Starting phenix.real_space_refine
on Sun Apr  5 18:53:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jzk_61916/04_2026/9jzk_61916.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jzk_61916/04_2026/9jzk_61916.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jzk_61916/04_2026/9jzk_61916.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jzk_61916/04_2026/9jzk_61916.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jzk_61916/04_2026/9jzk_61916.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jzk_61916/04_2026/9jzk_61916.map"
  }
  resolution = 3.84
  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=   0.082
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      65      5.16       5
     C    8063      2.51       5
     N    2164      2.21       5
     O    2341      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12633
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "D"
      Number of atoms: 2549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 327, 2549
          Classifications: {'peptide': 327}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 309}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 2555
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 2555
          Classifications: {'peptide': 328}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 310}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 327, 2549
          Classifications: {'peptide': 327}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 309}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 2560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2560
          Classifications: {'peptide': 329}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 311}
          Chain breaks: 2
    Chain: "E"
      Number of atoms: 2420
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 311, 2420
          Classifications: {'peptide': 311}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 16, 'TRANS': 294}
          Chain breaks: 2
  Time building chain proxies: 2.76, per 1000 atoms: 0.22
  Number of scatterers: 12633
  At special positions: 0
  Unit cell: (101.49, 105.072, 121.788, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      65     16.00
     O    2341      8.00
     N    2164      7.00
     C    8063      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: 0.90
  Conformation dependent library (CDL) restraints added in 559.4 milliseconds
  

