Starting phenix.real_space_refine
on Thu Jun 12 15:25:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9egt_47997/06_2025/9egt_47997.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9egt_47997/06_2025/9egt_47997.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9egt_47997/06_2025/9egt_47997.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9egt_47997/06_2025/9egt_47997.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9egt_47997/06_2025/9egt_47997.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9egt_47997/06_2025/9egt_47997.cif"
  }
  resolution = 2.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.074
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: 5
    Type Number    sf(0)   Gaussians
     Ca      5      9.91       5
     S      70      5.16       5
     C    9205      2.51       5
     N    2250      2.21       5
     O    2639      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.14s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14169
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2779
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 15, 'TRANS': 322}
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 42
          Unresolved non-hydrogen dihedrals: 28
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 29
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 54
          Classifications: {'water': 54}
          Link IDs: {None: 53}
    Chain: "B"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 53
          Classifications: {'water': 53}
          Link IDs: {None: 52}
    Chain: "C"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 53
          Classifications: {'water': 53}
          Link IDs: {None: 52}
    Chain: "D"
      Number of atoms: 55
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 55
          Classifications: {'water': 55}
          Link IDs: {None: 54}
    Chain: "E"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 54
          Classifications: {'water': 54}
          Link IDs: {None: 53}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 8.13, per 1000 atoms: 0.57
  Number of scatterers: 14169
  At special positions: 0
  Unit cell: (90.625, 89.9, 109.475, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      5     19.99
     S      70     16.00
     O    2639      8.00
     N    2250      7.00
     C    9205      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: 3.59
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3220

  Finding SS restraints...
    Secondary structure from input PDB file:
      85 helices and 0 sheets defined
      77.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 10
      removed outlier: 3.646A  pdb=" N   ALA A  10 " --> pdb=" O   SER A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 18 through 23
      removed outlier: 3.571A  pdb=" N   LEU A  22 " --> pdb=" O   ARG A  19 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   CYS A  23 " --> pdb=" O   LEU A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 27 through 52
      removed outlier: 3.569A  pdb=" N   LEU A  31 " --> pdb=" O   SER A  27 " (cutoff:3.500A)
      removed outlier: 5.474A  pdb=" N   GLY A  34 " --> pdb=" O   LYS A  30 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   GLU A  35 " --> pdb=" O   LEU A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 72
    Processing helix  chain 'A' and resid 73 through 76
    Processing helix  chain 'A' and resid 77 through 99
    Processing helix  chain 'A' and resid 103 through 114
    Processing helix  chain 'A' and resid 118 through 144
      removed outlier: 3.603A  pdb=" N   SER A 142 " --> pdb=" O   LEU A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 151
    Processing helix  chain 'A' and resid 153 through 160
    Processing helix  chain 'A' and resid 164 through 174
    Processing helix  chain 'A' and resid 182 through 198
      removed outlier: 3.611A  pdb=" N   VAL A 186 " --> pdb=" O   TRP A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 230
      removed outlier: 3.547A  pdb=" N   LEU A 207 " --> pdb=" O   ASP A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 255
      removed outlier: 3.563A  pdb=" N   THR A 237 " --> pdb=" O   PRO A 233 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   VAL A 253 " --> pdb=" O   LEU A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 263
    Processing helix  chain 'A' and resid 274 through 295
    Processing helix  chain 'A' and resid 306 through 324
    Processing helix  chain 'B' and resid 6 through 10
      removed outlier: 3.647A  pdb=" N   ALA B  10 " --> pdb=" O   SER B   7 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 23
      removed outlier: 3.571A  pdb=" N   LEU B  22 " --> pdb=" O   ARG B  19 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   CYS B  23 " --> pdb=" O   LEU B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 27 through 52
      removed outlier: 3.569A  pdb=" N   LEU B  31 " --> pdb=" O   SER B  27 " (cutoff:3.500A)
      removed outlier: 5.474A  pdb=" N   GLY B  34 " --> pdb=" O   LYS B  30 " (cutoff:3.500A)
      removed outlier: 5.562A  pdb=" N   GLU B  35 " --> pdb=" O   LEU B  31 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 72
    Processing helix  chain 'B' and resid 73 through 76
    Processing helix  chain 'B' and resid 77 through 99
    Processing helix  chain 'B' and resid 103 through 114
    Processing helix  chain 'B' and resid 118 through 144
      removed outlier: 3.604A  pdb=" N   SER B 142 " --> pdb=" O   LEU B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 151
    Processing helix  chain 'B' and resid 153 through 160
    Processing helix  chain 'B' and resid 164 through 174
    Processing helix  chain 'B' and resid 182 through 198
      removed outlier: 3.610A  pdb=" N   VAL B 186 " --> pdb=" O   TRP B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 230
      removed outlier: 3.547A  pdb=" N   LEU B 207 " --> pdb=" O   ASP B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 255
      removed outlier: 3.562A  pdb=" N   THR B 237 " --> pdb=" O   PRO B 233 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   VAL B 253 " --> pdb=" O   LEU B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 263
