Starting phenix.real_space_refine
on Thu Jul  2 03:48:21 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j8k_36072/07_2026/8j8k_36072.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j8k_36072/07_2026/8j8k_36072.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j8k_36072/07_2026/8j8k_36072.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j8k_36072/07_2026/8j8k_36072.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j8k_36072/07_2026/8j8k_36072.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j8k_36072/07_2026/8j8k_36072.cif"
  }
  resolution = 3.36
  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=   0.003 sd=   0.048
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
     P       3      5.49       5
     S      30      5.16       5
     C    4290      2.51       5
     N    1053      2.21       5
     O    1113      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6489
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2133
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2133
          Classifications: {'peptide': 285}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 277}
    Chain: "A"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 30
          Unusual residues: {'DSL': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'DSL:plan-3': 1, 'DSL:plan-4': 1, 'DSL:plan-5': 1, 'DSL:plan-6': 1, 'DSL:plan-7': 1}
          Unresolved non-hydrogen planarities: 25
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 1.17, per 1000 atoms: 0.18
  Number of scatterers: 6489
  At special positions: 0
  Unit cell: (98.88, 106.56, 70.08, 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      30     16.00
     P       3     15.00
     O    1113      8.00
     N    1053      7.00
     C    4290      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.48
  Conformation dependent library (CDL) restraints added in 287.9 milliseconds
  

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1590

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 0 sheets defined
      78.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 22
      removed outlier: 3.697A  pdb=" N   ILE A  21 " --> pdb=" O   VAL A  18 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ARG A  22 " --> pdb=" O   LYS A  19 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 18 through 22'
    Processing helix  chain 'A' and resid 26 through 32
      removed outlier: 3.567A  pdb=" N   LEU A  31 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   VAL A  32 " --> pdb=" O   ASN A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 33 through 43
      removed outlier: 3.923A  pdb=" N   LEU A  37 " --> pdb=" O   LEU A  33 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   GLY A  41 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   GLY A  42 " --> pdb=" O   ALA A  38 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLY A  43 " --> pdb=" O   ALA A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 77
      removed outlier: 3.693A  pdb=" N   SER A  56 " --> pdb=" O   LEU A  52 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LEU A  64 " --> pdb=" O   VAL A  60 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA A  65 " --> pdb=" O   VAL A  61 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   VAL A  72 " --> pdb=" O   ALA A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 83
      removed outlier: 3.799A  pdb=" N   ALA A  81 " --> pdb=" O   ASP A  77 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ALA A  82 " --> pdb=" O   VAL A  78 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ALA A  83 " --> pdb=" O   ALA A  79 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 77 through 83'
    Processing helix  chain 'A' and resid 100 through 121
    Processing helix  chain 'A' and resid 123 through 142
    Processing helix  chain 'A' and resid 147 through 168
      removed outlier: 3.616A  pdb=" N   CYS A 151 " --> pdb=" O   VAL A 147 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   VAL A 153 " --> pdb=" O   GLU A 149 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   ARG A 160 " --> pdb=" O   ALA A 156 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   ALA A 161 " --> pdb=" O   TYR A 157 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   THR A 168 " --> pdb=" O   GLY A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 197
      removed outlier: 3.915A  pdb=" N   LEU A 177 " --> pdb=" O   SER A 173 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LEU A 185 " --> pdb=" O   ALA A 181 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   VAL A 188 " --> pdb=" O   SER A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 241
      removed outlier: 4.057A  pdb=" N   LEU A 218 " --> pdb=" O   THR A 214 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ARG A 219 " --> pdb=" O   SER A 215 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   PHE A 220 " --> pdb=" O   THR A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 267
    Processing helix  chain 'A' and resid 273 through 281
      removed outlier: 3.541A  pdb=" N   ASP A 281 " --> pdb=" O   ILE A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 301
      removed outlier: 3.593A  pdb=" N   ALA A 290 " --> pdb=" O   LEU A 286 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   TRP A 291 " --> pdb=" O   LEU A 287 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   ILE A 292 " --> pdb=" O   ALA A 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 22
      removed outlier: 3.698A  pdb=" N   ILE B  21 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ARG B  22 " --> pdb=" O   LYS B  19 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 18 through 22'
    Processing helix  chain 'B' and resid 26 through 32
      removed outlier: 3.567A  pdb=" N   LEU B  31 " --> pdb=" O   LYS B  28 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   VAL B  32 " --> pdb=" O   ASN B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 43
      removed outlier: 3.923A  pdb=" N   LEU B  37 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   GLY B  41 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   GLY B  42 " --> pdb=" O   ALA B  38 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLY B  43 " --> pdb=" O   ALA B  39 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 48 through 77
