Starting phenix.real_space_refine
on Thu Sep 18 02:43:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9li2_63110/09_2025/9li2_63110_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9li2_63110/09_2025/9li2_63110.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9li2_63110/09_2025/9li2_63110_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9li2_63110/09_2025/9li2_63110_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9li2_63110/09_2025/9li2_63110.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9li2_63110/09_2025/9li2_63110.map"
  }
  resolution = 3.72
  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=   0.001 sd=   0.026
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
     S      27      5.16       5
     C    4254      2.51       5
     N    1065      2.21       5
     O    1170      1.98       5
     H    6333      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12849
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4255
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 4255
          Classifications: {'peptide': 268}
          Link IDs: {'PTRANS': 13, 'TRANS': 254}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "B"
      Number of atoms: 4255
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 4255
          Classifications: {'peptide': 268}
          Link IDs: {'PTRANS': 13, 'TRANS': 254}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "C"
      Number of atoms: 4255
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 4255
          Classifications: {'peptide': 268}
          Link IDs: {'PTRANS': 13, 'TRANS': 254}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'DXC': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'DXC': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'DXC': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.62, per 1000 atoms: 0.20
  Number of scatterers: 12849
  At special positions: 0
  Unit cell: (79.05, 81.84, 123.69, 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)
     S      27     16.00
     O    1170      8.00
     N    1065      7.00
     C    4254      6.00
     H    6333      1.00
    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=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.11
  Conformation dependent library (CDL) restraints added in 389.5 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1548

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 9 sheets defined
      34.3% alpha, 38.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 98
    Processing helix  chain 'A' and resid 206 through 213
      removed outlier: 3.674A  pdb=" N   PHE A 210 " --> pdb=" O   SER A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 227
      removed outlier: 3.900A  pdb=" N   PHE A 219 " --> pdb=" O   ASN A 215 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   SER A 225 " --> pdb=" O   GLN A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 278
      removed outlier: 3.548A  pdb=" N   SER A 277 " --> pdb=" O   ALA A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 332
    Processing helix  chain 'B' and resid 66 through 98
    Processing helix  chain 'B' and resid 206 through 213
      removed outlier: 3.649A  pdb=" N   PHE B 210 " --> pdb=" O   SER B 206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 227
      removed outlier: 3.881A  pdb=" N   PHE B 219 " --> pdb=" O   ASN B 215 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   SER B 225 " --> pdb=" O   GLN B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 278
      removed outlier: 3.557A  pdb=" N   SER B 277 " --> pdb=" O   ALA B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 332
    Processing helix  chain 'C' and resid 66 through 98
    Processing helix  chain 'C' and resid 206 through 213
      removed outlier: 3.646A  pdb=" N   PHE C 210 " --> pdb=" O   SER C 206 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 215 through 227
      removed outlier: 3.878A  pdb=" N   PHE C 219 " --> pdb=" O   ASN C 215 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   SER C 225 " --> pdb=" O   GLN C 221 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 272 through 278
      removed outlier: 3.560A  pdb=" N   SER C 277 " --> pdb=" O   ALA C 274 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 302 through 332
    Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 107
      removed outlier: 13.479A  pdb=" N   PHE A 291 " --> pdb=" O   VAL A 240 " (cutoff:3.500A)
      removed outlier: 9.248A  pdb=" N   MET A 242 " --> pdb=" O   PHE A 291 " (cutoff:3.500A)
      removed outlier: 9.237A  pdb=" N   GLN A 293 " --> pdb=" O   MET A 242 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   LEU A 244 " --> pdb=" O   GLN A 293 " (cutoff:3.500A)
      removed outlier: 7.543A  pdb=" N   VAL A 295 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   LYS A 246 " --> pdb=" O   VAL A 295 " (cutoff:3.500A)
      removed outlier: 7.795A  pdb=" N   ASP A 297 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   LYS A 248 " --> pdb=" O   ASP A 297 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   TRP A 287 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   GLU A 181 " --> pdb=" O   TRP A 287 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   ARG A 188 " --> pdb=" O   LEU A 125 " (cutoff:3.500A)
