Starting phenix.real_space_refine
on Thu Feb  5 00:53:05 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m6i_63663/02_2026/9m6i_63663.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m6i_63663/02_2026/9m6i_63663.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9m6i_63663/02_2026/9m6i_63663.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m6i_63663/02_2026/9m6i_63663.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9m6i_63663/02_2026/9m6i_63663.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m6i_63663/02_2026/9m6i_63663.cif"
  }
  resolution = 3.06
  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=   0.011
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      20      5.16       5
     C    8540      2.51       5
     N    2345      2.21       5
     O    2995      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13900
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2780
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 375, 2780
          Classifications: {'peptide': 375}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 370}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
    Chain: "B"
      Number of atoms: 2780
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 375, 2780
          Classifications: {'peptide': 375}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 370}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
    Chain: "C"
      Number of atoms: 2780
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 375, 2780
          Classifications: {'peptide': 375}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 370}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
    Chain: "D"
      Number of atoms: 2780
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 375, 2780
          Classifications: {'peptide': 375}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 370}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
    Chain: "E"
      Number of atoms: 2780
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 375, 2780
          Classifications: {'peptide': 375}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 370}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
  Time building chain proxies: 3.49, per 1000 atoms: 0.25
  Number of scatterers: 13900
  At special positions: 0
  Unit cell: (132.678, 133.245, 103.194, 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      20     16.00
     O    2995      8.00
     N    2345      7.00
     C    8540      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: 1.24
  Conformation dependent library (CDL) restraints added in 536.8 milliseconds
  