      removed outlier: 3.692A  pdb=" N   SER B  56 " --> pdb=" O   LEU B  52 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU B  64 " --> pdb=" O   VAL B  60 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA B  65 " --> pdb=" O   VAL B  61 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   VAL B  72 " --> pdb=" O   ALA B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 83
      removed outlier: 3.799A  pdb=" N   ALA B  81 " --> pdb=" O   ASP B  77 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ALA B  82 " --> pdb=" O   VAL B  78 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ALA B  83 " --> pdb=" O   ALA B  79 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 77 through 83'
    Processing helix  chain 'B' and resid 100 through 121
    Processing helix  chain 'B' and resid 123 through 142
    Processing helix  chain 'B' and resid 147 through 168
      removed outlier: 3.616A  pdb=" N   CYS B 151 " --> pdb=" O   VAL B 147 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   VAL B 153 " --> pdb=" O   GLU B 149 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   ARG B 160 " --> pdb=" O   ALA B 156 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   ALA B 161 " --> pdb=" O   TYR B 157 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   THR B 168 " --> pdb=" O   GLY B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 197
      removed outlier: 3.915A  pdb=" N   LEU B 177 " --> pdb=" O   SER B 173 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LEU B 185 " --> pdb=" O   ALA B 181 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   VAL B 188 " --> pdb=" O   SER B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 214 through 241
      removed outlier: 4.056A  pdb=" N   LEU B 218 " --> pdb=" O   THR B 214 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ARG B 219 " --> pdb=" O   SER B 215 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   PHE B 220 " --> pdb=" O   THR B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 267
    Processing helix  chain 'B' and resid 273 through 281
      removed outlier: 3.541A  pdb=" N   ASP B 281 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 301
      removed outlier: 3.593A  pdb=" N   ALA B 290 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   TRP B 291 " --> pdb=" O   LEU B 287 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   ILE B 292 " --> pdb=" O   ALA B 288 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 18 through 22
      removed outlier: 3.697A  pdb=" N   ILE C  21 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ARG C  22 " --> pdb=" O   LYS C  19 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 18 through 22'
    Processing helix  chain 'C' and resid 26 through 32
      removed outlier: 3.566A  pdb=" N   LEU C  31 " --> pdb=" O   LYS C  28 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   VAL C  32 " --> pdb=" O   ASN C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 33 through 43
      removed outlier: 3.923A  pdb=" N   LEU C  37 " --> pdb=" O   LEU C  33 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   GLY C  41 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   GLY C  42 " --> pdb=" O   ALA C  38 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLY C  43 " --> pdb=" O   ALA C  39 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 77
      removed outlier: 3.693A  pdb=" N   SER C  56 " --> pdb=" O   LEU C  52 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LEU C  64 " --> pdb=" O   VAL C  60 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA C  65 " --> pdb=" O   VAL C  61 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   VAL C  72 " --> pdb=" O   ALA C  68 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 77 through 83
      removed outlier: 3.799A  pdb=" N   ALA C  81 " --> pdb=" O   ASP C  77 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ALA C  82 " --> pdb=" O   VAL C  78 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ALA C  83 " --> pdb=" O   ALA C  79 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 77 through 83'
    Processing helix  chain 'C' and resid 100 through 121
    Processing helix  chain 'C' and resid 123 through 142
    Processing helix  chain 'C' and resid 147 through 168
      removed outlier: 3.615A  pdb=" N   CYS C 151 " --> pdb=" O   VAL C 147 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   VAL C 153 " --> pdb=" O   GLU C 149 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   ARG C 160 " --> pdb=" O   ALA C 156 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   ALA C 161 " --> pdb=" O   TYR C 157 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   THR C 168 " --> pdb=" O   GLY C 164 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 173 through 197
      removed outlier: 3.914A  pdb=" N   LEU C 177 " --> pdb=" O   SER C 173 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LEU C 185 " --> pdb=" O   ALA C 181 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   VAL C 188 " --> pdb=" O   SER C 184 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 214 through 241
      removed outlier: 4.057A  pdb=" N   LEU C 218 " --> pdb=" O   THR C 214 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ARG C 219 " --> pdb=" O   SER C 215 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   PHE C 220 " --> pdb=" O   THR C 216 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 251 through 267
    Processing helix  chain 'C' and resid 273 through 281
      removed outlier: 3.542A  pdb=" N   ASP C 281 " --> pdb=" O   ILE C 277 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 282 through 301
      removed outlier: 3.593A  pdb=" N   ALA C 290 " --> pdb=" O   LEU C 286 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   TRP C 291 " --> pdb=" O   LEU C 287 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   ILE C 292 " --> pdb=" O   ALA C 288 " (cutoff:3.500A)

    429 hydrogen bonds defined for protein.