      removed outlier: 5.727A  pdb=" N   LEU A 125 " --> pdb=" O   ARG A 188 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 107
      removed outlier: 13.479A  pdb=" N   PHE A 291 " --> pdb=" O   VAL A 240 " (cutoff:3.500A)
      removed outlier: 9.248A  pdb=" N   MET A 242 " --> pdb=" O   PHE A 291 " (cutoff:3.500A)
      removed outlier: 9.237A  pdb=" N   GLN A 293 " --> pdb=" O   MET A 242 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   LEU A 244 " --> pdb=" O   GLN A 293 " (cutoff:3.500A)
      removed outlier: 7.543A  pdb=" N   VAL A 295 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   LYS A 246 " --> pdb=" O   VAL A 295 " (cutoff:3.500A)
      removed outlier: 7.795A  pdb=" N   ASP A 297 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   LYS A 248 " --> pdb=" O   ASP A 297 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 157
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 107
      removed outlier: 13.472A  pdb=" N   PHE B 291 " --> pdb=" O   VAL B 240 " (cutoff:3.500A)
      removed outlier: 9.252A  pdb=" N   MET B 242 " --> pdb=" O   PHE B 291 " (cutoff:3.500A)
      removed outlier: 9.243A  pdb=" N   GLN B 293 " --> pdb=" O   MET B 242 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   LEU B 244 " --> pdb=" O   GLN B 293 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   VAL B 295 " --> pdb=" O   LEU B 244 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   LYS B 246 " --> pdb=" O   VAL B 295 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   ASP B 297 " --> pdb=" O   LYS B 246 " (cutoff:3.500A)
      removed outlier: 7.779A  pdb=" N   LYS B 248 " --> pdb=" O   ASP B 297 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   TRP B 287 " --> pdb=" O   GLU B 181 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   GLU B 181 " --> pdb=" O   TRP B 287 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   ARG B 188 " --> pdb=" O   LEU B 125 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   LEU B 125 " --> pdb=" O   ARG B 188 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 107
      removed outlier: 13.472A  pdb=" N   PHE B 291 " --> pdb=" O   VAL B 240 " (cutoff:3.500A)
      removed outlier: 9.252A  pdb=" N   MET B 242 " --> pdb=" O   PHE B 291 " (cutoff:3.500A)
      removed outlier: 9.243A  pdb=" N   GLN B 293 " --> pdb=" O   MET B 242 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   LEU B 244 " --> pdb=" O   GLN B 293 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   VAL B 295 " --> pdb=" O   LEU B 244 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   LYS B 246 " --> pdb=" O   VAL B 295 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   ASP B 297 " --> pdb=" O   LYS B 246 " (cutoff:3.500A)
      removed outlier: 7.779A  pdb=" N   LYS B 248 " --> pdb=" O   ASP B 297 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 151 through 157
    Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 107
      removed outlier: 13.471A  pdb=" N   PHE C 291 " --> pdb=" O   VAL C 240 " (cutoff:3.500A)
      removed outlier: 9.215A  pdb=" N   MET C 242 " --> pdb=" O   PHE C 291 " (cutoff:3.500A)
      removed outlier: 9.237A  pdb=" N   GLN C 293 " --> pdb=" O   MET C 242 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   LEU C 244 " --> pdb=" O   GLN C 293 " (cutoff:3.500A)
      removed outlier: 7.548A  pdb=" N   VAL C 295 " --> pdb=" O   LEU C 244 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   LYS C 246 " --> pdb=" O   VAL C 295 " (cutoff:3.500A)
      removed outlier: 7.770A  pdb=" N   ASP C 297 " --> pdb=" O   LYS C 246 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   LYS C 248 " --> pdb=" O   ASP C 297 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   TRP C 287 " --> pdb=" O   GLU C 181 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   GLU C 181 " --> pdb=" O   TRP C 287 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   ARG C 188 " --> pdb=" O   LEU C 125 " (cutoff:3.500A)
      removed outlier: 5.861A  pdb=" N   LEU C 125 " --> pdb=" O   ARG C 188 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 100 through 107
      removed outlier: 13.471A  pdb=" N   PHE C 291 " --> pdb=" O   VAL C 240 " (cutoff:3.500A)
      removed outlier: 9.215A  pdb=" N   MET C 242 " --> pdb=" O   PHE C 291 " (cutoff:3.500A)
      removed outlier: 9.237A  pdb=" N   GLN C 293 " --> pdb=" O   MET C 242 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   LEU C 244 " --> pdb=" O   GLN C 293 " (cutoff:3.500A)
      removed outlier: 7.548A  pdb=" N   VAL C 295 " --> pdb=" O   LEU C 244 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   LYS C 246 " --> pdb=" O   VAL C 295 " (cutoff:3.500A)
      removed outlier: 7.770A  pdb=" N   ASP C 297 " --> pdb=" O   LYS C 246 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   LYS C 248 " --> pdb=" O   ASP C 297 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 151 through 157
      removed outlier: 4.542A  pdb=" N   ASP C 200 " --> pdb=" O   TYR C 119 " (cutoff:3.500A)

    385 hydrogen bonds defined for protein.