    Processing helix  chain 'B' and resid 274 through 295
    Processing helix  chain 'B' and resid 306 through 324
    Processing helix  chain 'C' and resid 6 through 10
      removed outlier: 3.646A  pdb=" N   ALA C  10 " --> pdb=" O   SER C   7 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 18 through 23
      removed outlier: 3.571A  pdb=" N   LEU C  22 " --> pdb=" O   ARG C  19 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   CYS C  23 " --> pdb=" O   LEU C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 52
      removed outlier: 3.569A  pdb=" N   LEU C  31 " --> pdb=" O   SER C  27 " (cutoff:3.500A)
      removed outlier: 5.475A  pdb=" N   GLY C  34 " --> pdb=" O   LYS C  30 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   GLU C  35 " --> pdb=" O   LEU C  31 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 55 through 72
    Processing helix  chain 'C' and resid 73 through 76
    Processing helix  chain 'C' and resid 77 through 99
    Processing helix  chain 'C' and resid 103 through 114
    Processing helix  chain 'C' and resid 118 through 144
      removed outlier: 3.604A  pdb=" N   SER C 142 " --> pdb=" O   LEU C 138 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 144 through 151
    Processing helix  chain 'C' and resid 153 through 160
    Processing helix  chain 'C' and resid 164 through 174
    Processing helix  chain 'C' and resid 182 through 198
      removed outlier: 3.611A  pdb=" N   VAL C 186 " --> pdb=" O   TRP C 182 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 203 through 230
      removed outlier: 3.547A  pdb=" N   LEU C 207 " --> pdb=" O   ASP C 203 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 255
      removed outlier: 3.562A  pdb=" N   THR C 237 " --> pdb=" O   PRO C 233 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   VAL C 253 " --> pdb=" O   LEU C 249 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 259 through 263
    Processing helix  chain 'C' and resid 274 through 295
    Processing helix  chain 'C' and resid 306 through 324
    Processing helix  chain 'D' and resid 6 through 10
      removed outlier: 3.647A  pdb=" N   ALA D  10 " --> pdb=" O   SER D   7 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 18 through 23
      removed outlier: 3.571A  pdb=" N   LEU D  22 " --> pdb=" O   ARG D  19 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   CYS D  23 " --> pdb=" O   LEU D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 27 through 52
      removed outlier: 3.569A  pdb=" N   LEU D  31 " --> pdb=" O   SER D  27 " (cutoff:3.500A)
      removed outlier: 5.474A  pdb=" N   GLY D  34 " --> pdb=" O   LYS D  30 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   GLU D  35 " --> pdb=" O   LEU D  31 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 72
    Processing helix  chain 'D' and resid 73 through 76
    Processing helix  chain 'D' and resid 77 through 99
    Processing helix  chain 'D' and resid 103 through 114
    Processing helix  chain 'D' and resid 118 through 144
      removed outlier: 3.603A  pdb=" N   SER D 142 " --> pdb=" O   LEU D 138 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 144 through 151
    Processing helix  chain 'D' and resid 153 through 160
    Processing helix  chain 'D' and resid 164 through 174
    Processing helix  chain 'D' and resid 182 through 198
      removed outlier: 3.612A  pdb=" N   VAL D 186 " --> pdb=" O   TRP D 182 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 203 through 230
      removed outlier: 3.547A  pdb=" N   LEU D 207 " --> pdb=" O   ASP D 203 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 233 through 255
      removed outlier: 3.562A  pdb=" N   THR D 237 " --> pdb=" O   PRO D 233 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   VAL D 253 " --> pdb=" O   LEU D 249 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 259 through 263
    Processing helix  chain 'D' and resid 274 through 295
    Processing helix  chain 'D' and resid 306 through 324
    Processing helix  chain 'E' and resid 6 through 10
      removed outlier: 3.647A  pdb=" N   ALA E  10 " --> pdb=" O   SER E   7 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 18 through 23
      removed outlier: 3.570A  pdb=" N   LEU E  22 " --> pdb=" O   ARG E  19 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   CYS E  23 " --> pdb=" O   LEU E  20 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 27 through 52
      removed outlier: 3.570A  pdb=" N   LEU E  31 " --> pdb=" O   SER E  27 " (cutoff:3.500A)
      removed outlier: 5.474A  pdb=" N   GLY E  34 " --> pdb=" O   LYS E  30 " (cutoff:3.500A)
      removed outlier: 5.562A  pdb=" N   GLU E  35 " --> pdb=" O   LEU E  31 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 72
    Processing helix  chain 'E' and resid 73 through 76
    Processing helix  chain 'E' and resid 77 through 99
    Processing helix  chain 'E' and resid 103 through 114
    Processing helix  chain 'E' and resid 118 through 144
      removed outlier: 3.603A  pdb=" N   SER E 142 " --> pdb=" O   LEU E 138 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 144 through 151
    Processing helix  chain 'E' and resid 153 through 160
    Processing helix  chain 'E' and resid 164 through 174
    Processing helix  chain 'E' and resid 182 through 198
      removed outlier: 3.610A  pdb=" N   VAL E 186 " --> pdb=" O   TRP E 182 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 203 through 230
      removed outlier: 3.548A  pdb=" N   LEU E 207 " --> pdb=" O   ASP E 203 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 233 through 255
      removed outlier: 3.563A  pdb=" N   THR E 237 " --> pdb=" O   PRO E 233 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   VAL E 253 " --> pdb=" O   LEU E 249 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 259 through 263
    Processing helix  chain 'E' and resid 274 through 295
    Processing helix  chain 'E' and resid 306 through 324

    935 hydrogen bonds defined for protein.