  3730 Ramachandran restraints generated.
    1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3510

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 30 sheets defined
      39.8% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 66
      removed outlier: 4.171A  pdb=" N   LYS A  66 " --> pdb=" O   THR A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 70
    Processing helix  chain 'A' and resid 152 through 164
      removed outlier: 3.843A  pdb=" N   ASP A 164 " --> pdb=" O   ILE A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 192
      removed outlier: 3.816A  pdb=" N   THR A 192 " --> pdb=" O   THR A 189 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 189 through 192'
    Processing helix  chain 'A' and resid 201 through 208
      removed outlier: 3.632A  pdb=" N   ALA A 208 " --> pdb=" O   ASN A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 294
    Processing helix  chain 'A' and resid 315 through 330
      removed outlier: 3.538A  pdb=" N   ALA A 330 " --> pdb=" O   ARG A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 345
    Processing helix  chain 'A' and resid 358 through 369
    Processing helix  chain 'A' and resid 369 through 378
      removed outlier: 3.628A  pdb=" N   ALA A 373 " --> pdb=" O   ASN A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 399
    Processing helix  chain 'A' and resid 402 through 413
    Processing helix  chain 'B' and resid 40 through 66
      removed outlier: 3.940A  pdb=" N   LYS B  66 " --> pdb=" O   THR B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 164
      removed outlier: 3.763A  pdb=" N   ASP B 164 " --> pdb=" O   ILE B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 192
      removed outlier: 3.803A  pdb=" N   THR B 192 " --> pdb=" O   THR B 189 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 189 through 192'
    Processing helix  chain 'B' and resid 201 through 208
      removed outlier: 3.587A  pdb=" N   ALA B 208 " --> pdb=" O   ASN B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 294
    Processing helix  chain 'B' and resid 315 through 330
    Processing helix  chain 'B' and resid 358 through 369
    Processing helix  chain 'B' and resid 369 through 378
      removed outlier: 3.545A  pdb=" N   ALA B 373 " --> pdb=" O   ASN B 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 399
    Processing helix  chain 'B' and resid 402 through 413
    Processing helix  chain 'C' and resid 40 through 66
      removed outlier: 4.188A  pdb=" N   LYS C  66 " --> pdb=" O   THR C  62 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 70
    Processing helix  chain 'C' and resid 152 through 164
      removed outlier: 3.875A  pdb=" N   ASP C 164 " --> pdb=" O   ILE C 160 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 189 through 192
      removed outlier: 3.862A  pdb=" N   THR C 192 " --> pdb=" O   THR C 189 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 189 through 192'
    Processing helix  chain 'C' and resid 201 through 208
      removed outlier: 3.592A  pdb=" N   ALA C 208 " --> pdb=" O   ASN C 204 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 269 through 294
    Processing helix  chain 'C' and resid 315 through 330
    Processing helix  chain 'C' and resid 340 through 345
    Processing helix  chain 'C' and resid 358 through 369
    Processing helix  chain 'C' and resid 369 through 378
      removed outlier: 3.547A  pdb=" N   ALA C 373 " --> pdb=" O   ASN C 369 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 385 through 399
    Processing helix  chain 'C' and resid 402 through 413
    Processing helix  chain 'D' and resid 40 through 66
      removed outlier: 4.190A  pdb=" N   LYS D  66 " --> pdb=" O   THR D  62 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 70
    Processing helix  chain 'D' and resid 152 through 164
      removed outlier: 3.886A  pdb=" N   ASP D 164 " --> pdb=" O   ILE D 160 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 189 through 192
      removed outlier: 3.849A  pdb=" N   THR D 192 " --> pdb=" O   THR D 189 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 189 through 192'
    Processing helix  chain 'D' and resid 201 through 208
      removed outlier: 3.555A  pdb=" N   ALA D 208 " --> pdb=" O   ASN D 204 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 269 through 294
    Processing helix  chain 'D' and resid 315 through 330
      removed outlier: 4.070A  pdb=" N   ALA D 330 " --> pdb=" O   ARG D 326 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 340 through 345
      removed outlier: 3.537A  pdb=" N   ILE D 344 " --> pdb=" O   THR D 340 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 358 through 369
    Processing helix  chain 'D' and resid 369 through 378
      removed outlier: 3.834A  pdb=" N   ALA D 373 " --> pdb=" O   ASN D 369 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 385 through 399
    Processing helix  chain 'D' and resid 402 through 413
    Processing helix  chain 'E' and resid 40 through 66
      removed outlier: 3.937A  pdb=" N   LYS E  66 " --> pdb=" O   THR E  62 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 152 through 164
      removed outlier: 3.867A  pdb=" N   ASP E 164 " --> pdb=" O   ILE E 160 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 189 through 192
      removed outlier: 3.888A  pdb=" N   THR E 192 " --> pdb=" O   THR E 189 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 189 through 192'
    Processing helix  chain 'E' and resid 201 through 208
      removed outlier: 3.592A  pdb=" N   ALA E 208 " --> pdb=" O   ASN E 204 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 269 through 294
    Processing helix  chain 'E' and resid 315 through 330
    Processing helix  chain 'E' and resid 358 through 369
    Processing helix  chain 'E' and resid 369 through 378
      removed outlier: 3.504A  pdb=" N   ALA E 373 " --> pdb=" O   ASN E 369 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 385 through 399
    Processing helix  chain 'E' and resid 402 through 413
    Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 77
      removed outlier: 6.183A  pdb=" N   LYS A 228 " --> pdb=" O   THR A 100 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 86
    Processing sheet with id=AA3, first strand: chain 'A' and resid 168 through 172
      removed outlier: 5.021A  pdb=" N   GLN A 106 " --> pdb=" O   ALA A 185 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   SER A 107 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 146
    Processing sheet with id=AA5, first strand: chain 'A' and resid 209 through 210
    Processing sheet with id=AA6, first strand: chain 'A' and resid 346 through 348
    Processing sheet with id=AA7, first strand: chain 'B' and resid 73 through 77
      removed outlier: 6.180A  pdb=" N   LYS B 228 " --> pdb=" O   THR B 100 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 82 through 86
    Processing sheet with id=AA9, first strand: chain 'B' and resid 168 through 172
      removed outlier: 6.122A  pdb=" N   LEU B 181 " --> pdb=" O   THR B 110 " (cutoff:3.500A)
      removed outlier: 4.994A  pdb=" N   GLN B 106 " --> pdb=" O   ALA B 185 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   SER B 107 " --> pdb=" O   LEU B 221 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 142 through 146
    Processing sheet with id=AB2, first strand: chain 'B' and resid 209 through 210
    Processing sheet with id=AB3, first strand: chain 'B' and resid 346 through 348
    Processing sheet with id=AB4, first strand: chain 'C' and resid 73 through 77
      removed outlier: 6.173A  pdb=" N   LYS C 228 " --> pdb=" O   THR C 100 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 82 through 86
    Processing sheet with id=AB6, first strand: chain 'C' and resid 168 through 172
      removed outlier: 5.028A  pdb=" N   GLN C 106 " --> pdb=" O   ALA C 185 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   SER C 107 " --> pdb=" O   LEU C 221 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 142 through 146
    Processing sheet with id=AB8, first strand: chain 'C' and resid 209 through 210
    Processing sheet with id=AB9, first strand: chain 'C' and resid 346 through 348
    Processing sheet with id=AC1, first strand: chain 'D' and resid 73 through 77
      removed outlier: 6.183A  pdb=" N   LYS D 228 " --> pdb=" O   THR D 100 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 82 through 86
    Processing sheet with id=AC3, first strand: chain 'D' and resid 168 through 172
      removed outlier: 6.145A  pdb=" N   LEU D 181 " --> pdb=" O   THR D 110 " (cutoff:3.500A)
      removed outlier: 5.019A  pdb=" N   GLN D 106 " --> pdb=" O   ALA D 185 " (cutoff:3.500A)
      removed outlier: 6.202A  pdb=" N   SER D 107 " --> pdb=" O   LEU D 221 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'D' and resid 142 through 146
    Processing sheet with id=AC5, first strand: chain 'D' and resid 209 through 210
    Processing sheet with id=AC6, first strand: chain 'D' and resid 346 through 348
    Processing sheet with id=AC7, first strand: chain 'E' and resid 73 through 77
      removed outlier: 6.156A  pdb=" N   LYS E 228 " --> pdb=" O   THR E 100 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'E' and resid 82 through 86
    Processing sheet with id=AC9, first strand: chain 'E' and resid 168 through 172
      removed outlier: 5.017A  pdb=" N   GLN E 106 " --> pdb=" O   ALA E 185 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   SER E 107 " --> pdb=" O   LEU E 221 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'E' and resid 142 through 146
    Processing sheet with id=AD2, first strand: chain 'E' and resid 209 through 210
    Processing sheet with id=AD3, first strand: chain 'E' and resid 347 through 348

    769 hydrogen bonds defined for protein.
    2136 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.30