    1095 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: 2.87

  Time building geometry restraints manager: 1.50 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6321
        1.03 -     1.23: 15
        1.23 -     1.42: 2847
        1.42 -     1.61: 3783
        1.61 -     1.81: 60
  Bond restraints: 13026
  Sorted by residual:
  bond pdb=" C13 DXC C 401 "
       pdb=" C14 DXC C 401 "
    ideal  model  delta    sigma   weight residual
    1.534  1.681 -0.147 2.00e-02 2.50e+03 5.41e+01
  bond pdb=" C13 DXC A 401 "
       pdb=" C14 DXC A 401 "
    ideal  model  delta    sigma   weight residual
    1.534  1.681 -0.147 2.00e-02 2.50e+03 5.40e+01
  bond pdb=" C13 DXC B 401 "
       pdb=" C14 DXC B 401 "
    ideal  model  delta    sigma   weight residual
    1.534  1.680 -0.146 2.00e-02 2.50e+03 5.35e+01
  bond pdb=" C10 DXC A 401 "
       pdb=" C9  DXC A 401 "
    ideal  model  delta    sigma   weight residual
    1.540  1.673 -0.133 2.00e-02 2.50e+03 4.40e+01
  bond pdb=" C10 DXC B 401 "
       pdb=" C9  DXC B 401 "
    ideal  model  delta    sigma   weight residual
    1.540  1.672 -0.132 2.00e-02 2.50e+03 4.38e+01
  ... (remaining 13021 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.02: 23337
        2.02 -     4.03: 103
        4.03 -     6.05: 37
        6.05 -     8.06: 4
        8.06 -    10.08: 9
  Bond angle restraints: 23490
  Sorted by residual:
  angle pdb=" C17 DXC A 401 "
        pdb=" C19 DXC A 401 "
        pdb=" C21 DXC A 401 "
      ideal   model   delta    sigma   weight residual
     109.37  119.45  -10.08 3.00e+00 1.11e-01 1.13e+01
  angle pdb=" C17 DXC C 401 "
        pdb=" C19 DXC C 401 "
        pdb=" C21 DXC C 401 "
      ideal   model   delta    sigma   weight residual
     109.37  119.44  -10.07 3.00e+00 1.11e-01 1.13e+01
  angle pdb=" C17 DXC B 401 "
        pdb=" C19 DXC B 401 "
        pdb=" C21 DXC B 401 "
      ideal   model   delta    sigma   weight residual
     109.37  119.39  -10.02 3.00e+00 1.11e-01 1.11e+01
  angle pdb=" C2  DXC B 401 "
        pdb=" C1  DXC B 401 "
        pdb=" C6  DXC B 401 "
      ideal   model   delta    sigma   weight residual
     110.41  119.82   -9.41 3.00e+00 1.11e-01 9.84e+00
  angle pdb=" C2  DXC A 401 "
        pdb=" C1  DXC A 401 "
        pdb=" C6  DXC A 401 "
      ideal   model   delta    sigma   weight residual
     110.41  119.81   -9.40 3.00e+00 1.11e-01 9.82e+00
  ... (remaining 23485 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.38: 5913
       23.38 -    46.75: 342
       46.75 -    70.13: 47
       70.13 -    93.50: 19
       93.50 -   116.88: 39
  Dihedral angle restraints: 6360
    sinusoidal: 3429
      harmonic: 2931
  Sorted by residual:
  dihedral pdb=" CA  PHE B 204 "
           pdb=" C   PHE B 204 "
           pdb=" N   SER B 205 "
           pdb=" CA  SER B 205 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.39  -22.61     0      5.00e+00 4.00e-02 2.05e+01
  dihedral pdb=" CA  PHE A 204 "
           pdb=" C   PHE A 204 "
           pdb=" N   SER A 205 "
           pdb=" CA  SER A 205 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.92  -22.08     0      5.00e+00 4.00e-02 1.95e+01
  dihedral pdb=" CA  PHE C 204 "
           pdb=" C   PHE C 204 "
           pdb=" N   SER C 205 "
           pdb=" CA  SER C 205 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.95  -22.05     0      5.00e+00 4.00e-02 1.94e+01
  ... (remaining 6357 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.115: 977
       0.115 -    0.230: 28
       0.230 -    0.345: 6
       0.345 -    0.459: 0
       0.459 -    0.574: 3
  Chirality restraints: 1014
  Sorted by residual:
  chirality pdb=" C1  DXC C 401 "
            pdb=" C2  DXC C 401 "
            pdb=" C6  DXC C 401 "
            pdb=" O2  DXC C 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.42   -1.85   -0.57 2.00e-01 2.50e+01 8.25e+00
  chirality pdb=" C1  DXC A 401 "
            pdb=" C2  DXC A 401 "
            pdb=" C6  DXC A 401 "
            pdb=" O2  DXC A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.42   -1.85   -0.57 2.00e-01 2.50e+01 8.17e+00
  chirality pdb=" C1  DXC B 401 "
            pdb=" C2  DXC B 401 "
            pdb=" C6  DXC B 401 "
            pdb=" O2  DXC B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.42   -1.85   -0.57 2.00e-01 2.50e+01 8.17e+00
  ... (remaining 1011 not shown)

  Planarity restraints: 1905
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C 289 "   -0.041 5.00e-02 4.00e+02   6.28e-02 6.31e+00
        pdb=" N   PRO C 290 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO C 290 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO C 290 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 136 "   -0.038 5.00e-02 4.00e+02   5.80e-02 5.39e+00
        pdb=" N   PRO C 137 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO C 137 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO C 137 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 136 "    0.025 5.00e-02 4.00e+02   3.81e-02 2.32e+00
        pdb=" N   PRO A 137 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A 137 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 137 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1902 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 812
        2.20 -     2.80: 26172