    1269 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: 0.71

  Time building geometry restraints manager: 0.59 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 990
        1.31 -     1.43: 1821
        1.43 -     1.56: 3765
        1.56 -     1.68: 3
        1.68 -     1.81: 51
  Bond restraints: 6630
  Sorted by residual:
  bond pdb=" C   GLY C 190 "
       pdb=" O   GLY C 190 "
    ideal  model  delta    sigma   weight residual
    1.234  1.183  0.050 1.20e-02 6.94e+03 1.77e+01
  bond pdb=" C   GLY B 190 "
       pdb=" O   GLY B 190 "
    ideal  model  delta    sigma   weight residual
    1.234  1.183  0.050 1.20e-02 6.94e+03 1.76e+01
  bond pdb=" C   GLY A 190 "
       pdb=" O   GLY A 190 "
    ideal  model  delta    sigma   weight residual
    1.234  1.183  0.050 1.20e-02 6.94e+03 1.75e+01
  bond pdb=" CA  LYS C 191 "
       pdb=" C   LYS C 191 "
    ideal  model  delta    sigma   weight residual
    1.524  1.470  0.054 1.29e-02 6.01e+03 1.72e+01
  bond pdb=" CA  LYS A 191 "
       pdb=" C   LYS A 191 "
    ideal  model  delta    sigma   weight residual
    1.524  1.470  0.053 1.29e-02 6.01e+03 1.70e+01
  ... (remaining 6625 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 8509
        1.40 -     2.80: 421
        2.80 -     4.20: 73
        4.20 -     5.61: 27
        5.61 -     7.01: 24
  Bond angle restraints: 9054
  Sorted by residual:
  angle pdb=" N   GLU B 211 "
        pdb=" CA  GLU B 211 "
        pdb=" C   GLU B 211 "
      ideal   model   delta    sigma   weight residual
     113.21  108.06    5.15 1.15e+00 7.56e-01 2.01e+01
  angle pdb=" N   GLU C 211 "
        pdb=" CA  GLU C 211 "
        pdb=" C   GLU C 211 "
      ideal   model   delta    sigma   weight residual
     113.21  108.07    5.14 1.15e+00 7.56e-01 2.00e+01
  angle pdb=" N   GLU A 211 "
        pdb=" CA  GLU A 211 "
        pdb=" C   GLU A 211 "
      ideal   model   delta    sigma   weight residual
     113.21  108.07    5.14 1.15e+00 7.56e-01 1.99e+01
  angle pdb=" C   PHE C  62 "
        pdb=" CA  PHE C  62 "
        pdb=" CB  PHE C  62 "
      ideal   model   delta    sigma   weight residual
     110.90  104.41    6.49 1.58e+00 4.01e-01 1.69e+01
  angle pdb=" C   PHE A  62 "
        pdb=" CA  PHE A  62 "
        pdb=" CB  PHE A  62 "
      ideal   model   delta    sigma   weight residual
     110.90  104.41    6.49 1.58e+00 4.01e-01 1.69e+01
  ... (remaining 9049 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.42: 3420
       17.42 -    34.85: 300
       34.85 -    52.27: 81
       52.27 -    69.69: 12
       69.69 -    87.11: 3
  Dihedral angle restraints: 3816
    sinusoidal: 1335
      harmonic: 2481
  Sorted by residual:
  dihedral pdb=" CB  ARG B 282 "
           pdb=" CG  ARG B 282 "
           pdb=" CD  ARG B 282 "
           pdb=" NE  ARG B 282 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  126.48   53.52     3      1.50e+01 4.44e-03 9.21e+00
  dihedral pdb=" CB  ARG A 282 "
           pdb=" CG  ARG A 282 "
           pdb=" CD  ARG A 282 "
           pdb=" NE  ARG A 282 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  126.54   53.46     3      1.50e+01 4.44e-03 9.21e+00
  dihedral pdb=" CB  ARG C 282 "
           pdb=" CG  ARG C 282 "
           pdb=" CD  ARG C 282 "
           pdb=" NE  ARG C 282 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  126.55   53.45     3      1.50e+01 4.44e-03 9.21e+00
  ... (remaining 3813 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 937
       0.057 -    0.113: 134
       0.113 -    0.170: 3
       0.170 -    0.227: 6
       0.227 -    0.283: 3
  Chirality restraints: 1083
  Sorted by residual:
  chirality pdb=" CA  LEU B 210 "
            pdb=" N   LEU B 210 "
            pdb=" C   LEU B 210 "
            pdb=" CB  LEU B 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 2.01e+00
  chirality pdb=" CA  LEU A 210 "
            pdb=" N   LEU A 210 "
            pdb=" C   LEU A 210 "
            pdb=" CB  LEU A 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.96e+00
  chirality pdb=" CA  LEU C 210 "
            pdb=" N   LEU C 210 "
            pdb=" C   LEU C 210 "
            pdb=" CB  LEU C 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.92e+00
  ... (remaining 1080 not shown)

  Planarity restraints: 1104