    2730 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: 4.36

  Time building geometry restraints manager: 4.27 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4250
        1.34 -     1.46: 3099
        1.46 -     1.57: 6856
        1.57 -     1.69: 0
        1.69 -     1.81: 115
  Bond restraints: 14320
  Sorted by residual:
  bond pdb=" C   ARG D 130 "
       pdb=" O   ARG D 130 "
    ideal  model  delta    sigma   weight residual
    1.236  1.226  0.010 1.29e-02 6.01e+03 6.37e-01
  bond pdb=" CA  ILE A 230 "
       pdb=" CB  ILE A 230 "
    ideal  model  delta    sigma   weight residual
    1.540  1.529  0.011 1.36e-02 5.41e+03 6.20e-01
  bond pdb=" C   ARG E 130 "
       pdb=" O   ARG E 130 "
    ideal  model  delta    sigma   weight residual
    1.236  1.226  0.010 1.29e-02 6.01e+03 6.13e-01
  bond pdb=" CA  ILE B 230 "
       pdb=" CB  ILE B 230 "
    ideal  model  delta    sigma   weight residual
    1.540  1.530  0.010 1.36e-02 5.41e+03 5.90e-01
  bond pdb=" CA  ILE E 230 "
       pdb=" CB  ILE E 230 "
    ideal  model  delta    sigma   weight residual
    1.540  1.530  0.010 1.36e-02 5.41e+03 5.47e-01
  ... (remaining 14315 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.11: 18880
        1.11 -     2.23: 502
        2.23 -     3.34: 133
        3.34 -     4.45: 25
        4.45 -     5.56: 10
  Bond angle restraints: 19550
  Sorted by residual:
  angle pdb=" C   PHE D 247 "
        pdb=" N   PHE D 248 "
        pdb=" CA  PHE D 248 "
      ideal   model   delta    sigma   weight residual
     121.66  117.84    3.82 1.76e+00 3.23e-01 4.70e+00
  angle pdb=" C   PHE C 247 "
        pdb=" N   PHE C 248 "
        pdb=" CA  PHE C 248 "
      ideal   model   delta    sigma   weight residual
     121.66  117.87    3.79 1.76e+00 3.23e-01 4.63e+00
  angle pdb=" C   PHE E 247 "
        pdb=" N   PHE E 248 "
        pdb=" CA  PHE E 248 "
      ideal   model   delta    sigma   weight residual
     121.66  117.88    3.78 1.76e+00 3.23e-01 4.60e+00
  angle pdb=" C   PHE A 247 "
        pdb=" N   PHE A 248 "
        pdb=" CA  PHE A 248 "
      ideal   model   delta    sigma   weight residual
     121.66  117.89    3.77 1.76e+00 3.23e-01 4.58e+00
  angle pdb=" C   PHE B 247 "
        pdb=" N   PHE B 248 "
        pdb=" CA  PHE B 248 "
      ideal   model   delta    sigma   weight residual
     121.66  117.90    3.76 1.76e+00 3.23e-01 4.57e+00
  ... (remaining 19545 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.93: 7534
       15.93 -    31.85: 521
       31.85 -    47.78: 155
       47.78 -    63.70: 25
       63.70 -    79.63: 15
  Dihedral angle restraints: 8250
    sinusoidal: 3250
      harmonic: 5000
  Sorted by residual:
  dihedral pdb=" CA  ARG D 313 "
           pdb=" CB  ARG D 313 "
           pdb=" CG  ARG D 313 "
           pdb=" CD  ARG D 313 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.03   57.03     3      1.50e+01 4.44e-03 9.42e+00
  dihedral pdb=" CA  ARG E 313 "
           pdb=" CB  ARG E 313 "
           pdb=" CG  ARG E 313 "
           pdb=" CD  ARG E 313 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.02   57.02     3      1.50e+01 4.44e-03 9.42e+00
  dihedral pdb=" CA  ARG B 313 "
           pdb=" CB  ARG B 313 "
           pdb=" CG  ARG B 313 "
           pdb=" CD  ARG B 313 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.02   57.02     3      1.50e+01 4.44e-03 9.42e+00
  ... (remaining 8247 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1451
       0.032 -    0.063: 552
       0.063 -    0.095: 113
       0.095 -    0.127: 40
       0.127 -    0.159: 14
  Chirality restraints: 2170
  Sorted by residual:
  chirality pdb=" CA  ILE C 232 "
            pdb=" N   ILE C 232 "
            pdb=" C   ILE C 232 "
            pdb=" CB  ILE C 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.29e-01
  chirality pdb=" CA  PHE E 248 "
            pdb=" N   PHE E 248 "
            pdb=" C   PHE E 248 "
            pdb=" CB  PHE E 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.29e-01
  chirality pdb=" CA  ILE D 232 "
            pdb=" N   ILE D 232 "
            pdb=" C   ILE D 232 "
            pdb=" CB  ILE D 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.16e-01
  ... (remaining 2167 not shown)

  Planarity restraints: 2420
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE C 248 "    0.007 2.00e-02 2.50e+03   1.48e-02 2.19e+00
        pdb=" C   PHE C 248 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   PHE C 248 "    0.009 2.00e-02 2.50e+03
        pdb=" N   LEU C 249 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE D 248 "    0.007 2.00e-02 2.50e+03   1.48e-02 2.19e+00
        pdb=" C   PHE D 248 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   PHE D 248 "    0.009 2.00e-02 2.50e+03
        pdb=" N   LEU D 249 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 248 "    0.007 2.00e-02 2.50e+03   1.47e-02 2.17e+00
        pdb=" C   PHE B 248 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   PHE B 248 "    0.009 2.00e-02 2.50e+03
        pdb=" N   LEU B 249 "    0.009 2.00e-02 2.50e+03
  ... (remaining 2417 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 2446
        2.76 -     3.30: 14068
        3.30 -     3.83: 26781
        3.83 -     4.37: 32815
        4.37 -     4.90: 53574
  Nonbonded interactions: 129684
  Sorted by model distance:
  nonbonded pdb="CA    CA A 500 "
            pdb=" O   HOH A 604 "
     model   vdw
     2.231 2.510
  nonbonded pdb="CA    CA E 500 "
            pdb=" O   HOH E 605 "
     model   vdw
     2.240 2.510
  nonbonded pdb="CA    CA B 500 "
            pdb=" O   HOH B 604 "
     model   vdw
     2.246 2.510
  nonbonded pdb="CA    CA C 500 "
            pdb=" O   HOH C 603 "
     model   vdw
     2.254 2.510
  nonbonded pdb="CA    CA D 500 "
            pdb=" O   HOH D 606 "
     model   vdw
     2.256 2.510
  ... (remaining 129679 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: 0.10
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  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:             9.330
  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:          0.670
  Check model and map are aligned:         0.120
  Set scattering table:                    0.150
  Process input model:                     33.520
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   57.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
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   0.021  14320  Z= 0.118