        2.80 -     3.40: 33565
        3.40 -     4.00: 44598
        4.00 -     4.60: 67306
  Nonbonded interactions: 172453
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 200 "
            pdb=" HZ1 LYS A 231 "
     model   vdw
     1.603 2.450
  nonbonded pdb=" OD1 ASP B 200 "
            pdb=" HZ1 LYS B 231 "
     model   vdw
     1.646 2.450
  nonbonded pdb=" OD1 ASP C 200 "
            pdb=" HZ1 LYS C 231 "
     model   vdw
     1.648 2.450
  nonbonded pdb=" O   LEU A 189 "
            pdb=" H   GLN A 279 "
     model   vdw
     1.764 2.450
  nonbonded pdb="HH22 ARG B 271 "
            pdb=" O   ALA B 278 "
     model   vdw
     1.765 2.450
  ... (remaining 172448 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'
}

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 group one per residue
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:             1.520
  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:             0.080
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.460
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6933
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      :  0.014   0.502   6696  Z= 1.140
  Angle     :  0.667  10.081   9099  Z= 0.289
  Chirality :  0.059   0.574   1014
  Planarity :  0.004   0.063   1143
  Dihedral  : 20.734 116.879   2595
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  0.00 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.30), residues: 798
  helix:  3.36 (0.31), residues: 261
  sheet: -0.81 (0.27), residues: 300
  loop : -0.99 (0.40), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 237 
 TYR   0.006   0.001   TYR B 201 
 PHE   0.012   0.001   PHE C 204 
 TRP   0.002   0.000   TRP C 304 
 HIS   0.004   0.001   HIS B  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00856 ( 6693)
  covalent geometry    : angle       0.66724 ( 9099)
  hydrogen bonds       : bond        0.09676 (  361)
  hydrogen bonds       : angle       4.94250 ( 1095)
  Misc. bond           : bond        0.49973 (    3)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Evaluate side-chains
  103 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 100
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  260 GLN cc_start: 0.8472 (pp30) cc_final: 0.8134 (pp30)
  outliers start: 3
  outliers final: 3
  residues processed: 103
  average time/residue: 0.0971
  time to fit residues: 16.2180
Evaluate side-chains
  91 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 88
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 HIS
Chi-restraints excluded: chain B residue   98 HIS
Chi-restraints excluded: chain C residue   98 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.195767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.160114 restraints weight = 18218.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.166188 restraints weight = 12450.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.170749 restraints weight = 9468.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.173576 restraints weight = 7720.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.176194 restraints weight = 6590.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6671
moved from start:          0.0596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6696  Z= 0.136
  Angle     :  0.563   7.281   9099  Z= 0.264
  Chirality :  0.048   0.327   1014
  Planarity :  0.004   0.057   1143
  Dihedral  : 16.551 103.385   1083
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  4.06 %
    Favored  : 94.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.30), residues: 798
  helix:  3.70 (0.29), residues: 261
  sheet: -0.93 (0.26), residues: 300
  loop : -0.87 (0.40), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 271 
 TYR   0.003   0.001   TYR B 111 
 PHE   0.013   0.001   PHE B 258 
 TRP   0.003   0.001   TRP C 304 
 HIS   0.002   0.001   HIS C 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 6693)
  covalent geometry    : angle       0.56268 ( 9099)
  hydrogen bonds       : bond        0.03046 (  361)
  hydrogen bonds       : angle       4.01074 ( 1095)
  Misc. bond           : bond        0.00492 (    3)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Evaluate side-chains
  100 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  220 MET cc_start: 0.6816 (tpp) cc_final: 0.6586 (tpp)
REVERT: C  260 GLN cc_start: 0.8593 (pp30) cc_final: 0.8180 (pp30)
  outliers start: 7
  outliers final: 7
  residues processed: 99
  average time/residue: 0.1002
  time to fit residues: 15.7284
Evaluate side-chains
  93 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 HIS
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue   98 HIS
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue   98 HIS
Chi-restraints excluded: chain C residue  205 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 72 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
C 148 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.197647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.162254 restraints weight = 18372.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.168432 restraints weight = 12504.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.172869 restraints weight = 9511.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.175483 restraints weight = 7742.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.178272 restraints weight = 6630.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6673