  Time building geometry restraints manager: 1.55 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4724
        1.34 -     1.46: 1482
        1.46 -     1.57: 7744
        1.57 -     1.69: 0
        1.69 -     1.81: 40
  Bond restraints: 13990
  Sorted by residual:
  bond pdb=" N   ALA E 246 "
       pdb=" CA  ALA E 246 "
    ideal  model  delta    sigma   weight residual
    1.463  1.456  0.007 6.90e-03 2.10e+04 1.17e+00
  bond pdb=" C   ALA E 246 "
       pdb=" N   PRO E 247 "
    ideal  model  delta    sigma   weight residual
    1.334  1.359 -0.025 2.34e-02 1.83e+03 1.13e+00
  bond pdb=" C   ALA A 246 "
       pdb=" N   PRO A 247 "
    ideal  model  delta    sigma   weight residual
    1.334  1.359 -0.025 2.34e-02 1.83e+03 1.11e+00
  bond pdb=" C   ALA D 246 "
       pdb=" N   PRO D 247 "
    ideal  model  delta    sigma   weight residual
    1.334  1.358 -0.025 2.34e-02 1.83e+03 1.10e+00
  bond pdb=" C   ALA C 246 "
       pdb=" N   PRO C 247 "
    ideal  model  delta    sigma   weight residual
    1.334  1.358 -0.024 2.34e-02 1.83e+03 1.09e+00
  ... (remaining 13985 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 18639
        1.61 -     3.22: 264
        3.22 -     4.84: 26
        4.84 -     6.45: 15
        6.45 -     8.06: 1
  Bond angle restraints: 18945
  Sorted by residual:
  angle pdb=" N   ALA B 246 "
        pdb=" CA  ALA B 246 "
        pdb=" C   ALA B 246 "
      ideal   model   delta    sigma   weight residual
     112.17  107.14    5.03 1.36e+00 5.41e-01 1.37e+01
  angle pdb=" N   ALA A 246 "
        pdb=" CA  ALA A 246 "
        pdb=" C   ALA A 246 "
      ideal   model   delta    sigma   weight residual
     112.17  107.20    4.97 1.36e+00 5.41e-01 1.34e+01
  angle pdb=" N   ALA C 246 "
        pdb=" CA  ALA C 246 "
        pdb=" C   ALA C 246 "
      ideal   model   delta    sigma   weight residual
     112.17  107.21    4.96 1.36e+00 5.41e-01 1.33e+01
  angle pdb=" N   ALA D 246 "
        pdb=" CA  ALA D 246 "
        pdb=" C   ALA D 246 "
      ideal   model   delta    sigma   weight residual
     112.17  107.21    4.96 1.36e+00 5.41e-01 1.33e+01
  angle pdb=" N   ALA E 246 "
        pdb=" CA  ALA E 246 "
        pdb=" C   ALA E 246 "
      ideal   model   delta    sigma   weight residual
     112.17  107.22    4.95 1.36e+00 5.41e-01 1.32e+01
  ... (remaining 18940 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.42: 7920
       17.42 -    34.83: 636
       34.83 -    52.25: 62
       52.25 -    69.66: 6
       69.66 -    87.08: 16
  Dihedral angle restraints: 8640
    sinusoidal: 3230
      harmonic: 5410
  Sorted by residual:
  dihedral pdb=" CA  ALA B 246 "
           pdb=" C   ALA B 246 "
           pdb=" N   PRO B 247 "
           pdb=" CA  PRO B 247 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.59   34.41     0      5.00e+00 4.00e-02 4.74e+01
  dihedral pdb=" CA  ALA C 246 "
           pdb=" C   ALA C 246 "
           pdb=" N   PRO C 247 "
           pdb=" CA  PRO C 247 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.11   33.89     0      5.00e+00 4.00e-02 4.59e+01
  dihedral pdb=" CA  ALA E 246 "
           pdb=" C   ALA E 246 "
           pdb=" N   PRO E 247 "
           pdb=" CA  PRO E 247 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.11   33.89     0      5.00e+00 4.00e-02 4.59e+01
  ... (remaining 8637 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1574
       0.029 -    0.057: 518
       0.057 -    0.086: 172
       0.086 -    0.114: 92
       0.114 -    0.143: 34
  Chirality restraints: 2390
  Sorted by residual:
  chirality pdb=" CA  ILE D 131 "
            pdb=" N   ILE D 131 "
            pdb=" C   ILE D 131 "
            pdb=" CB  ILE D 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.11e-01
  chirality pdb=" CA  ILE A 131 "
            pdb=" N   ILE A 131 "
            pdb=" C   ILE A 131 "
            pdb=" CB  ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.04e-01
  chirality pdb=" CA  ILE E 131 "
            pdb=" N   ILE E 131 "
            pdb=" C   ILE E 131 "
            pdb=" CB  ILE E 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.03e-01
  ... (remaining 2387 not shown)