  Angle     :  0.479   5.564  19550  Z= 0.258
  Chirality :  0.037   0.159   2170
  Planarity :  0.004   0.030   2420
  Dihedral  : 12.753  79.630   5030
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  5.03 %
    Favored  : 94.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.20), residues: 1680
  helix:  0.73 (0.15), residues: 1165
  sheet:  None (None), residues: 0
  loop : -0.60 (0.26), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  94 
 HIS   0.003   0.001   HIS E 326 
 PHE   0.020   0.001   PHE D 248 
 TYR   0.016   0.001   TYR E  97 
 ARG   0.002   0.000   ARG C 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13348 (  935)
  hydrogen bonds       : angle       5.75750 ( 2730)
  covalent geometry    : bond        0.00225 (14320)
  covalent geometry    : angle       0.47897 (19550)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 241
  time to evaluate  : 1.565 
Fit side-chains
REVERT: B   70 ASP cc_start: 0.8010 (t0) cc_final: 0.7494 (t0)
REVERT: B  332 MET cc_start: 0.8688 (ttp) cc_final: 0.8344 (ttp)
REVERT: C   60 LEU cc_start: 0.7771 (tp) cc_final: 0.7402 (tm)
REVERT: D   60 LEU cc_start: 0.7761 (tp) cc_final: 0.7465 (tm)
REVERT: D  115 GLU cc_start: 0.8479 (mt-10) cc_final: 0.7809 (mm-30)
REVERT: D  300 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8388 (mt-10)
  outliers start: 10
  outliers final: 0
  residues processed: 251
  average time/residue: 1.5705
  time to fit residues: 428.2787
Evaluate side-chains
  214 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 2.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 139 optimal weight:    0.6980
   chunk 125 optimal weight:    6.9990
   chunk 69 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 84 optimal weight:    0.8980
   chunk 66 optimal weight:    4.9990
   chunk 129 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 96 optimal weight:    1.9990
   chunk 149 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 159 GLN
A 212 ASN
B 133 ASN
B 212 ASN
C 212 ASN
D 159 GLN
D 212 ASN
E 159 GLN
E 212 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.135486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.113527 restraints weight = 14351.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 1.09
r_work: 0.3264 rms_B_bonded: 1.59 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.1170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  14320  Z= 0.170
  Angle     :  0.532   6.451  19550  Z= 0.287
  Chirality :  0.039   0.159   2170
  Planarity :  0.005   0.031   2420
  Dihedral  :  4.193  16.776   1865
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  8.79 %
    Favored  : 90.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.20), residues: 1680
  helix:  1.57 (0.15), residues: 1150
  sheet:  None (None), residues: 0
  loop : -0.43 (0.27), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A  94 
 HIS   0.003   0.001   HIS E 326 
 PHE   0.025   0.002   PHE E 248 
 TYR   0.022   0.002   TYR D  97 
 ARG   0.002   0.000   ARG D 313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06131 (  935)
  hydrogen bonds       : angle       4.53557 ( 2730)
  covalent geometry    : bond        0.00372 (14320)
  covalent geometry    : angle       0.53173 (19550)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 207
  time to evaluate  : 1.720 
Fit side-chains
REVERT: D  324 GLU cc_start: 0.8477 (mp0) cc_final: 0.8237 (mp0)
REVERT: E   57 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7338 (pt0)
  outliers start: 17
  outliers final: 5
  residues processed: 218
  average time/residue: 1.2702
  time to fit residues: 304.2246
Evaluate side-chains
  205 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 199
  time to evaluate  : 1.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain B residue  336 MET
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue  336 MET
Chi-restraints excluded: chain E residue   57 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 153 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 111 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 124 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 3 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A  11 ASN
A 159 GLN
D 159 GLN
E  11 ASN
E 159 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.132694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.110572 restraints weight = 14411.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 1.09
r_work: 0.3225 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 2.70 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8672
moved from start:          0.1536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  14320  Z= 0.204
  Angle     :  0.566   6.876  19550  Z= 0.303
  Chirality :  0.041   0.163   2170
  Planarity :  0.005   0.033   2420
  Dihedral  :  4.375  16.999   1865
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  :  9.40 %
    Favored  : 88.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.20), residues: 1680
  helix:  1.58 (0.15), residues: 1150
  sheet:  None (None), residues: 0
  loop : -0.43 (0.27), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  94 
 HIS   0.003   0.001   HIS E 326 
 PHE   0.029   0.002   PHE E 248 
 TYR   0.026   0.002   TYR C  97 
 ARG   0.003   0.000   ARG B 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06470 (  935)
  hydrogen bonds       : angle       4.53096 ( 2730)
  covalent geometry    : bond        0.00463 (14320)
  covalent geometry    : angle       0.56627 (19550)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 191
  time to evaluate  : 1.548 
Fit side-chains
REVERT: B  130 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8547 (ttp80)
REVERT: E  203 ASP cc_start: 0.8917 (OUTLIER) cc_final: 0.8445 (t70)
  outliers start: 38
  outliers final: 16
  residues processed: 223
  average time/residue: 1.3435
  time to fit residues: 328.3781
Evaluate side-chains
  204 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 186
  time to evaluate  : 1.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain A residue  203 ASP
Chi-restraints excluded: chain A residue  336 MET
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue  130 ARG
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  336 MET
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue  129 ILE
Chi-restraints excluded: chain D residue   57 GLU
Chi-restraints excluded: chain D residue  129 ILE