moved from start:          0.0912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6696  Z= 0.137
  Angle     :  0.554   5.904   9099  Z= 0.260
  Chirality :  0.048   0.335   1014
  Planarity :  0.003   0.044   1143
  Dihedral  : 12.849  84.044   1083
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  5.36 %
    Favored  : 93.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.30), residues: 798
  helix:  3.85 (0.29), residues: 261
  sheet: -1.03 (0.26), residues: 300
  loop : -0.91 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 271 
 TYR   0.004   0.001   TYR A 201 
 PHE   0.013   0.001   PHE B 232 
 TRP   0.005   0.001   TRP A 239 
 HIS   0.002   0.001   HIS C 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 6693)
  covalent geometry    : angle       0.55350 ( 9099)
  hydrogen bonds       : bond        0.02659 (  361)
  hydrogen bonds       : angle       3.81246 ( 1095)
  Misc. bond           : bond        0.00403 (    3)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Evaluate side-chains
  104 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  260 GLN cc_start: 0.8608 (pp30) cc_final: 0.8159 (pp30)
  outliers start: 7
  outliers final: 5
  residues processed: 101
  average time/residue: 0.1002
  time to fit residues: 15.6790
Evaluate side-chains
  97 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  297 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   chunk 34 optimal weight:    6.9990
   chunk 29 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.194469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.157969 restraints weight = 18260.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.164259 restraints weight = 12356.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.168758 restraints weight = 9375.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.172012 restraints weight = 7592.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.174226 restraints weight = 6453.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6686
moved from start:          0.1078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6696  Z= 0.129
  Angle     :  0.508   5.918   9099  Z= 0.248
  Chirality :  0.045   0.223   1014
  Planarity :  0.003   0.038   1143
  Dihedral  :  8.615  71.478   1077
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  6.09 %
    Favored  : 92.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.30), residues: 798
  helix:  3.87 (0.30), residues: 261
  sheet: -1.08 (0.26), residues: 300
  loop : -0.88 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 237 
 TYR   0.005   0.001   TYR A 201 
 PHE   0.015   0.001   PHE B 232 
 TRP   0.004   0.001   TRP C 239 
 HIS   0.002   0.001   HIS A 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6693)
  covalent geometry    : angle       0.50831 ( 9099)
  hydrogen bonds       : bond        0.02579 (  361)
  hydrogen bonds       : angle       3.73622 ( 1095)
  Misc. bond           : bond        0.00245 (    3)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Evaluate side-chains
  105 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.6700 (tpp) cc_final: 0.6137 (tpp)
REVERT: C  260 GLN cc_start: 0.8597 (pp30) cc_final: 0.8148 (pp30)
  outliers start: 10
  outliers final: 10
  residues processed: 101
  average time/residue: 0.1011
  time to fit residues: 15.9101
Evaluate side-chains
  105 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  221 GLN
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  221 GLN
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain C residue  200 ASP
Chi-restraints excluded: chain C residue  205 SER
Chi-restraints excluded: chain C residue  221 GLN
Chi-restraints excluded: chain C residue  297 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 34 optimal weight:    5.9990
   overall best weight:    0.8980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.193834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.158061 restraints weight = 18451.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.164201 restraints weight = 12648.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.168656 restraints weight = 9621.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.171681 restraints weight = 7827.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.173814 restraints weight = 6668.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.3873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6690
moved from start:          0.1209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   6696  Z= 0.131
  Angle     :  0.481   4.037   9099  Z= 0.243
  Chirality :  0.044   0.181   1014
  Planarity :  0.003   0.033   1143
  Dihedral  :  7.073  54.853   1077
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  7.68 %
    Favored  : 90.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.30), residues: 798
  helix:  3.63 (0.30), residues: 270
  sheet: -1.12 (0.26), residues: 300
  loop : -0.74 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 237 
 TYR   0.004   0.001   TYR A 201 
 PHE   0.016   0.001   PHE B 232 
 TRP   0.004   0.001   TRP C 239 
