REVERT: A   86 LYS cc_start: 0.8359 (mtpp) cc_final: 0.8079 (mttp)
REVERT: A  107 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8427 (tmmm)
REVERT: A  199 LYS cc_start: 0.8285 (mmtp) cc_final: 0.7513 (mptp)
REVERT: A  330 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.6256 (mmm160)
REVERT: B   52 GLU cc_start: 0.7686 (tt0) cc_final: 0.7353 (tt0)
REVERT: B   86 LYS cc_start: 0.8407 (mtpp) cc_final: 0.8158 (mttp)
REVERT: B  107 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8405 (tmmm)
REVERT: B  173 TYR cc_start: 0.9146 (OUTLIER) cc_final: 0.8759 (t80)
REVERT: B  199 LYS cc_start: 0.8263 (ttpt) cc_final: 0.7713 (mptp)
REVERT: B  242 LYS cc_start: 0.7586 (mmtt) cc_final: 0.7374 (mmtt)
REVERT: B  246 GLU cc_start: 0.8130 (mp0) cc_final: 0.7922 (mp0)
REVERT: B  330 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.6313 (mmm160)
REVERT: C   86 LYS cc_start: 0.8379 (mtpp) cc_final: 0.8121 (mttp)
REVERT: C  199 LYS cc_start: 0.8277 (ttpt) cc_final: 0.7690 (mptp)
REVERT: C  242 LYS cc_start: 0.7601 (mmtt) cc_final: 0.7392 (mmtt)
REVERT: D   52 GLU cc_start: 0.7663 (tt0) cc_final: 0.7326 (tt0)
REVERT: D  107 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8346 (tmmm)
REVERT: D  139 LYS cc_start: 0.8434 (mttp) cc_final: 0.7806 (mtmt)
REVERT: D  173 TYR cc_start: 0.9147 (OUTLIER) cc_final: 0.8761 (t80)
REVERT: D  199 LYS cc_start: 0.8299 (ttpt) cc_final: 0.7678 (mptp)
  outliers start: 11
  outliers final: 4
  residues processed: 101
  average time/residue: 0.9475
  time to fit residues: 101.3516
Evaluate side-chains
  100 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  330 ARG
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain B residue  173 TYR
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  107 LYS
Chi-restraints excluded: chain D residue  173 TYR
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 90 optimal weight:    0.6980
   chunk 116 optimal weight:    5.9990
   chunk 92 optimal weight:    4.9990
   chunk 117 optimal weight:    2.9990
   chunk 112 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 132 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 123 optimal weight:    0.5980
   overall best weight:    1.4584

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.149792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.111716 restraints weight = 9378.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 1.15
r_work: 0.3087 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.2968 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.1779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  10672  Z= 0.148
  Angle     :  0.567   8.410  14464  Z= 0.296
  Chirality :  0.043   0.152   1644
  Planarity :  0.004   0.026   1880
  Dihedral  :  5.637  54.788   1484
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  8.00 %
    Favored  : 91.01 %
  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:  1.87 (0.23), residues: 1364
  helix:  2.70 (0.19), residues: 712
  sheet: -1.34 (0.30), residues: 248
  loop :  0.40 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 148 
 TYR   0.028   0.002   TYR C 213 
 PHE   0.017   0.002   PHE A 144 
 TRP   0.011   0.002   TRP B 147 
 HIS   0.004   0.001   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (10672)
  covalent geometry    : angle       0.56669 (14464)
  hydrogen bonds       : bond        0.06164 (  571)
  hydrogen bonds       : angle       4.51565 ( 1656)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4785.28 seconds
wall clock time: 82 minutes 32.43 seconds (4952.43 seconds total)