Chi-restraints excluded: chain D residue  175 SER
Chi-restraints excluded: chain D residue  203 ASP
Chi-restraints excluded: chain E residue   57 GLU
Chi-restraints excluded: chain E residue  129 ILE
Chi-restraints excluded: chain E residue  203 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 122 optimal weight:    0.9990
   chunk 49 optimal weight:    0.4980
   chunk 56 optimal weight:    0.6980
   chunk 112 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 156 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 145 optimal weight:    0.9990
   chunk 88 optimal weight:    0.5980
   chunk 128 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 159 GLN
D 159 GLN
E 159 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.134981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.112983 restraints weight = 14334.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 1.09
r_work: 0.3258 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3156 rms_B_bonded: 2.73 restraints_weight: 0.2500
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.1496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  14320  Z= 0.153
  Angle     :  0.517   6.227  19550  Z= 0.278
  Chirality :  0.038   0.158   2170
  Planarity :  0.004   0.028   2420
  Dihedral  :  4.204  16.112   1865
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 10.54 %
    Favored  : 87.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.20), residues: 1680
  helix:  1.75 (0.15), residues: 1150
  sheet:  None (None), residues: 0
  loop : -0.43 (0.27), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  94 
 HIS   0.003   0.000   HIS E 326 
 PHE   0.026   0.002   PHE E 248 
 TYR   0.027   0.002   TYR C  33 
 ARG   0.002   0.000   ARG D 130 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05842 (  935)
  hydrogen bonds       : angle       4.38305 ( 2730)
  covalent geometry    : bond        0.00328 (14320)
  covalent geometry    : angle       0.51659 (19550)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 190
  time to evaluate  : 1.932 
Fit side-chains
REVERT: A  300 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8417 (mt-10)
REVERT: E   57 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7264 (pt0)
REVERT: E  203 ASP cc_start: 0.8909 (OUTLIER) cc_final: 0.8450 (t70)
REVERT: E  300 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8382 (mt-10)
  outliers start: 31
  outliers final: 13
  residues processed: 212
  average time/residue: 1.3971
  time to fit residues: 323.6761
Evaluate side-chains
  201 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 184
  time to evaluate  : 1.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain A residue  203 ASP
Chi-restraints excluded: chain A residue  300 GLU
Chi-restraints excluded: chain A residue  336 MET
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  336 MET
Chi-restraints excluded: chain C residue  129 ILE
Chi-restraints excluded: chain D residue  129 ILE
Chi-restraints excluded: chain D residue  175 SER
Chi-restraints excluded: chain D residue  336 MET
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   57 GLU
Chi-restraints excluded: chain E residue  163 MET
Chi-restraints excluded: chain E residue  203 ASP
Chi-restraints excluded: chain E residue  300 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 101 optimal weight:    0.5980
   chunk 89 optimal weight:    0.5980
   chunk 147 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 158 optimal weight:    0.7980
   chunk 96 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 159 GLN
D 159 GLN
E 159 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.133950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.111964 restraints weight = 14442.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 1.09
r_work: 0.3243 rms_B_bonded: 1.59 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 2.77 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026  14320  Z= 0.171
  Angle     :  0.533   6.662  19550  Z= 0.286
  Chirality :  0.039   0.160   2170
  Planarity :  0.004   0.029   2420
  Dihedral  :  4.250  16.236   1865
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 11.41 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.20), residues: 1680
  helix:  1.78 (0.15), residues: 1150
  sheet:  None (None), residues: 0
  loop : -0.43 (0.27), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  94 
 HIS   0.003   0.001   HIS E 326 
 PHE   0.027   0.002   PHE E 248 
 TYR   0.029   0.002   TYR C  33 
 ARG   0.002   0.000   ARG B 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06023 (  935)
  hydrogen bonds       : angle       4.38991 ( 2730)
  covalent geometry    : bond        0.00380 (14320)
  covalent geometry    : angle       0.53312 (19550)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 184
  time to evaluate  : 1.579 
Fit side-chains
REVERT: A  300 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8436 (mt-10)
REVERT: B  203 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8498 (t70)
REVERT: D  300 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8616 (mt-10)
REVERT: E   57 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7316 (pt0)
REVERT: E  203 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.8440 (t70)
REVERT: E  300 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8435 (mt-10)
  outliers start: 36
  outliers final: 14
  residues processed: 211
  average time/residue: 1.5385
  time to fit residues: 354.4591
Evaluate side-chains
  203 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 183
  time to evaluate  : 1.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain A residue  203 ASP
Chi-restraints excluded: chain A residue  300 GLU
Chi-restraints excluded: chain A residue  336 MET
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  203 ASP
Chi-restraints excluded: chain B residue  332 MET
Chi-restraints excluded: chain C residue  129 ILE
Chi-restraints excluded: chain C residue  231 SER
Chi-restraints excluded: chain D residue  129 ILE
Chi-restraints excluded: chain D residue  175 SER
Chi-restraints excluded: chain D residue  203 ASP
Chi-restraints excluded: chain D residue  231 SER
Chi-restraints excluded: chain D residue  300 GLU
Chi-restraints excluded: chain D residue  336 MET
Chi-restraints excluded: chain E residue   57 GLU
Chi-restraints excluded: chain E residue  163 MET
Chi-restraints excluded: chain E residue  203 ASP