 HIS   0.002   0.001   HIS C 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6693)
  covalent geometry    : angle       0.48052 ( 9099)
  hydrogen bonds       : bond        0.02575 (  361)
  hydrogen bonds       : angle       3.72021 ( 1095)
  Misc. bond           : bond        0.00248 (    3)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Evaluate side-chains
  108 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.6718 (tpp) cc_final: 0.6154 (tpp)
REVERT: B   78 MET cc_start: 0.6596 (tpp) cc_final: 0.6114 (tpp)
REVERT: C  196 PHE cc_start: 0.8094 (m-80) cc_final: 0.7846 (m-80)
REVERT: C  260 GLN cc_start: 0.8603 (pp30) cc_final: 0.8143 (pp30)
  outliers start: 10
  outliers final: 10
  residues processed: 104
  average time/residue: 0.0947
  time to fit residues: 15.4809
Evaluate side-chains
  107 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  221 GLN
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  221 GLN
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  200 ASP
Chi-restraints excluded: chain C residue  205 SER
Chi-restraints excluded: chain C residue  221 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 70 optimal weight:    0.8980
   chunk 76 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 69 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   chunk 52 optimal weight:   10.0000
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.9982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.196064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.159280 restraints weight = 18334.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.165730 restraints weight = 12259.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.170416 restraints weight = 9222.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.173348 restraints weight = 7421.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.176098 restraints weight = 6302.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6695
moved from start:          0.1314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   6696  Z= 0.139
  Angle     :  0.474   4.062   9099  Z= 0.244
  Chirality :  0.043   0.146   1014
  Planarity :  0.003   0.030   1143
  Dihedral  :  6.763  52.951   1077
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  :  8.55 %
    Favored  : 89.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.76 (0.30), residues: 798
  helix:  3.58 (0.30), residues: 270
  sheet: -1.17 (0.26), residues: 300
  loop : -0.81 (0.41), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 237 
 TYR   0.005   0.001   TYR B 201 
 PHE   0.017   0.001   PHE B 232 
 TRP   0.004   0.001   TRP C 239 
 HIS   0.002   0.001   HIS A 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6693)
  covalent geometry    : angle       0.47379 ( 9099)
  hydrogen bonds       : bond        0.02632 (  361)
  hydrogen bonds       : angle       3.76566 ( 1095)
  Misc. bond           : bond        0.00182 (    3)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Evaluate side-chains
  108 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.6690 (tpp) cc_final: 0.6154 (tpp)
REVERT: B   78 MET cc_start: 0.6783 (tpp) cc_final: 0.6313 (tpp)
REVERT: C  260 GLN cc_start: 0.8601 (pp30) cc_final: 0.8140 (pp30)
  outliers start: 13
  outliers final: 13
  residues processed: 103
  average time/residue: 0.1001
  time to fit residues: 16.4037
Evaluate side-chains
  106 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  221 GLN
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  221 GLN
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  297 ASP
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  200 ASP
Chi-restraints excluded: chain C residue  205 SER
Chi-restraints excluded: chain C residue  221 GLN
Chi-restraints excluded: chain C residue  297 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 8 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 57 optimal weight:    0.4980
   overall best weight:    1.2988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.194813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.160270 restraints weight = 18506.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.166231 restraints weight = 12733.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.170449 restraints weight = 9728.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.173446 restraints weight = 7930.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.175255 restraints weight = 6749.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6736
moved from start:          0.1493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   6696  Z= 0.169
  Angle     :  0.490   4.178   9099  Z= 0.257
  Chirality :  0.043   0.145   1014
  Planarity :  0.003   0.030   1143
  Dihedral  :  6.639  51.646   1077
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  :  9.57 %
    Favored  : 88.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.30), residues: 798
  helix:  3.41 (0.30), residues: 270
  sheet: -1.26 (0.26), residues: 306
  loop : -0.82 (0.42), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 237 
 TYR   0.007   0.001   TYR A 119 
 PHE   0.019   0.002   PHE B 232 
 TRP   0.005   0.001   TRP C 287 
 HIS   0.002   0.001   HIS B 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 6693)
  covalent geometry    : angle       0.49032 ( 9099)