  Planarity restraints: 2435
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 329 "    0.014 2.00e-02 2.50e+03   1.25e-02 2.75e+00
        pdb=" CG  PHE B 329 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 329 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 329 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 329 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 329 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 329 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 246 "    0.021 5.00e-02 4.00e+02   3.18e-02 1.62e+00
        pdb=" N   PRO B 247 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO B 247 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 247 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA E 246 "    0.020 5.00e-02 4.00e+02   3.03e-02 1.47e+00
        pdb=" N   PRO E 247 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO E 247 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO E 247 "    0.017 5.00e-02 4.00e+02
  ... (remaining 2432 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 322
        2.70 -     3.25: 13672
        3.25 -     3.80: 21347
        3.80 -     4.35: 27818
        4.35 -     4.90: 46943
  Nonbonded interactions: 110102
  Sorted by model distance:
  nonbonded pdb=" O   CYS C  91 "
            pdb=" OH  TYR C  95 "
     model   vdw
     2.149 3.040
  nonbonded pdb=" O   CYS E  91 "
            pdb=" OH  TYR E  95 "
     model   vdw
     2.161 3.040
  nonbonded pdb=" O   CYS D  91 "
            pdb=" OH  TYR D  95 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" O   CYS B  91 "
            pdb=" OH  TYR B  95 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" O   CYS A  91 "
            pdb=" OH  TYR A  95 "
     model   vdw
     2.166 3.040
  ... (remaining 110097 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             9.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     13.780
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5834
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      :  0.002   0.025  13990  Z= 0.117
  Angle     :  0.517   8.062  18945  Z= 0.295
  Chirality :  0.039   0.143   2390
  Planarity :  0.003   0.033   2435
  Dihedral  : 12.926  87.080   5130
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 25.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.89 (0.20), residues: 1865
  helix:  2.93 (0.20), residues: 660
  sheet:  0.80 (0.22), residues: 540
  loop : -0.05 (0.26), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 129 
 TYR   0.006   0.001   TYR B 209 
 PHE   0.029   0.001   PHE B 329 
 TRP   0.007   0.001   TRP E 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 (13990)
  covalent geometry    : angle       0.51706 (18945)
  hydrogen bonds       : bond        0.11737 (  769)
  hydrogen bonds       : angle       5.32925 ( 2136)

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

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

  3730 Ramachandran restraints generated.
    1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3730 Ramachandran restraints generated.
    1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  341 MET cc_start: 0.3371 (ppp) cc_final: 0.3009 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1067
  time to fit residues: 23.2727
Evaluate side-chains
  108 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    0.6980
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    0.0040
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    4.9990
   chunk 149 optimal weight:   20.0000
   overall best weight:    0.6592

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

Flipped N/Q/H residues before XYZ refinement:
A 214 ASN
B 214 ASN
C  61 ASN
D 214 ASN
E  61 ASN
E 348 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4960 r_free = 0.4960 target = 0.270795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4572 r_free = 0.4572 target = 0.223715 restraints weight = 16610.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.4553 rms_B_bonded: 3.11
r_work: 0.3948 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6868
moved from start:          0.1018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  13990  Z= 0.105
  Angle     :  0.456   6.003  18945  Z= 0.249
  Chirality :  0.039   0.138   2390
  Planarity :  0.003   0.070   2435
  Dihedral  :  4.411  37.673   1935
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  4.71 %
    Favored  : 94.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 25.00 %
    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 (0.20), residues: 1865
  helix:  2.78 (0.20), residues: 675
  sheet:  1.27 (0.23), residues: 535
  loop : -0.05 (0.26), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 374 
 TYR   0.006   0.001   TYR E 397 
 PHE   0.013   0.001   PHE E 329 
 TRP   0.006   0.001   TRP B 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 (13990)
  covalent geometry    : angle       0.45605 (18945)
  hydrogen bonds       : bond        0.03098 (  769)
  hydrogen bonds       : angle       4.50864 ( 2136)

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

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

  3730 Ramachandran restraints generated.
    1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3730 Ramachandran restraints generated.
    1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 119
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   56 LYS cc_start: 0.6748 (mttt) cc_final: 0.6446 (tmtt)
REVERT: D   69 LEU cc_start: 0.7474 (pp) cc_final: 0.7223 (pp)
REVERT: E   56 LYS cc_start: 0.6643 (mttt) cc_final: 0.6215 (tmtt)
REVERT: E   69 LEU cc_start: 0.7637 (pp) cc_final: 0.7426 (pp)
  outliers start: 9
  outliers final: 8
  residues processed: 124
  average time/residue: 0.0947
  time to fit residues: 19.0224
Evaluate side-chains
  119 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain E residue   73 THR
Chi-restraints excluded: chain E residue  121 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 110 optimal weight:   20.0000
   chunk 17 optimal weight:    1.9990
   chunk 158 optimal weight:    0.7980
   chunk 84 optimal weight:    0.5980
   chunk 136 optimal weight:    9.9990
   chunk 121 optimal weight:    0.8980
   chunk 144 optimal weight:    1.9990
   chunk 164 optimal weight:    0.5980
   chunk 87 optimal weight:    2.9990
   chunk 132 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
D 214 ASN
D 322 GLN
D 348 GLN
E 214 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4957 r_free = 0.4957 target = 0.270454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.221081 restraints weight = 16723.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.4511 rms_B_bonded: 2.07
r_work: 0.4077 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3903 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6948
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  13990  Z= 0.104
  Angle     :  0.429   5.409  18945  Z= 0.236
  Chirality :  0.039   0.137   2390
  Planarity :  0.003   0.067   2435
  Dihedral  :  4.290  37.723   1935
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  6.08 %
    Favored  : 93.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 25.00 %
    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:  2.15 (0.20), residues: 1865
  helix:  2.87 (0.20), residues: 675
  sheet:  1.31 (0.23), residues: 535
  loop : -0.02 (0.26), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 326 
 TYR   0.005   0.001   TYR E 397 
 PHE   0.027   0.001   PHE B 329 
 TRP   0.006   0.001   TRP C 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (13990)
  covalent geometry    : angle       0.42894 (18945)
  hydrogen bonds       : bond        0.02749 (  769)
  hydrogen bonds       : angle       4.31222 ( 2136)