Chi-restraints excluded: chain E residue  300 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 126 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 59 optimal weight:    6.9990
   chunk 130 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9980
   chunk 98 optimal weight:    0.6980
   chunk 151 optimal weight:    0.7980
   chunk 110 optimal weight:    0.7980
   chunk 164 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 159 GLN
D 159 GLN
E 159 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.134032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.112059 restraints weight = 14549.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 1.09
r_work: 0.3245 rms_B_bonded: 1.59 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 2.77 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8647
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  14320  Z= 0.168
  Angle     :  0.527   6.456  19550  Z= 0.283
  Chirality :  0.039   0.160   2170
  Planarity :  0.004   0.029   2420
  Dihedral  :  4.238  16.543   1865
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 12.35 %
    Favored  : 85.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.20), residues: 1680
  helix:  1.80 (0.15), residues: 1150
  sheet:  None (None), residues: 0
  loop : -0.46 (0.27), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  94 
 HIS   0.003   0.001   HIS E 326 
 PHE   0.026   0.002   PHE E 248 
 TYR   0.029   0.002   TYR C  33 
 ARG   0.002   0.000   ARG A 130 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05967 (  935)
  hydrogen bonds       : angle       4.37854 ( 2730)
  covalent geometry    : bond        0.00374 (14320)
  covalent geometry    : angle       0.52748 (19550)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 189
  time to evaluate  : 1.577 
Fit side-chains
REVERT: A  290 VAL cc_start: 0.8692 (m) cc_final: 0.8479 (t)
REVERT: A  300 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8419 (mt-10)
REVERT: B  203 ASP cc_start: 0.8875 (OUTLIER) cc_final: 0.8515 (t70)
REVERT: C   57 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7370 (pt0)
REVERT: C  130 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8289 (ttp80)
REVERT: D  235 VAL cc_start: 0.8774 (OUTLIER) cc_final: 0.8505 (m)
REVERT: E   57 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7382 (pt0)
REVERT: E  203 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8445 (t70)
REVERT: E  300 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8424 (mt-10)
  outliers start: 32
  outliers final: 17
  residues processed: 214
  average time/residue: 1.5920
  time to fit residues: 372.2856
Evaluate side-chains
  208 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 183
  time to evaluate  : 3.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain A residue  203 ASP
Chi-restraints excluded: chain A residue  300 GLU
Chi-restraints excluded: chain A residue  336 MET
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  203 ASP
Chi-restraints excluded: chain B residue  332 MET
Chi-restraints excluded: chain B residue  336 MET
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue  129 ILE
Chi-restraints excluded: chain C residue  130 ARG
Chi-restraints excluded: chain C residue  231 SER
Chi-restraints excluded: chain D residue  129 ILE
Chi-restraints excluded: chain D residue  175 SER
Chi-restraints excluded: chain D residue  203 ASP
Chi-restraints excluded: chain D residue  231 SER
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain D residue  336 MET
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   57 GLU
Chi-restraints excluded: chain E residue  163 MET
Chi-restraints excluded: chain E residue  203 ASP
Chi-restraints excluded: chain E residue  231 SER
Chi-restraints excluded: chain E residue  300 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 124 optimal weight:    0.3980
   chunk 117 optimal weight:    0.8980
   chunk 113 optimal weight:    0.9980
   chunk 76 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 59 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 159 GLN
D 159 GLN
E 159 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.134893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.112893 restraints weight = 14486.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 1.10
r_work: 0.3255 rms_B_bonded: 1.60 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 2.78 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8639
moved from start:          0.1577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  14320  Z= 0.155
  Angle     :  0.514   6.266  19550  Z= 0.276
  Chirality :  0.038   0.160   2170
  Planarity :  0.004   0.029   2420
  Dihedral  :  4.179  15.835   1865
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 12.89 %
    Favored  : 84.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.20), residues: 1680
  helix:  1.84 (0.15), residues: 1150
  sheet:  None (None), residues: 0
  loop : -0.47 (0.27), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP E  94 
 HIS   0.003   0.000   HIS E 326 
 PHE   0.025   0.002   PHE E 248 
 TYR   0.029   0.002   TYR C  33 
 ARG   0.002   0.000   ARG B 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05794 (  935)
  hydrogen bonds       : angle       4.34866 ( 2730)
  covalent geometry    : bond        0.00337 (14320)
  covalent geometry    : angle       0.51427 (19550)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 184
  time to evaluate  : 1.770 
Fit side-chains
REVERT: A  300 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8414 (mt-10)
REVERT: B  203 ASP cc_start: 0.8886 (OUTLIER) cc_final: 0.8538 (t70)
REVERT: B  290 VAL cc_start: 0.8667 (m) cc_final: 0.8451 (t)
REVERT: C   57 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7327 (pt0)
REVERT: C  130 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8290 (ttp80)
REVERT: D  300 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8576 (mt-10)
REVERT: E   57 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7347 (pt0)
REVERT: E  203 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8453 (t70)
REVERT: E  300 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8393 (mt-10)
  outliers start: 34
  outliers final: 13
  residues processed: 212
  average time/residue: 1.3559
  time to fit residues: 313.8978
Evaluate side-chains
  207 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 186
  time to evaluate  : 1.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  203 ASP