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3016

  Finding SS restraints...
    Secondary structure from input PDB file:
      96 helices and 6 sheets defined
      68.7% alpha, 0.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'D' and resid 52 through 61
    Processing helix  chain 'D' and resid 62 through 69
    Processing helix  chain 'D' and resid 72 through 83
    Processing helix  chain 'D' and resid 85 through 93
    Processing helix  chain 'D' and resid 129 through 149
    Processing helix  chain 'D' and resid 152 through 158
      removed outlier: 3.874A  pdb=" N   LYS D 156 " --> pdb=" O   SER D 152 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 158 through 173
      removed outlier: 3.590A  pdb=" N   ILE D 162 " --> pdb=" O   GLY D 158 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 177 through 182
    Processing helix  chain 'D' and resid 183 through 187
      removed outlier: 4.556A  pdb=" N   MET D 187 " --> pdb=" O   LEU D 184 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 190 through 200
    Processing helix  chain 'D' and resid 202 through 213
    Processing helix  chain 'D' and resid 216 through 231
      removed outlier: 3.620A  pdb=" N   GLN D 225 " --> pdb=" O   GLU D 221 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 235 through 248
    Processing helix  chain 'D' and resid 250 through 254
      removed outlier: 4.088A  pdb=" N   LEU D 253 " --> pdb=" O   ASP D 250 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 255 through 277
    Processing helix  chain 'D' and resid 278 through 283
      Proline residue:  D 281  - end of helix
      No H-bonds generated for 'chain 'D' and resid 278 through 283'
    Processing helix  chain 'D' and resid 288 through 295
    Processing helix  chain 'D' and resid 299 through 314
    Processing helix  chain 'D' and resid 332 through 342
      removed outlier: 3.968A  pdb=" N   ARG D 342 " --> pdb=" O   ARG D 338 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 354 through 365
    Processing helix  chain 'A' and resid 53 through 61
    Processing helix  chain 'A' and resid 62 through 69
    Processing helix  chain 'A' and resid 72 through 83
    Processing helix  chain 'A' and resid 85 through 93
    Processing helix  chain 'A' and resid 129 through 150
    Processing helix  chain 'A' and resid 152 through 157
    Processing helix  chain 'A' and resid 158 through 174
      removed outlier: 4.321A  pdb=" N   ILE A 162 " --> pdb=" O   GLY A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 182
    Processing helix  chain 'A' and resid 190 through 200
    Processing helix  chain 'A' and resid 202 through 213
    Processing helix  chain 'A' and resid 216 through 231
    Processing helix  chain 'A' and resid 235 through 247
    Processing helix  chain 'A' and resid 250 through 254
      removed outlier: 4.188A  pdb=" N   LEU A 253 " --> pdb=" O   ASP A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 277
    Processing helix  chain 'A' and resid 278 through 283
      Proline residue:  A 281  - end of helix
      No H-bonds generated for 'chain 'A' and resid 278 through 283'
    Processing helix  chain 'A' and resid 288 through 295
    Processing helix  chain 'A' and resid 299 through 314
    Processing helix  chain 'A' and resid 332 through 342
    Processing helix  chain 'A' and resid 354 through 365
    Processing helix  chain 'B' and resid 52 through 61
    Processing helix  chain 'B' and resid 62 through 69
    Processing helix  chain 'B' and resid 72 through 83
    Processing helix  chain 'B' and resid 85 through 93
    Processing helix  chain 'B' and resid 129 through 149
    Processing helix  chain 'B' and resid 152 through 158
    Processing helix  chain 'B' and resid 159 through 173
    Processing helix  chain 'B' and resid 175 through 182
      removed outlier: 3.754A  pdb=" N   GLY B 179 " --> pdb=" O   ARG B 175 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLU B 180 " --> pdb=" O   PRO B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 200
    Processing helix  chain 'B' and resid 202 through 213
    Processing helix  chain 'B' and resid 216 through 231
    Processing helix  chain 'B' and resid 235 through 246
    Processing helix  chain 'B' and resid 250 through 254
      removed outlier: 3.909A  pdb=" N   LEU B 253 " --> pdb=" O   ASP B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 277
    Processing helix  chain 'B' and resid 278 through 283
      Proline residue:  B 281  - end of helix
      No H-bonds generated for 'chain 'B' and resid 278 through 283'