  hydrogen bonds       : bond        0.02823 (  361)
  hydrogen bonds       : angle       3.93736 ( 1095)
  Misc. bond           : bond        0.00173 (    3)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Evaluate side-chains
  109 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.6685 (tpp) cc_final: 0.6174 (tpp)
REVERT: B   78 MET cc_start: 0.6786 (tpp) cc_final: 0.6328 (tpp)
REVERT: C  260 GLN cc_start: 0.8599 (pp30) cc_final: 0.7954 (pp30)
  outliers start: 14
  outliers final: 14
  residues processed: 103
  average time/residue: 0.0908
  time to fit residues: 14.8163
Evaluate side-chains
  107 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  221 GLN
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  221 GLN
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  297 ASP
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  200 ASP
Chi-restraints excluded: chain C residue  205 SER
Chi-restraints excluded: chain C residue  221 GLN
Chi-restraints excluded: chain C residue  297 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0980
   chunk 40 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 63 optimal weight:    0.8980
   chunk 31 optimal weight:    0.1980
   chunk 67 optimal weight:    2.9990
   chunk 60 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.4980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.191526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.156733 restraints weight = 18160.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.162723 restraints weight = 12494.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.167134 restraints weight = 9509.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.169939 restraints weight = 7754.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.172375 restraints weight = 6607.370|
|-----------------------------------------------------------------------------|
r_work (final): 0.3884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6723
moved from start:          0.1471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6696  Z= 0.095
  Angle     :  0.445   4.253   9099  Z= 0.229
  Chirality :  0.042   0.145   1014
  Planarity :  0.003   0.029   1143
  Dihedral  :  6.113  49.268   1077
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 10.00 %
    Favored  : 88.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.31), residues: 798
  helix:  3.76 (0.30), residues: 270
  sheet: -1.11 (0.26), residues: 306
  loop : -0.82 (0.41), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 237 
 TYR   0.006   0.001   TYR B 201 
 PHE   0.015   0.001   PHE C 232 
 TRP   0.003   0.000   TRP A 239 
 HIS   0.002   0.001   HIS C 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 6693)
  covalent geometry    : angle       0.44469 ( 9099)
  hydrogen bonds       : bond        0.02461 (  361)
  hydrogen bonds       : angle       3.61066 ( 1095)
  Misc. bond           : bond        0.00180 (    3)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Evaluate side-chains
  110 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.6625 (tpp) cc_final: 0.6133 (tpp)
REVERT: B   78 MET cc_start: 0.6788 (tpp) cc_final: 0.6288 (tpp)
  outliers start: 12
  outliers final: 12
  residues processed: 104
  average time/residue: 0.0980
  time to fit residues: 16.1872
Evaluate side-chains
  108 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  221 GLN
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  221 GLN
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  205 SER
Chi-restraints excluded: chain C residue  221 GLN
Chi-restraints excluded: chain C residue  297 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 37 optimal weight:    0.1980
   chunk 32 optimal weight:    0.5980
   chunk 64 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 72 optimal weight:    0.4980
   chunk 50 optimal weight:    0.3980
   overall best weight:    0.4980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.193140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.156768 restraints weight = 18278.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.163165 restraints weight = 12344.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.167726 restraints weight = 9299.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.170988 restraints weight = 7530.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.172923 restraints weight = 6397.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6660
moved from start:          0.1487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6696  Z= 0.097
  Angle     :  0.440   4.467   9099  Z= 0.228
  Chirality :  0.042   0.146   1014
  Planarity :  0.003   0.029   1143
  Dihedral  :  5.926  49.562   1077
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 10.29 %
    Favored  : 87.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.31), residues: 798
  helix:  3.86 (0.29), residues: 270
  sheet: -0.99 (0.27), residues: 306
  loop : -0.84 (0.41), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 237 
 TYR   0.005   0.000   TYR A 201 
 PHE   0.015   0.001   PHE C 232 
 TRP   0.004   0.000   TRP A 239 
 HIS   0.002   0.001   HIS A 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 6693)
  covalent geometry    : angle       0.44036 ( 9099)
  hydrogen bonds       : bond        0.02385 (  361)