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C51 DSL B 401 "   -0.024 2.00e-02 2.50e+03   2.55e-01 8.14e+02
        pdb=" C52 DSL B 401 "    0.094 2.00e-02 2.50e+03
        pdb=" C53 DSL B 401 "   -0.196 2.00e-02 2.50e+03
        pdb=" C54 DSL B 401 "    0.430 2.00e-02 2.50e+03
        pdb=" C55 DSL B 401 "   -0.304 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C51 DSL A 401 "   -0.024 2.00e-02 2.50e+03   2.55e-01 8.12e+02
        pdb=" C52 DSL A 401 "    0.094 2.00e-02 2.50e+03
        pdb=" C53 DSL A 401 "   -0.196 2.00e-02 2.50e+03
        pdb=" C54 DSL A 401 "    0.430 2.00e-02 2.50e+03
        pdb=" C55 DSL A 401 "   -0.304 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C51 DSL C 401 "   -0.024 2.00e-02 2.50e+03   2.55e-01 8.12e+02
        pdb=" C52 DSL C 401 "    0.094 2.00e-02 2.50e+03
        pdb=" C53 DSL C 401 "   -0.196 2.00e-02 2.50e+03
        pdb=" C54 DSL C 401 "    0.430 2.00e-02 2.50e+03
        pdb=" C55 DSL C 401 "   -0.304 2.00e-02 2.50e+03
  ... (remaining 1101 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 737
        2.74 -     3.28: 6502
        3.28 -     3.82: 10208
        3.82 -     4.36: 11617
        4.36 -     4.90: 20301
  Nonbonded interactions: 49365
  Sorted by model distance:
  nonbonded pdb=" O   ALA C 146 "
            pdb=" OH  TYR C 213 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   ALA A 146 "
            pdb=" OH  TYR A 213 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   ALA B 146 "
            pdb=" OH  TYR B 213 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   VAL C  61 "
            pdb=" OG  SER C 113 "
     model   vdw
     2.469 3.040
  nonbonded pdb=" O   VAL B  61 "
            pdb=" OG  SER B 113 "
     model   vdw
     2.469 3.040
  ... (remaining 49360 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.870
  Find NCS groups from input model:        0.030
  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:             0.000
  Load rotamer database and sin/cos tables:0.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
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      :  0.006   0.082   6630  Z= 0.328
  Angle     :  0.768   7.007   9054  Z= 0.468
  Chirality :  0.043   0.283   1083
  Planarity :  0.020   0.255   1104
  Dihedral  : 14.575  87.113   2226
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 18.43 %
    Favored  : 81.57 %
  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 are not related in a simple way.
  whole: -2.74 (0.25), residues: 849
  helix: -1.25 (0.19), residues: 600
  sheet:  None (None), residues: 0
  loop : -2.96 (0.31), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG B 160 
 TYR   0.010   0.001   TYR C 131 
 PHE   0.047   0.004   PHE A  62 
 TRP   0.026   0.001   TRP C 222 
 HIS   0.001   0.000   HIS B 197 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00555 /  0.33 ( 6630)
  covalent geometry    : angle       0.76838 /  0.47 ( 9054)
  hydrogen bonds       : bond        0.09878 /  6.68 (  429)
  hydrogen bonds       : angle       4.74126 /  3.33 ( 1269)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.228 
Fit side-chains
REVERT: B   48 TYR cc_start: 0.6509 (m-80) cc_final: 0.6250 (m-80)
REVERT: B   99 GLU cc_start: 0.7881 (mp0) cc_final: 0.7675 (mp0)
REVERT: B  119 MET cc_start: 0.7733 (ppp) cc_final: 0.7450 (tmm)
REVERT: C   99 GLU cc_start: 0.8208 (mp0) cc_final: 0.7937 (mp0)
REVERT: C  119 MET cc_start: 0.7845 (ppp) cc_final: 0.7462 (tmm)
REVERT: C  239 GLU cc_start: 0.7976 (tt0) cc_final: 0.7759 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.0814
  time to fit residues: 10.3741
Evaluate side-chains
  54 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.115742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.085031 restraints weight = 11104.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 2.42
r_work: 0.3122 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.1418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6630  Z= 0.118
  Angle     :  0.627  10.516   9054  Z= 0.302
  Chirality :  0.037   0.168   1083
  Planarity :  0.004   0.037   1104
  Dihedral  :  7.407  59.899    975
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 22.12 %
    Favored  : 75.48 %
  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 are not related in a simple way.