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

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

  3730 Ramachandran restraints generated.
    1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3730 Ramachandran restraints generated.
    1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  341 MET cc_start: 0.7899 (mpp) cc_final: 0.6575 (ptp)
REVERT: B   64 LEU cc_start: 0.5084 (OUTLIER) cc_final: 0.4701 (tp)
REVERT: D  389 LYS cc_start: 0.8135 (pptt) cc_final: 0.7745 (ttpt)
REVERT: E   56 LYS cc_start: 0.6553 (mttt) cc_final: 0.6146 (tmtt)
REVERT: E   69 LEU cc_start: 0.7656 (pp) cc_final: 0.7448 (pp)
REVERT: E  329 PHE cc_start: 0.6654 (m-10) cc_final: 0.6443 (m-10)
REVERT: E  341 MET cc_start: 0.5131 (OUTLIER) cc_final: 0.4372 (ppp)
  outliers start: 12
  outliers final: 9
  residues processed: 123
  average time/residue: 0.0932
  time to fit residues: 18.7656
Evaluate side-chains
  116 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain E residue   73 THR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  121 LEU
Chi-restraints excluded: chain E residue  341 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 120 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 107 optimal weight:   10.0000
   chunk 104 optimal weight:    0.4980
   chunk 179 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 136 optimal weight:   20.0000
   chunk 118 optimal weight:    6.9990
   chunk 128 optimal weight:    4.9990
   chunk 158 optimal weight:    0.0040
   chunk 26 optimal weight:   40.0000
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
B 214 ASN
D 214 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4976 r_free = 0.4976 target = 0.274122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4581 r_free = 0.4581 target = 0.225369 restraints weight = 16659.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.4522 rms_B_bonded: 2.00
r_work: 0.4098 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3915 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6913
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  13990  Z= 0.090
  Angle     :  0.409   5.618  18945  Z= 0.224
  Chirality :  0.038   0.134   2390
  Planarity :  0.003   0.063   2435
  Dihedral  :  4.086  37.088   1935
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  7.65 %
    Favored  : 91.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 25.00 %
    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:  2.35 (0.20), residues: 1865
  helix:  3.03 (0.20), residues: 675
  sheet:  1.50 (0.23), residues: 535
  loop :  0.01 (0.26), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 326 
 TYR   0.004   0.001   TYR A 283 
 PHE   0.012   0.001   PHE B 329 
 TRP   0.010   0.001   TRP A 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00194 (13990)
  covalent geometry    : angle       0.40855 (18945)
  hydrogen bonds       : bond        0.02466 (  769)
  hydrogen bonds       : angle       4.11413 ( 2136)

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

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

  3730 Ramachandran restraints generated.
    1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3730 Ramachandran restraints generated.
    1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
REVERT: D   56 LYS cc_start: 0.6592 (mttt) cc_final: 0.6346 (tmtt)
REVERT: D   69 LEU cc_start: 0.7463 (pp) cc_final: 0.7147 (pp)
REVERT: D  329 PHE cc_start: 0.6361 (m-80) cc_final: 0.6121 (m-80)
REVERT: D  389 LYS cc_start: 0.8114 (pptt) cc_final: 0.7900 (ttpt)
REVERT: E   56 LYS cc_start: 0.6565 (mttt) cc_final: 0.6156 (tmtt)
REVERT: E   69 LEU cc_start: 0.7617 (pp) cc_final: 0.7383 (pp)
REVERT: E  341 MET cc_start: 0.5164 (ppp) cc_final: 0.4962 (ptm)
  outliers start: 9
  outliers final: 6
  residues processed: 118
  average time/residue: 0.0967
  time to fit residues: 18.3303
Evaluate side-chains
  115 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 109
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain C residue   64 LEU
Chi-restraints excluded: chain E residue  121 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 154 optimal weight:    1.9990
   chunk 83 optimal weight:    6.9990
   chunk 81 optimal weight:    5.9990
   chunk 164 optimal weight:    0.8980
   chunk 182 optimal weight:    9.9990
   chunk 89 optimal weight:    0.8980
   chunk 151 optimal weight:    0.6980
   chunk 176 optimal weight:    9.9990
   chunk 71 optimal weight:    0.5980
   chunk 119 optimal weight:    5.9990
   chunk 26 optimal weight:   50.0000
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
B 214 ASN
D 214 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4961 r_free = 0.4961 target = 0.272137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.222049 restraints weight = 16562.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.4495 rms_B_bonded: 1.99
r_work: 0.4074 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3888 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6967
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13990  Z= 0.118
  Angle     :  0.442   6.616  18945  Z= 0.240
  Chirality :  0.040   0.140   2390
  Planarity :  0.003   0.068   2435
  Dihedral  :  4.227  37.659   1935
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  8.24 %
    Favored  : 90.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 25.00 %
    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:  2.28 (0.20), residues: 1865
  helix:  3.08 (0.20), residues: 675
  sheet:  1.39 (0.23), residues: 535
  loop : -0.08 (0.25), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 138 
 TYR   0.004   0.001   TYR C  95 
 PHE   0.035   0.001   PHE B 329 
 TRP   0.003   0.000   TRP E 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (13990)
  covalent geometry    : angle       0.44217 (18945)
  hydrogen bonds       : bond        0.02612 (  769)
  hydrogen bonds       : angle       4.17432 ( 2136)