    Processing helix  chain 'B' and resid 288 through 295
    Processing helix  chain 'B' and resid 299 through 314
    Processing helix  chain 'B' and resid 332 through 342
      removed outlier: 3.521A  pdb=" N   ARG B 341 " --> pdb=" O   ALA B 337 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   ARG B 342 " --> pdb=" O   ARG B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 365
    Processing helix  chain 'C' and resid 52 through 61
    Processing helix  chain 'C' and resid 62 through 68
      removed outlier: 3.789A  pdb=" N   MET C  68 " --> pdb=" O   SER C  64 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 83
    Processing helix  chain 'C' and resid 85 through 93
    Processing helix  chain 'C' and resid 129 through 150
      removed outlier: 3.504A  pdb=" N   PHE C 137 " --> pdb=" O   ILE C 133 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 152 through 157
    Processing helix  chain 'C' and resid 160 through 173
    Processing helix  chain 'C' and resid 175 through 182
    Processing helix  chain 'C' and resid 190 through 200
    Processing helix  chain 'C' and resid 202 through 213
    Processing helix  chain 'C' and resid 216 through 231
    Processing helix  chain 'C' and resid 235 through 247
    Processing helix  chain 'C' and resid 250 through 254
      removed outlier: 3.908A  pdb=" N   LEU C 253 " --> pdb=" O   ASP C 250 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 255 through 276
      removed outlier: 4.211A  pdb=" N   GLU C 261 " --> pdb=" O   VAL C 257 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ASP C 264 " --> pdb=" O   TYR C 260 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 279 through 283
    Processing helix  chain 'C' and resid 288 through 295
    Processing helix  chain 'C' and resid 299 through 314
    Processing helix  chain 'C' and resid 332 through 342
      removed outlier: 3.903A  pdb=" N   ARG C 342 " --> pdb=" O   ARG C 338 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 354 through 365
    Processing helix  chain 'E' and resid 52 through 61
    Processing helix  chain 'E' and resid 62 through 69
    Processing helix  chain 'E' and resid 72 through 83
    Processing helix  chain 'E' and resid 85 through 94
    Processing helix  chain 'E' and resid 129 through 150
    Processing helix  chain 'E' and resid 158 through 173
      removed outlier: 4.152A  pdb=" N   ILE E 162 " --> pdb=" O   GLY E 158 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 175 through 182
      removed outlier: 3.842A  pdb=" N   GLU E 180 " --> pdb=" O   PRO E 176 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 191 through 200
      removed outlier: 3.889A  pdb=" N   ASP E 195 " --> pdb=" O   HIS E 191 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 202 through 213
    Processing helix  chain 'E' and resid 216 through 231
      removed outlier: 3.592A  pdb=" N   PHE E 222 " --> pdb=" O   PRO E 218 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 235 through 248
    Processing helix  chain 'E' and resid 250 through 254
      removed outlier: 3.603A  pdb=" N   LEU E 253 " --> pdb=" O   ASP E 250 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 255 through 276
      removed outlier: 3.507A  pdb=" N   GLU E 274 " --> pdb=" O   ALA E 270 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 279 through 283
    Processing helix  chain 'E' and resid 288 through 294
      removed outlier: 3.806A  pdb=" N   ILE E 292 " --> pdb=" O   HIS E 288 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 295 through 298
    Processing helix  chain 'E' and resid 299 through 314
    Processing helix  chain 'E' and resid 332 through 343
      removed outlier: 3.504A  pdb=" N   ARG E 341 " --> pdb=" O   ALA E 337 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 354 through 365
    Processing sheet with id=AA1, first strand: chain 'D' and resid 99 through 100
    Processing sheet with id=AA2, first strand: chain 'D' and resid 344 through 345
      removed outlier: 3.993A  pdb=" N   GLY E 368 " --> pdb=" O   SER D 345 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 368 through 369
      removed outlier: 3.904A  pdb=" N   GLY D 368 " --> pdb=" O   SER C 345 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 99 through 100
    Processing sheet with id=AA5, first strand: chain 'A' and resid 344 through 345
      removed outlier: 3.769A  pdb=" N   GLY B 368 " --> pdb=" O   SER A 345 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 99 through 100