  whole: -0.91 (0.28), residues: 849
  helix:  0.16 (0.21), residues: 612
  sheet:  None (None), residues: 0
  loop : -2.52 (0.32), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 207 
 TYR   0.011   0.001   TYR C 213 
 PHE   0.014   0.001   PHE A  59 
 TRP   0.025   0.001   TRP C 222 
 HIS   0.008   0.001   HIS C 197 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00250 /  0.12 ( 6630)
  covalent geometry    : angle       0.62677 /  0.30 ( 9054)
  hydrogen bonds       : bond        0.04436 /  2.84 (  429)
  hydrogen bonds       : angle       3.55548 /  2.52 ( 1269)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.166 
Fit side-chains
REVERT: B   48 TYR cc_start: 0.6620 (m-80) cc_final: 0.6372 (m-80)
REVERT: B  119 MET cc_start: 0.7910 (ppp) cc_final: 0.7695 (tmm)
REVERT: C   99 GLU cc_start: 0.8403 (mp0) cc_final: 0.8127 (mp0)
REVERT: C  119 MET cc_start: 0.7982 (ppp) cc_final: 0.7697 (tmm)
REVERT: C  285 GLN cc_start: 0.8860 (mt0) cc_final: 0.8468 (mp10)
  outliers start: 15
  outliers final: 13
  residues processed: 86
  average time/residue: 0.0561
  time to fit residues: 6.5764
Evaluate side-chains
  73 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  173 SER
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  173 SER
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  266 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 7 optimal weight:    9.9990
   chunk 55 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 62 optimal weight:    0.4980
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.117178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.086122 restraints weight = 11075.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 2.43
r_work: 0.3132 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.1875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6630  Z= 0.106
  Angle     :  0.514   5.991   9054  Z= 0.265
  Chirality :  0.036   0.163   1083
  Planarity :  0.004   0.036   1104
  Dihedral  :  7.505  56.982    975
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 23.72 %
    Favored  : 73.40 %
  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 are not related in a simple way.
  whole: -0.05 (0.29), residues: 849
  helix:  0.82 (0.22), residues: 609
  sheet:  None (None), residues: 0
  loop : -2.23 (0.33), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 207 
 TYR   0.009   0.001   TYR C 131 
 PHE   0.013   0.001   PHE A  59 
 TRP   0.024   0.001   TRP C 222 
 HIS   0.004   0.001   HIS A 197 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00222 /  0.11 ( 6630)
  covalent geometry    : angle       0.51412 /  0.27 ( 9054)
  hydrogen bonds       : bond        0.04073 /  2.60 (  429)
  hydrogen bonds       : angle       3.30028 /  2.35 ( 1269)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A   25 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7828 (mm110)
REVERT: A   99 GLU cc_start: 0.7901 (mp0) cc_final: 0.7529 (tm-30)
REVERT: C  119 MET cc_start: 0.7936 (ppp) cc_final: 0.7693 (tmm)
REVERT: C  201 ARG cc_start: 0.7337 (ptt180) cc_final: 0.7056 (ptt-90)
  outliers start: 18
  outliers final: 13
  residues processed: 86
  average time/residue: 0.0678
  time to fit residues: 7.6411
Evaluate side-chains
  70 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 GLN
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  119 MET
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  173 SER
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain C residue  173 SER
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  266 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 28 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 49 optimal weight:    0.5980
   chunk 55 optimal weight:    2.9990
   chunk 62 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    1.7188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.112490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.080564 restraints weight = 11232.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 2.42
r_work: 0.3035 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.2109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6630  Z= 0.167
  Angle     :  0.600   7.228   9054  Z= 0.307
  Chirality :  0.038   0.192   1083
  Planarity :  0.004   0.041   1104
  Dihedral  :  7.594  57.929    975
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 21.96 %
    Favored  : 73.88 %
  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 are not related in a simple way.
  whole:  0.10 (0.29), residues: 849
  helix:  0.90 (0.22), residues: 600
  sheet:  None (None), residues: 0
  loop : -1.97 (0.33), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 201 
 TYR   0.012   0.001   TYR C 193 
 PHE   0.018   0.002   PHE A 186 
 TRP   0.029   0.002   TRP B 222 
 HIS   0.001   0.000   HIS A 197 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00394 /  0.17 ( 6630)
  covalent geometry    : angle       0.59959 /  0.31 ( 9054)
  hydrogen bonds       : bond        0.05657 /  3.60 (  429)
  hydrogen bonds       : angle       3.46140 /  2.47 ( 1269)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 57
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
REVERT: C  119 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7731 (tmm)
REVERT: C  128 MET cc_start: 0.8369 (mmp) cc_final: 0.7953 (mmp)
  outliers start: 26
  outliers final: 16
  residues processed: 76
  average time/residue: 0.0589
  time to fit residues: 6.0254
Evaluate side-chains
  66 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 49
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  119 MET
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  173 SER
Chi-restraints excluded: chain B residue  191 LYS
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  119 MET
Chi-restraints excluded: chain C residue  173 SER
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  289 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 60 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 28 optimal weight:    8.9990
   chunk 78 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 71 optimal weight:    0.0060
   chunk 23 optimal weight:    0.1980
   chunk 11 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.6196

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.116785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.085615 restraints weight = 11116.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 2.41
r_work: 0.3125 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6630  Z= 0.102
  Angle     :  0.517   6.734   9054  Z= 0.264
  Chirality :  0.036   0.158   1083
  Planarity :  0.004   0.036   1104
  Dihedral  :  7.503  58.134    975
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 23.72 %
    Favored  : 74.04 %
  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 are not related in a simple way.