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

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

  3730 Ramachandran restraints generated.
    1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3730 Ramachandran restraints generated.
    1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.555 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LEU cc_start: 0.5445 (mp) cc_final: 0.4576 (mp)
REVERT: A  341 MET cc_start: 0.7597 (mpp) cc_final: 0.6231 (ptp)
REVERT: C  121 LEU cc_start: 0.5444 (mp) cc_final: 0.4570 (mp)
REVERT: D   56 LYS cc_start: 0.6608 (mttt) cc_final: 0.6365 (tmtt)
REVERT: E   56 LYS cc_start: 0.6585 (mttt) cc_final: 0.6193 (tmtt)
REVERT: E   69 LEU cc_start: 0.7572 (pp) cc_final: 0.7337 (pp)
REVERT: E  341 MET cc_start: 0.5100 (OUTLIER) cc_final: 0.4878 (ptm)
  outliers start: 16
  outliers final: 12
  residues processed: 116
  average time/residue: 0.0938
  time to fit residues: 17.7114
Evaluate side-chains
  117 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain C residue   64 LEU
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain E residue   73 THR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  121 LEU
Chi-restraints excluded: chain E residue  250 ILE
Chi-restraints excluded: chain E residue  341 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 142 optimal weight:    7.9990
   chunk 55 optimal weight:    0.9990
   chunk 38 optimal weight:   20.0000
   chunk 107 optimal weight:    9.9990
   chunk 168 optimal weight:    0.0570
   chunk 74 optimal weight:   40.0000
   chunk 140 optimal weight:    1.9990
   chunk 166 optimal weight:    0.6980
   chunk 115 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 148 optimal weight:   40.0000
   overall best weight:    0.7100

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

Flipped N/Q/H residues before XYZ refinement:
B 214 ASN
D 214 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4962 r_free = 0.4962 target = 0.270986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.226064 restraints weight = 16594.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.4561 rms_B_bonded: 3.20
r_work: 0.3929 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.3929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6876
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  13990  Z= 0.098
  Angle     :  0.422   7.418  18945  Z= 0.229
  Chirality :  0.039   0.141   2390
  Planarity :  0.003   0.068   2435
  Dihedral  :  4.106  37.199   1935
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  9.41 %
    Favored  : 89.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 25.00 %
    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:  2.39 (0.20), residues: 1865
  helix:  3.12 (0.20), residues: 675
  sheet:  1.51 (0.23), residues: 535
  loop : -0.03 (0.25), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 138 
 TYR   0.004   0.001   TYR B 209 
 PHE   0.020   0.001   PHE E 329 
 TRP   0.005   0.001   TRP A 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 (13990)
  covalent geometry    : angle       0.42242 (18945)
  hydrogen bonds       : bond        0.02444 (  769)
  hydrogen bonds       : angle       4.11306 ( 2136)

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

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

  3730 Ramachandran restraints generated.
    1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3730 Ramachandran restraints generated.
    1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.554 
Fit side-chains
REVERT: A  121 LEU cc_start: 0.5412 (mp) cc_final: 0.4545 (mp)
REVERT: B  376 LEU cc_start: 0.8252 (tp) cc_final: 0.7928 (mt)
REVERT: C  121 LEU cc_start: 0.5359 (mp) cc_final: 0.4483 (mp)
REVERT: D   56 LYS cc_start: 0.6786 (mttt) cc_final: 0.6483 (tmtt)
REVERT: D   69 LEU cc_start: 0.7345 (pp) cc_final: 0.7032 (pp)
REVERT: D  389 LYS cc_start: 0.8172 (pttp) cc_final: 0.7557 (mtpt)
REVERT: E   56 LYS cc_start: 0.6730 (mttt) cc_final: 0.6302 (tmtt)
REVERT: E   69 LEU cc_start: 0.7559 (pp) cc_final: 0.7297 (pp)
  outliers start: 15
  outliers final: 11
  residues processed: 117
  average time/residue: 0.0998
  time to fit residues: 18.9379
Evaluate side-chains
  116 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain C residue   64 LEU
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain E residue   73 THR
Chi-restraints excluded: chain E residue  121 LEU
Chi-restraints excluded: chain E residue  250 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 128 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 96 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 149 optimal weight:   20.0000
   chunk 160 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 39 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A  61 ASN
B 214 ASN
C  61 ASN
** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4962 r_free = 0.4962 target = 0.272291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.221229 restraints weight = 16611.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.4482 rms_B_bonded: 2.04
r_work: 0.4061 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3888 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6967
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13990  Z= 0.116
  Angle     :  0.454   8.071  18945  Z= 0.241
  Chirality :  0.040   0.141   2390
  Planarity :  0.003   0.066   2435
  Dihedral  :  4.181  37.361   1935
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 10.07 %
    Favored  : 89.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 25.00 %
    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:  2.33 (0.20), residues: 1865
  helix:  3.15 (0.20), residues: 675
  sheet:  1.40 (0.22), residues: 535
  loop : -0.09 (0.25), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 138 
 TYR   0.005   0.001   TYR C  95 
 PHE   0.040   0.001   PHE B 329 
 TRP   0.009   0.001   TRP E 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (13990)
  covalent geometry    : angle       0.45437 (18945)
  hydrogen bonds       : bond        0.02550 (  769)
  hydrogen bonds       : angle       4.16397 ( 2136)