    719 hydrogen bonds defined for protein.
    2055 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: 2.18

  Time building geometry restraints manager: 1.25 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 2098
        1.32 -     1.44: 3331
        1.44 -     1.57: 7355
        1.57 -     1.70: 15
        1.70 -     1.83: 110
  Bond restraints: 12909
  Sorted by residual:
  bond pdb=" NE  ARG A 362 "
       pdb=" CZ  ARG A 362 "
    ideal  model  delta    sigma   weight residual
    1.326  1.391 -0.065 1.10e-02 8.26e+03 3.49e+01
  bond pdb=" NE  ARG D 362 "
       pdb=" CZ  ARG D 362 "
    ideal  model  delta    sigma   weight residual
    1.326  1.390 -0.064 1.10e-02 8.26e+03 3.38e+01
  bond pdb=" CA  SER D  75 "
       pdb=" CB  SER D  75 "
    ideal  model  delta    sigma   weight residual
    1.530  1.461  0.069 1.56e-02 4.11e+03 1.96e+01
  bond pdb=" CA  SER C  75 "
       pdb=" CB  SER C  75 "
    ideal  model  delta    sigma   weight residual
    1.529  1.461  0.068 1.55e-02 4.16e+03 1.92e+01
  bond pdb=" CA  SER A  75 "
       pdb=" CB  SER A  75 "
    ideal  model  delta    sigma   weight residual
    1.529  1.464  0.065 1.55e-02 4.16e+03 1.76e+01
  ... (remaining 12904 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.57: 14867
        2.57 -     5.13: 2316
        5.13 -     7.70: 240
        7.70 -    10.26: 26
       10.26 -    12.83: 4
  Bond angle restraints: 17453
  Sorted by residual:
  angle pdb=" CA  ASP A  52 "
        pdb=" CB  ASP A  52 "
        pdb=" CG  ASP A  52 "
      ideal   model   delta    sigma   weight residual
     112.60  119.43   -6.83 1.00e+00 1.00e+00 4.66e+01
  angle pdb=" CA  THR B  73 "
        pdb=" CB  THR B  73 "
        pdb=" OG1 THR B  73 "
      ideal   model   delta    sigma   weight residual
     109.60   99.66    9.94 1.50e+00 4.44e-01 4.40e+01
  angle pdb=" CA  ASP E  52 "
        pdb=" CB  ASP E  52 "
        pdb=" CG  ASP E  52 "
      ideal   model   delta    sigma   weight residual
     112.60  119.20   -6.60 1.00e+00 1.00e+00 4.35e+01
  angle pdb=" OG1 THR C 237 "
        pdb=" CB  THR C 237 "
        pdb=" CG2 THR C 237 "
      ideal   model   delta    sigma   weight residual
     109.30  122.13  -12.83 2.00e+00 2.50e-01 4.12e+01
  angle pdb=" CA  THR D 254 "
        pdb=" CB  THR D 254 "
        pdb=" OG1 THR D 254 "
      ideal   model   delta    sigma   weight residual
     109.60  100.09    9.51 1.50e+00 4.44e-01 4.02e+01
  ... (remaining 17448 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.75: 7024
       14.75 -    29.51: 572
       29.51 -    44.26: 123
       44.26 -    59.02: 43
       59.02 -    73.77: 40
  Dihedral angle restraints: 7802
    sinusoidal: 3136
      harmonic: 4666
  Sorted by residual:
  dihedral pdb=" CA  GLY D  94 "
           pdb=" C   GLY D  94 "
           pdb=" N   VAL D  95 "
           pdb=" CA  VAL D  95 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.99   23.01     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  GLN C 125 "
           pdb=" C   GLN C 125 "
           pdb=" N   ARG C 126 "
           pdb=" CA  ARG C 126 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.78  -20.22     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  PRO D  27 "
           pdb=" C   PRO D  27 "
           pdb=" N   LYS D  28 "
           pdb=" CA  LYS D  28 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.95   19.05     0      5.00e+00 4.00e-02 1.45e+01
  ... (remaining 7799 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 1157
       0.077 -    0.153: 590
       0.153 -    0.230: 180
       0.230 -    0.306: 32
       0.306 -    0.383: 9
  Chirality restraints: 1968
  Sorted by residual:
  chirality pdb=" CB  VAL C  95 "
            pdb=" CA  VAL C  95 "
            pdb=" CG1 VAL C  95 "
            pdb=" CG2 VAL C  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.25   -0.38 2.00e-01 2.50e+01 3.66e+00
  chirality pdb=" CB  VAL E  77 "
            pdb=" CA  VAL E  77 "
            pdb=" CG1 VAL E  77 "
            pdb=" CG2 VAL E  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.25   -0.38 2.00e-01 2.50e+01 3.55e+00
  chirality pdb=" CA  PRO A 190 "
            pdb=" N   PRO A 190 "
            pdb=" C   PRO A 190 "
            pdb=" CB  PRO A 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.36    0.36 2.00e-01 2.50e+01 3.16e+00
  ... (remaining 1965 not shown)