Chi-restraints excluded: chain A residue  300 GLU
Chi-restraints excluded: chain A residue  336 MET
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  203 ASP
Chi-restraints excluded: chain B residue  332 MET
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue  129 ILE
Chi-restraints excluded: chain C residue  130 ARG
Chi-restraints excluded: chain C residue  231 SER
Chi-restraints excluded: chain D residue  129 ILE
Chi-restraints excluded: chain D residue  175 SER
Chi-restraints excluded: chain D residue  203 ASP
Chi-restraints excluded: chain D residue  231 SER
Chi-restraints excluded: chain D residue  300 GLU
Chi-restraints excluded: chain E residue   57 GLU
Chi-restraints excluded: chain E residue  163 MET
Chi-restraints excluded: chain E residue  203 ASP
Chi-restraints excluded: chain E residue  231 SER
Chi-restraints excluded: chain E residue  300 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 148 optimal weight:    0.5980
   chunk 54 optimal weight:    0.5980
   chunk 84 optimal weight:    0.5980
   chunk 109 optimal weight:    0.7980
   chunk 155 optimal weight:    0.3980
   chunk 143 optimal weight:    1.9990
   chunk 91 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 159 GLN
D 159 GLN
E 159 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.135423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.113454 restraints weight = 14478.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 1.09
r_work: 0.3259 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.3156 rms_B_bonded: 2.78 restraints_weight: 0.2500
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.1583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  14320  Z= 0.149
  Angle     :  0.509   6.224  19550  Z= 0.273
  Chirality :  0.038   0.158   2170
  Planarity :  0.004   0.029   2420
  Dihedral  :  4.138  15.683   1865
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 13.36 %
    Favored  : 84.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.20), residues: 1680
  helix:  1.86 (0.15), residues: 1150
  sheet:  None (None), residues: 0
  loop : -0.47 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  94 
 HIS   0.003   0.000   HIS E 326 
 PHE   0.024   0.002   PHE E 248 
 TYR   0.031   0.002   TYR C  33 
 ARG   0.002   0.000   ARG E 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05689 (  935)
  hydrogen bonds       : angle       4.33199 ( 2730)
  covalent geometry    : bond        0.00324 (14320)
  covalent geometry    : angle       0.50876 (19550)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 194
  time to evaluate  : 1.527 
Fit side-chains
REVERT: A  300 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8389 (mt-10)
REVERT: B  115 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7795 (mm-30)
REVERT: B  203 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8532 (t70)
REVERT: D  300 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8562 (mt-10)
REVERT: E  203 ASP cc_start: 0.8914 (OUTLIER) cc_final: 0.8446 (t70)
REVERT: E  300 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8391 (mt-10)
  outliers start: 26
  outliers final: 14
  residues processed: 214
  average time/residue: 1.3128
  time to fit residues: 307.4724
Evaluate side-chains
  200 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 181
  time to evaluate  : 1.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  203 ASP
Chi-restraints excluded: chain A residue  300 GLU
Chi-restraints excluded: chain A residue  336 MET
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  203 ASP
Chi-restraints excluded: chain B residue  332 MET
Chi-restraints excluded: chain B residue  336 MET
Chi-restraints excluded: chain C residue  129 ILE
Chi-restraints excluded: chain C residue  231 SER
Chi-restraints excluded: chain D residue  129 ILE
Chi-restraints excluded: chain D residue  175 SER
Chi-restraints excluded: chain D residue  203 ASP
Chi-restraints excluded: chain D residue  231 SER
Chi-restraints excluded: chain D residue  300 GLU
Chi-restraints excluded: chain E residue  163 MET
Chi-restraints excluded: chain E residue  203 ASP
Chi-restraints excluded: chain E residue  231 SER
Chi-restraints excluded: chain E residue  300 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 62 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 142 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 82 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 87 optimal weight:    0.5980
   chunk 120 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 159 GLN
D 159 GLN
E 159 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.134314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.112335 restraints weight = 14392.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 1.08
r_work: 0.3247 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3144 rms_B_bonded: 2.75 restraints_weight: 0.2500
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.1647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  14320  Z= 0.168
  Angle     :  0.532   6.506  19550  Z= 0.285
  Chirality :  0.039   0.162   2170
  Planarity :  0.004   0.030   2420
  Dihedral  :  4.209  16.129   1865
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 13.69 %
    Favored  : 84.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.20), residues: 1680
  helix:  1.81 (0.15), residues: 1150
  sheet:  None (None), residues: 0
  loop : -0.48 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  94 
 HIS   0.003   0.001   HIS E 326 
 PHE   0.025   0.002   PHE E 248 
 TYR   0.032   0.002   TYR C  33 
 ARG   0.003   0.000   ARG B 130 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05928 (  935)
  hydrogen bonds       : angle       4.37050 ( 2730)
  covalent geometry    : bond        0.00375 (14320)
  covalent geometry    : angle       0.53169 (19550)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 183
  time to evaluate  : 1.716 
Fit side-chains
REVERT: A  300 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8417 (mt-10)
REVERT: B  203 ASP cc_start: 0.8879 (OUTLIER) cc_final: 0.8521 (t70)
REVERT: C  130 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8305 (ttp80)
REVERT: D  300 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8587 (mt-10)
REVERT: E  203 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8434 (t70)
REVERT: E  300 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8422 (mt-10)
  outliers start: 28
  outliers final: 14
  residues processed: 206