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

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

  3730 Ramachandran restraints generated.
    1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3730 Ramachandran restraints generated.
    1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.571 
Fit side-chains
REVERT: A  121 LEU cc_start: 0.5420 (mp) cc_final: 0.4515 (mp)
REVERT: B  376 LEU cc_start: 0.8258 (tp) cc_final: 0.7962 (mt)
REVERT: C  121 LEU cc_start: 0.5356 (mp) cc_final: 0.4458 (mp)
REVERT: D   56 LYS cc_start: 0.6571 (mttt) cc_final: 0.6342 (tmtt)
REVERT: D  341 MET cc_start: 0.7333 (mpp) cc_final: 0.6517 (pmm)
REVERT: D  389 LYS cc_start: 0.8243 (pttp) cc_final: 0.7622 (mtpt)
REVERT: E   56 LYS cc_start: 0.6594 (mttt) cc_final: 0.6208 (tmtt)
  outliers start: 14
  outliers final: 11
  residues processed: 110
  average time/residue: 0.0947
  time to fit residues: 16.9376
Evaluate side-chains
  111 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain C residue   64 LEU
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain E residue   73 THR
Chi-restraints excluded: chain E residue  121 LEU
Chi-restraints excluded: chain E residue  250 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 165 optimal weight:    5.9990
   chunk 74 optimal weight:   30.0000
   chunk 70 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 183 optimal weight:   30.0000
   chunk 23 optimal weight:    0.7980
   chunk 39 optimal weight:    5.9990
   chunk 103 optimal weight:   10.0000
   chunk 163 optimal weight:    0.0470
   chunk 34 optimal weight:    0.0470
   overall best weight:    0.9780

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

Flipped N/Q/H residues before XYZ refinement:
B 214 ASN
** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4964 r_free = 0.4964 target = 0.272507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.221138 restraints weight = 16624.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.4482 rms_B_bonded: 1.71
r_work: 0.4115 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3968 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6865
moved from start:          0.2257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13990  Z= 0.114
  Angle     :  0.449   8.184  18945  Z= 0.239
  Chirality :  0.040   0.142   2390
  Planarity :  0.003   0.066   2435
  Dihedral  :  4.183  37.268   1935
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 10.07 %
    Favored  : 88.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 25.00 %
    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:  2.30 (0.20), residues: 1865
  helix:  3.15 (0.20), residues: 675
  sheet:  1.38 (0.22), residues: 535
  loop : -0.10 (0.25), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 138 
 TYR   0.004   0.001   TYR C  95 
 PHE   0.023   0.001   PHE B 329 
 TRP   0.004   0.000   TRP E 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (13990)
  covalent geometry    : angle       0.44920 (18945)
  hydrogen bonds       : bond        0.02513 (  769)
  hydrogen bonds       : angle       4.15344 ( 2136)

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

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

  3730 Ramachandran restraints generated.
    1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3730 Ramachandran restraints generated.
    1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 LEU cc_start: 0.5350 (mp) cc_final: 0.4452 (mp)
REVERT: A  341 MET cc_start: 0.7245 (mpp) cc_final: 0.6073 (ppp)
REVERT: C  121 LEU cc_start: 0.5296 (mp) cc_final: 0.4391 (mp)
REVERT: D   56 LYS cc_start: 0.6775 (mttt) cc_final: 0.6476 (tmtt)
REVERT: D  329 PHE cc_start: 0.5825 (m-80) cc_final: 0.5621 (m-80)
REVERT: D  341 MET cc_start: 0.7062 (mpp) cc_final: 0.6272 (pmm)
REVERT: D  389 LYS cc_start: 0.8052 (pttp) cc_final: 0.7331 (mtpt)
REVERT: E   56 LYS cc_start: 0.6792 (mttt) cc_final: 0.6366 (tmtt)
  outliers start: 16
  outliers final: 16
  residues processed: 112
  average time/residue: 0.0896
  time to fit residues: 16.6812
Evaluate side-chains
  117 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue   64 LEU
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain D residue   64 LEU
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain E residue   73 THR
Chi-restraints excluded: chain E residue  121 LEU
Chi-restraints excluded: chain E residue  250 ILE
Chi-restraints excluded: chain E residue  341 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 140 optimal weight:   30.0000
   chunk 50 optimal weight:    0.9990
   chunk 142 optimal weight:   10.0000
   chunk 130 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 69 optimal weight:    8.9990
   chunk 32 optimal weight:    3.9990
   chunk 183 optimal weight:    0.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
B 214 ASN
** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 328 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4933 r_free = 0.4933 target = 0.268669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.217703 restraints weight = 16473.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.4498 rms_B_bonded: 2.18
r_work: 0.4058 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3910 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6922
moved from start:          0.2342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13990  Z= 0.122
  Angle     :  0.459   8.690  18945  Z= 0.246
  Chirality :  0.040   0.143   2390
  Planarity :  0.003   0.065   2435
  Dihedral  :  4.230  37.412   1935
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 10.65 %
    Favored  : 88.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 25.00 %
    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:  2.26 (0.20), residues: 1865
  helix:  3.14 (0.20), residues: 675
  sheet:  1.27 (0.22), residues: 540
  loop : -0.11 (0.25), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 138 
 TYR   0.005   0.001   TYR C  95 
 PHE   0.013   0.001   PHE E 114 
 TRP   0.004   0.001   TRP C 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (13990)
  covalent geometry    : angle       0.45940 (18945)
  hydrogen bonds       : bond        0.02565 (  769)
  hydrogen bonds       : angle       4.21257 ( 2136)