  whole:  0.54 (0.29), residues: 849
  helix:  1.20 (0.22), residues: 606
  sheet:  None (None), residues: 0
  loop : -1.81 (0.35), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 207 
 TYR   0.011   0.001   TYR B  48 
 PHE   0.012   0.001   PHE A  59 
 TRP   0.024   0.001   TRP C 222 
 HIS   0.011   0.003   HIS B 197 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00215 /  0.10 ( 6630)
  covalent geometry    : angle       0.51692 /  0.26 ( 9054)
  hydrogen bonds       : bond        0.03979 /  2.53 (  429)
  hydrogen bonds       : angle       3.23266 /  2.30 ( 1269)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
REVERT: C  119 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7736 (tmm)
REVERT: C  128 MET cc_start: 0.8256 (mmp) cc_final: 0.7834 (mmp)
REVERT: C  201 ARG cc_start: 0.7352 (ptt180) cc_final: 0.6799 (ttp-170)
REVERT: C  285 GLN cc_start: 0.8874 (mt0) cc_final: 0.8522 (mp10)
  outliers start: 14
  outliers final: 10
  residues processed: 72
  average time/residue: 0.0613
  time to fit residues: 6.1202
Evaluate side-chains
  68 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 MET
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  173 SER
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain C residue  119 MET
Chi-restraints excluded: chain C residue  173 SER
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  289 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 76 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 47 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   overall best weight:    1.0182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.115722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.083760 restraints weight = 11181.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 2.43
r_work: 0.3089 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.2457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6630  Z= 0.119
  Angle     :  0.527   6.547   9054  Z= 0.269
  Chirality :  0.037   0.171   1083
  Planarity :  0.004   0.036   1104
  Dihedral  :  7.229  54.181    975
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 22.76 %
    Favored  : 74.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.29), residues: 849
  helix:  1.37 (0.22), residues: 600
  sheet:  None (None), residues: 0
  loop : -1.77 (0.35), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 207 
 TYR   0.009   0.001   TYR C 131 
 PHE   0.013   0.002   PHE A  59 
 TRP   0.027   0.001   TRP C 222 
 HIS   0.007   0.002   HIS C 197 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.12 ( 6630)
  covalent geometry    : angle       0.52729 /  0.27 ( 9054)
  hydrogen bonds       : bond        0.04501 /  2.86 (  429)
  hydrogen bonds       : angle       3.23893 /  2.31 ( 1269)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 59
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
REVERT: A  192 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8529 (tpp-160)
REVERT: A  292 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.9022 (mt)
REVERT: C   25 GLN cc_start: 0.8246 (mm-40) cc_final: 0.8039 (mm-40)
REVERT: C  119 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7709 (tmm)
REVERT: C  201 ARG cc_start: 0.7306 (ptt180) cc_final: 0.7002 (ptt-90)
  outliers start: 18
  outliers final: 14
  residues processed: 72
  average time/residue: 0.0685
  time to fit residues: 6.5664
Evaluate side-chains
  71 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 54
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 MET
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  192 ARG
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  173 SER
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  119 MET
Chi-restraints excluded: chain C residue  173 SER
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  289 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 41 optimal weight:    0.4980
   chunk 42 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 6 optimal weight:   20.0000
   chunk 61 optimal weight:    0.7980
   chunk 72 optimal weight:    3.9990
   chunk 66 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.116852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.085455 restraints weight = 10974.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 2.41
r_work: 0.3123 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.2613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6630  Z= 0.103
  Angle     :  0.513   6.772   9054  Z= 0.259
  Chirality :  0.036   0.161   1083
  Planarity :  0.003   0.032   1104
  Dihedral  :  7.139  52.161    975
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 22.60 %
    Favored  : 74.04 %
  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 are not related in a simple way.