  Planarity restraints: 2227
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  36 "   -0.105 2.00e-02 2.50e+03   5.41e-02 5.86e+01
        pdb=" CG  TYR A  36 "    0.051 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  36 "    0.056 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  36 "    0.037 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  36 "    0.012 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  36 "    0.023 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  36 "   -0.007 2.00e-02 2.50e+03
        pdb=" OH  TYR A  36 "   -0.068 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 244 "   -0.057 2.00e-02 2.50e+03   4.10e-02 3.36e+01
        pdb=" CG  TYR C 244 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 244 "    0.039 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 244 "    0.055 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 244 "    0.040 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 244 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 244 "   -0.050 2.00e-02 2.50e+03
        pdb=" OH  TYR C 244 "   -0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 346 "   -0.497 9.50e-02 1.11e+02   2.23e-01 3.10e+01
        pdb=" NE  ARG B 346 "    0.034 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 346 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 346 "    0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 346 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 2224 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.78: 1331
        2.78 -     3.31: 14301
        3.31 -     3.84: 21785
        3.84 -     4.37: 25950
        4.37 -     4.90: 41493
  Nonbonded interactions: 104860
  Sorted by model distance:
  nonbonded pdb=" O   VAL C 147 "
            pdb=" NH2 ARG C 287 "
     model   vdw
     2.244 3.120
  nonbonded pdb=" OG  SER B 134 "
            pdb=" NH2 ARG B 175 "
     model   vdw
     2.377 3.120
  nonbonded pdb=" O   PHE D 206 "
            pdb=" OG  SER D 209 "
     model   vdw
     2.378 3.040
  nonbonded pdb=" O   PRO D 300 "
            pdb=" OG  SER D 304 "
     model   vdw
     2.388 3.040
  nonbonded pdb=" O   GLU D 132 "
            pdb=" OG  SER D 135 "
     model   vdw
     2.389 3.040
  ... (remaining 104855 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 27 through 99 or resid 123 through 314 or resid 325 throug \ 
h 370))
  selection = (chain 'B' and (resid 27 through 99 or resid 123 through 314 or resid 325 throug \ 
h 370))
  selection = (chain 'C' and (resid 27 through 99 or resid 123 through 314 or resid 325 throug \ 
h 370))
  selection = (chain 'D' and (resid 27 through 99 or resid 123 through 314 or resid 325 throug \ 
h 370))
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.43 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:             0.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.120
  Find NCS groups from input model:        0.240
  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:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
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      :  0.011   0.105  12909  Z= 0.709
  Angle     :  1.877  12.830  17453  Z= 1.259
  Chirality :  0.097   0.383   1968
  Planarity :  0.016   0.223   2227
  Dihedral  : 13.176  73.774   4786
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  6.65 %
    Favored  : 92.25 %
  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: -2.72 (0.18), residues: 1592
  helix: -1.66 (0.14), residues: 1000
  sheet:  None (None), residues: 0
  loop : -1.81 (0.23), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.028   0.004   ARG D 340 
 TYR   0.105   0.012   TYR A  36 
 PHE   0.081   0.012   PHE E 282 
 TRP   0.062   0.015   TRP C 202 
 HIS   0.027   0.006   HIS D  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.01147 (12909)
  covalent geometry    : angle       1.87701 (17453)
  hydrogen bonds       : bond        0.20703 (  719)
  hydrogen bonds       : angle       7.11506 ( 2055)