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

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

  3730 Ramachandran restraints generated.
    1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3730 Ramachandran restraints generated.
    1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 LEU cc_start: 0.5444 (mp) cc_final: 0.4533 (mp)
REVERT: C  121 LEU cc_start: 0.5340 (mp) cc_final: 0.4416 (mp)
REVERT: C  376 LEU cc_start: 0.7721 (tt) cc_final: 0.7238 (mt)
REVERT: D   56 LYS cc_start: 0.6769 (mttt) cc_final: 0.6477 (tmtt)
REVERT: D  341 MET cc_start: 0.7086 (mpp) cc_final: 0.6290 (pmm)
REVERT: D  389 LYS cc_start: 0.8065 (pttp) cc_final: 0.7299 (mtpt)
REVERT: E   56 LYS cc_start: 0.6788 (mttt) cc_final: 0.6362 (tmtt)
  outliers start: 15
  outliers final: 15
  residues processed: 112
  average time/residue: 0.0897
  time to fit residues: 16.3485
Evaluate side-chains
  118 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue   64 LEU
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain D residue   64 LEU
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain E residue   73 THR
Chi-restraints excluded: chain E residue  121 LEU
Chi-restraints excluded: chain E residue  250 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 161 optimal weight:    3.9990
   chunk 160 optimal weight:    0.8980
   chunk 103 optimal weight:    0.2980
   chunk 129 optimal weight:    1.9990
   chunk 184 optimal weight:   30.0000
   chunk 28 optimal weight:    5.9990
   chunk 54 optimal weight:    7.9990
   chunk 97 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 138 optimal weight:    9.9990
   chunk 167 optimal weight:    1.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
B 214 ASN
C 214 ASN
** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4954 r_free = 0.4954 target = 0.271376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.219023 restraints weight = 16684.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.4467 rms_B_bonded: 1.76
r_work: 0.4100 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3966 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6878
moved from start:          0.2403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  13990  Z= 0.133
  Angle     :  0.474   8.561  18945  Z= 0.253
  Chirality :  0.040   0.146   2390
  Planarity :  0.003   0.065   2435
  Dihedral  :  4.303  37.425   1935
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 10.65 %
    Favored  : 88.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 25.00 %
    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:  2.17 (0.20), residues: 1865
  helix:  3.11 (0.20), residues: 675
  sheet:  1.20 (0.22), residues: 540
  loop : -0.17 (0.25), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 138 
 TYR   0.005   0.001   TYR C  95 
 PHE   0.013   0.001   PHE B 329 
 TRP   0.005   0.001   TRP C 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (13990)
  covalent geometry    : angle       0.47413 (18945)
  hydrogen bonds       : bond        0.02659 (  769)
  hydrogen bonds       : angle       4.26074 ( 2136)

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

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

  3730 Ramachandran restraints generated.
    1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3730 Ramachandran restraints generated.
    1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.474 
Fit side-chains
REVERT: A  121 LEU cc_start: 0.5372 (mp) cc_final: 0.4483 (mp)
REVERT: A  341 MET cc_start: 0.7199 (mpp) cc_final: 0.6091 (ppp)
REVERT: B  328 GLN cc_start: 0.6783 (mt0) cc_final: 0.5768 (tp40)
REVERT: C  121 LEU cc_start: 0.5263 (mp) cc_final: 0.4364 (mp)
REVERT: C  376 LEU cc_start: 0.7693 (tt) cc_final: 0.7222 (mt)
REVERT: D   56 LYS cc_start: 0.6772 (mttt) cc_final: 0.6496 (tmtt)
REVERT: D  121 LEU cc_start: 0.5179 (mp) cc_final: 0.4375 (mp)
REVERT: D  389 LYS cc_start: 0.8023 (pttp) cc_final: 0.7246 (mtpt)
REVERT: E   56 LYS cc_start: 0.6801 (mttt) cc_final: 0.6381 (tmtt)
  outliers start: 15
  outliers final: 14
  residues processed: 111
  average time/residue: 0.0862
  time to fit residues: 15.6415
Evaluate side-chains
  117 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue   64 LEU
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain D residue   64 LEU
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain E residue   73 THR
Chi-restraints excluded: chain E residue  121 LEU
Chi-restraints excluded: chain E residue  250 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 149 optimal weight:    8.9990
   chunk 37 optimal weight:   40.0000
   chunk 106 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 93 optimal weight:    0.5980
   chunk 26 optimal weight:    8.9990
   chunk 95 optimal weight:    0.7980
   chunk 59 optimal weight:    0.7980
   chunk 168 optimal weight:    0.9990
   chunk 105 optimal weight:    6.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 214 ASN
B 214 ASN
C 214 ASN
** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 328 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4960 r_free = 0.4960 target = 0.272119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.222000 restraints weight = 16653.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.4498 rms_B_bonded: 2.15
r_work: 0.4057 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3909 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6922
moved from start:          0.2466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13990  Z= 0.119
  Angle     :  0.461   8.651  18945  Z= 0.246
  Chirality :  0.040   0.144   2390
  Planarity :  0.003   0.065   2435
  Dihedral  :  4.245  37.476   1935
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 10.78 %
    Favored  : 88.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 25.00 %
    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:  2.22 (0.20), residues: 1865
  helix:  3.12 (0.20), residues: 675
  sheet:  1.25 (0.22), residues: 540
  loop : -0.13 (0.25), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 138 
 TYR   0.004   0.001   TYR C  95 
 PHE   0.016   0.001   PHE A 329 
 TRP   0.005   0.001   TRP C 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (13990)
  covalent geometry    : angle       0.46131 (18945)
  hydrogen bonds       : bond        0.02571 (  769)
  hydrogen bonds       : angle       4.27314 ( 2136)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4534.83 seconds
wall clock time: 78 minutes 19.87 seconds (4699.87 seconds total)