  whole:  0.92 (0.30), residues: 849
  helix:  1.46 (0.22), residues: 606
  sheet:  None (None), residues: 0
  loop : -1.57 (0.36), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  76 
 TYR   0.008   0.001   TYR C 131 
 PHE   0.012   0.001   PHE A  59 
 TRP   0.024   0.001   TRP C 222 
 HIS   0.005   0.001   HIS A 197 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00225 /  0.10 ( 6630)
  covalent geometry    : angle       0.51308 /  0.26 ( 9054)
  hydrogen bonds       : bond        0.03962 /  2.52 (  429)
  hydrogen bonds       : angle       3.14676 /  2.24 ( 1269)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 62
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: A  192 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8430 (tpp-160)
REVERT: C  119 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7695 (tmm)
REVERT: C  128 MET cc_start: 0.8308 (mmp) cc_final: 0.7784 (mmp)
REVERT: C  201 ARG cc_start: 0.7366 (ptt180) cc_final: 0.7052 (ptt-90)
REVERT: C  285 GLN cc_start: 0.8923 (mt0) cc_final: 0.8667 (mp10)
REVERT: C  292 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8998 (mt)
  outliers start: 21
  outliers final: 17
  residues processed: 77
  average time/residue: 0.0607
  time to fit residues: 6.3151
Evaluate side-chains
  77 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 57
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 MET
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  192 ARG
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  220 PHE
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  173 SER
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  119 MET
Chi-restraints excluded: chain C residue  173 SER
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  289 LEU
Chi-restraints excluded: chain C residue  292 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0870
   chunk 23 optimal weight:    0.0010
   chunk 79 optimal weight:    0.0070
   chunk 16 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0870
   chunk 32 optimal weight:    7.9990
   chunk 61 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   overall best weight:    0.1760

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.121380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.090738 restraints weight = 11046.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 2.43
r_work: 0.3216 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.2950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6630  Z= 0.087
  Angle     :  0.480   7.441   9054  Z= 0.239
  Chirality :  0.035   0.138   1083
  Planarity :  0.003   0.029   1104
  Dihedral  :  6.972  58.483    975
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 22.92 %
    Favored  : 74.20 %
  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 are not related in a simple way.
  whole:  1.14 (0.30), residues: 849
  helix:  1.62 (0.22), residues: 612
  sheet:  None (None), residues: 0
  loop : -1.58 (0.37), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 282 
 TYR   0.007   0.001   TYR C 131 
 PHE   0.010   0.001   PHE C  59 
 TRP   0.018   0.001   TRP B 222 
 HIS   0.003   0.001   HIS A 197 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00175 /  0.09 ( 6630)
  covalent geometry    : angle       0.48047 /  0.24 ( 9054)
  hydrogen bonds       : bond        0.02864 /  1.81 (  429)
  hydrogen bonds       : angle       3.01066 /  2.14 ( 1269)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
REVERT: A   19 LYS cc_start: 0.7177 (tppt) cc_final: 0.6337 (mptt)
REVERT: C   19 LYS cc_start: 0.7247 (tppt) cc_final: 0.6168 (mptt)
REVERT: C  119 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7690 (tmm)
REVERT: C  128 MET cc_start: 0.8315 (mmp) cc_final: 0.7791 (mmp)
REVERT: C  285 GLN cc_start: 0.8974 (mt0) cc_final: 0.8704 (mp10)
  outliers start: 18
  outliers final: 13
  residues processed: 86
  average time/residue: 0.0563
  time to fit residues: 6.6482
Evaluate side-chains
  75 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 MET
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  220 PHE
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  173 SER
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  220 PHE
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain C residue  119 MET
Chi-restraints excluded: chain C residue  173 SER
Chi-restraints excluded: chain C residue  220 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 30 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 4 optimal weight:    7.9990
   chunk 55 optimal weight:    0.9990
   chunk 28 optimal weight:    8.9990
   chunk 59 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    1.7986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  25 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.114195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.081962 restraints weight = 11233.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 2.45
r_work: 0.3056 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.2683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6630  Z= 0.171
  Angle     :  0.610   8.604   9054  Z= 0.312
  Chirality :  0.038   0.184   1083
  Planarity :  0.004   0.031   1104
  Dihedral  :  7.112  52.967    975
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 24.52 %
    Favored  : 72.92 %
  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 are not related in a simple way.