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

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

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  339 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 324
  time to evaluate  : 0.500 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   47 ILE cc_start: 0.7882 (tp) cc_final: 0.7414 (tp)
REVERT: D  188 PHE cc_start: 0.7800 (t80) cc_final: 0.7510 (t80)
REVERT: D  191 HIS cc_start: 0.8326 (p90) cc_final: 0.8031 (p90)
REVERT: D  341 ARG cc_start: 0.9116 (mmm-85) cc_final: 0.8619 (mtm-85)
REVERT: D  364 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8217 (tp)
REVERT: A   34 LEU cc_start: 0.8270 (tp) cc_final: 0.8037 (tt)
REVERT: A   35 GLN cc_start: 0.6686 (mm110) cc_final: 0.6412 (mm110)
REVERT: A   68 MET cc_start: 0.8296 (ptp) cc_final: 0.7930 (ptp)
REVERT: A   78 PHE cc_start: 0.8135 (m-10) cc_final: 0.7717 (m-10)
REVERT: A  124 THR cc_start: 0.8364 (p) cc_final: 0.8083 (p)
REVERT: A  139 HIS cc_start: 0.5885 (t70) cc_final: 0.5664 (t70)
REVERT: A  202 TRP cc_start: 0.8422 (p-90) cc_final: 0.8187 (p-90)
REVERT: A  235 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8474 (mtm)
REVERT: A  248 CYS cc_start: 0.8569 (t) cc_final: 0.8321 (p)
REVERT: A  250 ASP cc_start: 0.8668 (m-30) cc_final: 0.8349 (p0)
REVERT: A  345 SER cc_start: 0.8010 (m) cc_final: 0.7678 (p)
REVERT: B   33 PHE cc_start: 0.8596 (t80) cc_final: 0.8190 (t80)
REVERT: B   69 PHE cc_start: 0.6915 (m-80) cc_final: 0.6712 (m-80)
REVERT: B  134 SER cc_start: 0.8750 (m) cc_final: 0.8460 (p)
REVERT: B  170 MET cc_start: 0.8506 (mmt) cc_final: 0.8038 (mmt)
REVERT: B  178 HIS cc_start: 0.8329 (m-70) cc_final: 0.8103 (m170)
REVERT: B  250 ASP cc_start: 0.8770 (m-30) cc_final: 0.8489 (m-30)
REVERT: B  339 TYR cc_start: 0.7685 (m-80) cc_final: 0.7464 (m-80)
REVERT: B  340 ARG cc_start: 0.8674 (mtp85) cc_final: 0.8451 (mmm160)
REVERT: B  352 GLU cc_start: 0.8229 (mt-10) cc_final: 0.8028 (pm20)
REVERT: C  221 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8391 (mt-10)
REVERT: C  294 LEU cc_start: 0.8217 (mt) cc_final: 0.8012 (mp)
REVERT: E   33 PHE cc_start: 0.8968 (t80) cc_final: 0.8179 (t80)
REVERT: E   44 HIS cc_start: 0.8803 (p-80) cc_final: 0.8535 (p-80)
REVERT: E  187 MET cc_start: 0.7737 (mmp) cc_final: 0.6518 (tmm)
REVERT: E  235 MET cc_start: 0.8939 (mmm) cc_final: 0.8677 (mmm)
REVERT: E  243 GLU cc_start: 0.8622 (tt0) cc_final: 0.8206 (tp30)
REVERT: E  244 TYR cc_start: 0.8289 (t80) cc_final: 0.7219 (t80)
REVERT: E  247 GLU cc_start: 0.9331 (mt-10) cc_final: 0.9031 (tp30)
REVERT: E  326 GLN cc_start: 0.7315 (mt0) cc_final: 0.6986 (tt0)
REVERT: E  363 MET cc_start: 0.9458 (ttp) cc_final: 0.9091 (mtp)
  outliers start: 15
  outliers final: 3
  residues processed: 334
  average time/residue: 0.1278
  time to fit residues: 58.7119
Evaluate side-chains
  210 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 205
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  364 ILE
Chi-restraints excluded: chain A residue  235 MET
Chi-restraints excluded: chain B residue   62 ASP
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain C residue  272 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    7.9990
   chunk 130 optimal weight:   20.0000
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    8.9990
   chunk 91 optimal weight:    7.9990
   chunk 149 optimal weight:    5.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
D  44 HIS
D 186 GLN
A  35 GLN
B  35 GLN
B  44 HIS
B  55 GLN
** B 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 326 GLN
** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 234 GLN
C 276 HIS
E  56 ASN
E 186 GLN
** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 326 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.141389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.114852 restraints weight = 26607.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.114512 restraints weight = 24134.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.115302 restraints weight = 21260.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.115923 restraints weight = 18036.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.116005 restraints weight = 16627.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3613
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3613 r_free = 0.3613    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3613 r_free = 0.3613    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3613
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.3114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12909  Z= 0.177
  Angle     :  0.646   9.313  17453  Z= 0.334
  Chirality :  0.041   0.145   1968
  Planarity :  0.004   0.062   2227
  Dihedral  :  4.483  50.075   1745
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 10.96 %
    Favored  : 86.26 %
  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 are not related in a simple way.
  whole:  0.24 (0.20), residues: 1592
  helix:  0.72 (0.15), residues: 1025
  sheet:  None (None), residues: 0
  loop : -0.76 (0.25), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 362 
 TYR   0.029   0.002   TYR D 260 
 PHE   0.026   0.002   PHE A 166 
 TRP   0.011   0.001   TRP C 309 
 HIS   0.004   0.001   HIS B 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 (12909)
  covalent geometry    : angle       0.64599 (17453)
  hydrogen bonds       : bond        0.05610 (  719)
  hydrogen bonds       : angle       4.78368 ( 2055)