  average time/residue: 1.3476
  time to fit residues: 303.6373
Evaluate side-chains
  201 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 181
  time to evaluate  : 1.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  203 ASP
Chi-restraints excluded: chain A residue  300 GLU
Chi-restraints excluded: chain A residue  336 MET
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  203 ASP
Chi-restraints excluded: chain B residue  332 MET
Chi-restraints excluded: chain C residue  129 ILE
Chi-restraints excluded: chain C residue  130 ARG
Chi-restraints excluded: chain C residue  231 SER
Chi-restraints excluded: chain D residue  129 ILE
Chi-restraints excluded: chain D residue  175 SER
Chi-restraints excluded: chain D residue  203 ASP
Chi-restraints excluded: chain D residue  231 SER
Chi-restraints excluded: chain D residue  300 GLU
Chi-restraints excluded: chain E residue  129 ILE
Chi-restraints excluded: chain E residue  163 MET
Chi-restraints excluded: chain E residue  203 ASP
Chi-restraints excluded: chain E residue  231 SER
Chi-restraints excluded: chain E residue  300 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 144 optimal weight:    1.9990
   chunk 157 optimal weight:    0.6980
   chunk 124 optimal weight:    0.8980
   chunk 112 optimal weight:    0.7980
   chunk 20 optimal weight:    0.2980
   chunk 67 optimal weight:    2.9990
   chunk 84 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9990
   chunk 72 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 159 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.134556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.112574 restraints weight = 14493.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 1.09
r_work: 0.3249 rms_B_bonded: 1.59 restraints_weight: 0.5000
r_work: 0.3147 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8640
moved from start:          0.1638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  14320  Z= 0.163
  Angle     :  0.525   6.271  19550  Z= 0.281
  Chirality :  0.039   0.160   2170
  Planarity :  0.004   0.029   2420
  Dihedral  :  4.194  15.913   1865
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 14.23 %
    Favored  : 84.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.20), residues: 1680
  helix:  1.82 (0.15), residues: 1150
  sheet:  None (None), residues: 0
  loop : -0.48 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  94 
 HIS   0.003   0.000   HIS E 326 
 PHE   0.025   0.002   PHE E 248 
 TYR   0.032   0.002   TYR C  33 
 ARG   0.003   0.000   ARG E 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05849 (  935)
  hydrogen bonds       : angle       4.36137 ( 2730)
  covalent geometry    : bond        0.00362 (14320)
  covalent geometry    : angle       0.52484 (19550)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 181
  time to evaluate  : 1.622 
Fit side-chains
REVERT: A  300 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8410 (mt-10)
REVERT: B  203 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8535 (t70)
REVERT: B  290 VAL cc_start: 0.8665 (m) cc_final: 0.8422 (t)
REVERT: C  130 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8306 (ttp80)
REVERT: D  300 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8583 (mt-10)
REVERT: E  203 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.8439 (t70)
REVERT: E  300 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8414 (mt-10)
  outliers start: 21
  outliers final: 13
  residues processed: 199
  average time/residue: 1.3514
  time to fit residues: 294.7991
Evaluate side-chains
  199 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 180
  time to evaluate  : 1.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  203 ASP
Chi-restraints excluded: chain A residue  300 GLU
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  203 ASP
Chi-restraints excluded: chain B residue  332 MET
Chi-restraints excluded: chain C residue  129 ILE
Chi-restraints excluded: chain C residue  130 ARG
Chi-restraints excluded: chain C residue  231 SER
Chi-restraints excluded: chain D residue  129 ILE
Chi-restraints excluded: chain D residue  175 SER
Chi-restraints excluded: chain D residue  203 ASP
Chi-restraints excluded: chain D residue  231 SER
Chi-restraints excluded: chain D residue  300 GLU
Chi-restraints excluded: chain E residue  129 ILE
Chi-restraints excluded: chain E residue  163 MET
Chi-restraints excluded: chain E residue  203 ASP
Chi-restraints excluded: chain E residue  231 SER
Chi-restraints excluded: chain E residue  300 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 159 optimal weight:    0.0010
   chunk 102 optimal weight:    2.9990
   chunk 147 optimal weight:    0.0770
   chunk 64 optimal weight:    0.9990
   chunk 131 optimal weight:    0.9980
   chunk 160 optimal weight:    0.5980
   chunk 80 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 98 optimal weight:    0.5980
   overall best weight:    0.4144

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

Flipped N/Q/H residues before XYZ refinement:
A 159 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.137090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.115125 restraints weight = 14432.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 1.10
r_work: 0.3286 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.3183 rms_B_bonded: 2.81 restraints_weight: 0.2500
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8602
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  14320  Z= 0.132
  Angle     :  0.489   5.775  19550  Z= 0.262
  Chirality :  0.037   0.158   2170
  Planarity :  0.004   0.029   2420
  Dihedral  :  4.046  14.879   1865
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 14.63 %
    Favored  : 84.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.20), residues: 1680
  helix:  1.92 (0.15), residues: 1150
  sheet:  None (None), residues: 0
  loop : -0.46 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  94 
 HIS   0.002   0.000   HIS E 326 
 PHE   0.023   0.002   PHE C 248 
 TYR   0.032   0.002   TYR C  33 
 ARG   0.002   0.000   ARG E 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05399 (  935)
  hydrogen bonds       : angle       4.28536 ( 2730)
  covalent geometry    : bond        0.00273 (14320)
  covalent geometry    : angle       0.48865 (19550)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10622.60 seconds
wall clock time: 187 minutes 5.52 seconds (11225.52 seconds total)