  whole:  0.74 (0.30), residues: 849
  helix:  1.34 (0.22), residues: 615
  sheet:  None (None), residues: 0
  loop : -1.82 (0.36), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  22 
 TYR   0.011   0.001   TYR C 193 
 PHE   0.016   0.002   PHE A 186 
 TRP   0.033   0.002   TRP B 222 
 HIS   0.005   0.001   HIS B 197 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00409 /  0.17 ( 6630)
  covalent geometry    : angle       0.61036 /  0.31 ( 9054)
  hydrogen bonds       : bond        0.05406 /  3.42 (  429)
  hydrogen bonds       : angle       3.27272 /  2.34 ( 1269)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
REVERT: B   48 TYR cc_start: 0.6795 (m-10) cc_final: 0.6559 (m-10)
REVERT: B  201 ARG cc_start: 0.7062 (ttp-170) cc_final: 0.6784 (ttp-170)
REVERT: C   25 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7542 (mp-120)
REVERT: C  119 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7707 (tmm)
REVERT: C  128 MET cc_start: 0.8476 (mmp) cc_final: 0.8020 (mmp)
  outliers start: 16
  outliers final: 13
  residues processed: 69
  average time/residue: 0.0578
  time to fit residues: 5.5417
Evaluate side-chains
  66 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 MET
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  173 SER
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain C residue   25 GLN
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  119 MET
Chi-restraints excluded: chain C residue  173 SER
Chi-restraints excluded: chain C residue  266 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 54 optimal weight:    0.1980
   chunk 26 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0070
   chunk 80 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 82 optimal weight:    0.0470
   chunk 30 optimal weight:    8.9990
   chunk 74 optimal weight:    6.9990
   chunk 61 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.4096

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  25 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.114628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.082289 restraints weight = 10983.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 2.44
r_work: 0.3061 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.2711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.094   6630  Z= 0.169
  Angle     :  1.008  59.170   9054  Z= 0.583
  Chirality :  0.037   0.176   1083
  Planarity :  0.004   0.031   1104
  Dihedral  :  7.107  53.110    975
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 23.88 %
    Favored  : 73.08 %
  Cbeta Deviations :  0.13 %
  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 are not related in a simple way.
  whole:  0.75 (0.30), residues: 849
  helix:  1.34 (0.22), residues: 615
  sheet:  None (None), residues: 0
  loop : -1.78 (0.36), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  22 
 TYR   0.010   0.001   TYR C 193 
 PHE   0.015   0.002   PHE A 186 
 TRP   0.031   0.001   TRP B 222 
 HIS   0.009   0.002   HIS B 197 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.17 ( 6630)
  covalent geometry    : angle       1.00821 /  0.58 ( 9054)
  hydrogen bonds       : bond        0.05190 /  3.28 (  429)
  hydrogen bonds       : angle       3.26863 /  2.34 ( 1269)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 54
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
REVERT: A  192 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8414 (tpp-160)
REVERT: A  292 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.9024 (mt)
REVERT: B   48 TYR cc_start: 0.6764 (m-10) cc_final: 0.6535 (m-10)
REVERT: B  201 ARG cc_start: 0.6973 (ttp-170) cc_final: 0.6746 (ttp-170)
REVERT: C  119 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7697 (tmm)
REVERT: C  128 MET cc_start: 0.8464 (mmp) cc_final: 0.8008 (mmp)
  outliers start: 19
  outliers final: 14
  residues processed: 66
  average time/residue: 0.0591
  time to fit residues: 5.2755
Evaluate side-chains
  69 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 52
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  119 MET
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  192 ARG
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  173 SER
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  119 MET
Chi-restraints excluded: chain C residue  173 SER
Chi-restraints excluded: chain C residue  266 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 35 optimal weight:   20.0000
   chunk 5 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 78 optimal weight:    0.0670
   chunk 37 optimal weight:    2.9990
   chunk 13 optimal weight:    0.4980
   chunk 11 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.6522

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.114640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.082185 restraints weight = 11083.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 2.44
r_work: 0.3065 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.2705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.094   6630  Z= 0.169
  Angle     :  1.008  59.170   9054  Z= 0.583
  Chirality :  0.037   0.176   1083
  Planarity :  0.004   0.031   1104
  Dihedral  :  7.107  53.110    975
  Min Nonbonded Distance : 1.510

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 24.20 %
    Favored  : 73.08 %
  Cbeta Deviations :  0.13 %
  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 are not related in a simple way.
  whole:  0.75 (0.30), residues: 849
  helix:  1.34 (0.22), residues: 615
  sheet:  None (None), residues: 0
  loop : -1.78 (0.36), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  22 
 TYR   0.010   0.001   TYR C 193 
 PHE   0.015   0.002   PHE A 186 
 TRP   0.031   0.001   TRP B 222 
 HIS   0.009   0.002   HIS B 197 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.17 ( 6630)
  covalent geometry    : angle       1.00821 /  0.58 ( 9054)
  hydrogen bonds       : bond        0.05190 /  3.28 (  429)
  hydrogen bonds       : angle       3.26863 /  2.34 ( 1269)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1046.99 seconds
wall clock time: 18 minutes 40.38 seconds (1120.38 seconds total)