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

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

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 191
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   52 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7731 (p0)
REVERT: D   63 GLN cc_start: 0.6891 (tm-30) cc_final: 0.6670 (tm-30)
REVERT: D   67 ASP cc_start: 0.7065 (m-30) cc_final: 0.6730 (m-30)
REVERT: D  361 MET cc_start: 0.8446 (mmp) cc_final: 0.8237 (mmp)
REVERT: A   78 PHE cc_start: 0.7440 (m-10) cc_final: 0.7073 (m-10)
REVERT: A  170 MET cc_start: 0.8270 (mmt) cc_final: 0.7825 (mmm)
REVERT: A  336 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8109 (mm)
REVERT: A  370 ASN cc_start: 0.5799 (OUTLIER) cc_final: 0.5343 (m-40)
REVERT: B   29 LEU cc_start: 0.7328 (mm) cc_final: 0.6907 (mm)
REVERT: E  186 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7917 (pp30)
REVERT: E  244 TYR cc_start: 0.7969 (t80) cc_final: 0.7320 (t80)
  outliers start: 38
  outliers final: 17
  residues processed: 218
  average time/residue: 0.1118
  time to fit residues: 34.9773
Evaluate side-chains
  166 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 145
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   44 HIS
Chi-restraints excluded: chain D residue   52 ASP
Chi-restraints excluded: chain D residue  100 TYR
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  370 ASN
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue  102 SER
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  237 THR
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain C residue  273 LYS
Chi-restraints excluded: chain C residue  330 SER
Chi-restraints excluded: chain C residue  344 ILE
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  341 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 57 optimal weight:   10.0000
   chunk 138 optimal weight:   40.0000
   chunk 59 optimal weight:   10.0000
   chunk 103 optimal weight:    0.9990
   chunk 1 optimal weight:   20.0000
   chunk 61 optimal weight:   10.0000
   chunk 120 optimal weight:    0.7980
   chunk 55 optimal weight:   10.0000
   chunk 130 optimal weight:   20.0000
   chunk 98 optimal weight:   30.0000
   chunk 90 optimal weight:   10.0000
   overall best weight:    6.3594

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

Flipped N/Q/H residues before XYZ refinement:
D  44 HIS
D 186 GLN
** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.135181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.104732 restraints weight = 26640.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.105255 restraints weight = 20268.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.106521 restraints weight = 15350.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.107125 restraints weight = 14056.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.107208 restraints weight = 12469.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3497
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3497 r_free = 0.3497    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3497 r_free = 0.3497    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3497
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.3839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  12909  Z= 0.211
  Angle     :  0.637   7.095  17453  Z= 0.333
  Chirality :  0.042   0.158   1968
  Planarity :  0.005   0.047   2227
  Dihedral  :  4.152  33.335   1738
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 13.38 %
    Favored  : 83.26 %
  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 are not related in a simple way.
  whole:  0.70 (0.21), residues: 1592
  helix:  1.06 (0.16), residues: 1019
  sheet:  None (None), residues: 0
  loop : -0.51 (0.26), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 342 
 TYR   0.034   0.002   TYR D 260 
 PHE   0.063   0.002   PHE E  78 
 TRP   0.008   0.001   TRP C 309 
 HIS   0.007   0.001   HIS D  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 (12909)
  covalent geometry    : angle       0.63720 (17453)
  hydrogen bonds       : bond        0.05609 (  719)
  hydrogen bonds       : angle       4.74036 ( 2055)