  hydrogen bonds       : angle       3.51701 ( 1095)
  Misc. bond           : bond        0.00164 (    3)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Evaluate side-chains
  109 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.6624 (tpp) cc_final: 0.6148 (tpp)
REVERT: B   78 MET cc_start: 0.6744 (tpp) cc_final: 0.6257 (tpp)
  outliers start: 12
  outliers final: 12
  residues processed: 103
  average time/residue: 0.1002
  time to fit residues: 16.2057
Evaluate side-chains
  108 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  221 GLN
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  221 GLN
Chi-restraints excluded: chain B residue  297 ASP
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  205 SER
Chi-restraints excluded: chain C residue  221 GLN
Chi-restraints excluded: chain C residue  297 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 52 optimal weight:   10.0000
   chunk 28 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.9182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.191164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.155529 restraints weight = 18356.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.161564 restraints weight = 12580.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.165908 restraints weight = 9592.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.168496 restraints weight = 7835.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.171190 restraints weight = 6720.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6698
moved from start:          0.1535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6696  Z= 0.130
  Angle     :  0.458   4.925   9099  Z= 0.239
  Chirality :  0.042   0.145   1014
  Planarity :  0.003   0.029   1143
  Dihedral  :  6.022  52.639   1077
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 10.43 %
    Favored  : 87.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.31), residues: 798
  helix:  3.76 (0.29), residues: 270
  sheet: -1.07 (0.27), residues: 306
  loop : -0.83 (0.41), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 237 
 TYR   0.005   0.001   TYR A 201 
 PHE   0.017   0.001   PHE C 232 
 TRP   0.004   0.001   TRP A 239 
 HIS   0.002   0.001   HIS B 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6693)
  covalent geometry    : angle       0.45772 ( 9099)
  hydrogen bonds       : bond        0.02546 (  361)
  hydrogen bonds       : angle       3.63275 ( 1095)
  Misc. bond           : bond        0.00155 (    3)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS  325 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue ILE  328 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Evaluate side-chains
  107 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.6635 (tpp) cc_final: 0.6158 (tpp)
REVERT: B   78 MET cc_start: 0.6707 (tpp) cc_final: 0.6232 (tpp)
REVERT: C  196 PHE cc_start: 0.8056 (m-80) cc_final: 0.7828 (m-80)
REVERT: C  260 GLN cc_start: 0.8543 (pp30) cc_final: 0.8031 (pp30)
  outliers start: 12
  outliers final: 12
  residues processed: 102
  average time/residue: 0.1006
  time to fit residues: 16.1450
Evaluate side-chains
  107 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  221 GLN
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  221 GLN
Chi-restraints excluded: chain B residue  297 ASP
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  205 SER
Chi-restraints excluded: chain C residue  221 GLN
Chi-restraints excluded: chain C residue  297 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 37 optimal weight:    0.1980
   chunk 50 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.7984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.192936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.157564 restraints weight = 18309.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.163633 restraints weight = 12549.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.167960 restraints weight = 9568.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.170528 restraints weight = 7803.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.173104 restraints weight = 6695.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6740
moved from start:          0.1570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6696  Z= 0.116
  Angle     :  0.450   4.911   9099  Z= 0.234
  Chirality :  0.042   0.145   1014
  Planarity :  0.003   0.029   1143
  Dihedral  :  5.834  52.878   1077
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 10.29 %
    Favored  : 87.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.31), residues: 798
  helix:  3.81 (0.29), residues: 270
  sheet: -1.06 (0.27), residues: 306
  loop : -0.86 (0.41), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 237 
 TYR   0.005   0.001   TYR B 201 
 PHE   0.017   0.001   PHE C 232 
 TRP   0.003   0.001   TRP A 239 
 HIS   0.002   0.001   HIS C 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 6693)
  covalent geometry    : angle       0.45019 ( 9099)
  hydrogen bonds       : bond        0.02502 (  361)
  hydrogen bonds       : angle       3.58745 ( 1095)
  Misc. bond           : bond        0.00156 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 2128.80 seconds
wall clock time: 36 minutes 59.09 seconds (2219.09 seconds total)