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

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

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 152
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   52 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.7998 (p0)
REVERT: D   63 GLN cc_start: 0.7158 (tm-30) cc_final: 0.6890 (tm-30)
REVERT: D   67 ASP cc_start: 0.7367 (m-30) cc_final: 0.6882 (m-30)
REVERT: D  126 ARG cc_start: 0.7543 (tmm-80) cc_final: 0.7013 (tmm160)
REVERT: D  185 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8524 (mm)
REVERT: A  170 MET cc_start: 0.8369 (mmt) cc_final: 0.7953 (mmm)
REVERT: A  336 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8094 (mm)
REVERT: A  370 ASN cc_start: 0.5752 (OUTLIER) cc_final: 0.5381 (m-40)
REVERT: B   29 LEU cc_start: 0.7670 (mm) cc_final: 0.7120 (mm)
REVERT: B   68 MET cc_start: 0.8808 (ptm) cc_final: 0.8099 (tmm)
REVERT: C  361 MET cc_start: 0.8326 (mmt) cc_final: 0.7998 (mmt)
REVERT: E  211 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8516 (pp)
REVERT: E  244 TYR cc_start: 0.7961 (t80) cc_final: 0.7182 (t80)
REVERT: E  247 GLU cc_start: 0.7020 (tp30) cc_final: 0.6748 (tp30)
  outliers start: 46
  outliers final: 27
  residues processed: 189
  average time/residue: 0.1086
  time to fit residues: 29.6997
Evaluate side-chains
  173 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 141
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   44 HIS
Chi-restraints excluded: chain D residue   52 ASP
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  100 TYR
Chi-restraints excluded: chain D residue  118 PHE
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  185 LEU
Chi-restraints excluded: chain D residue  207 VAL
Chi-restraints excluded: chain D residue  258 VAL
Chi-restraints excluded: chain D residue  262 ILE
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  370 ASN
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue  102 SER
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  235 MET
Chi-restraints excluded: chain C residue  237 THR
Chi-restraints excluded: chain C residue  273 LYS
Chi-restraints excluded: chain C residue  330 SER
Chi-restraints excluded: chain C residue  344 ILE
Chi-restraints excluded: chain E residue   51 LYS
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue   80 CYS
Chi-restraints excluded: chain E residue  166 PHE
Chi-restraints excluded: chain E residue  211 LEU
Chi-restraints excluded: chain E residue  341 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 118 optimal weight:    3.9990
   chunk 65 optimal weight:   20.0000
   chunk 110 optimal weight:    0.9990
   chunk 146 optimal weight:   30.0000
   chunk 75 optimal weight:    8.9990
   chunk 108 optimal weight:   20.0000
   chunk 52 optimal weight:    0.8980
   chunk 89 optimal weight:   10.0000
   chunk 6 optimal weight:    6.9990
   chunk 26 optimal weight:    9.9990
   chunk 67 optimal weight:   10.0000
   overall best weight:    4.3788

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

Flipped N/Q/H residues before XYZ refinement:
D  44 HIS
** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 326 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.136447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.106642 restraints weight = 26071.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.106617 restraints weight = 23716.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.107918 restraints weight = 17985.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.108630 restraints weight = 15217.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.108719 restraints weight = 13999.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3516
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3516 r_free = 0.3516    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3516 r_free = 0.3516    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3516
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.4168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12909  Z= 0.161
  Angle     :  0.578   8.344  17453  Z= 0.296
  Chirality :  0.040   0.219   1968
  Planarity :  0.005   0.070   2227
  Dihedral  :  3.944  27.443   1736
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 14.69 %
    Favored  : 82.16 %
  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:  0.89 (0.21), residues: 1592
  helix:  1.16 (0.16), residues: 1021
  sheet:  None (None), residues: 0
  loop : -0.35 (0.26), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 340 
 TYR   0.036   0.002   TYR D 260 
 PHE   0.046   0.002   PHE E  78 
 TRP   0.008   0.001   TRP D 196 
 HIS   0.011   0.001   HIS D  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (12909)
  covalent geometry    : angle       0.57801 (17453)
  hydrogen bonds       : bond        0.04889 (  719)
  hydrogen bonds       : angle       4.45305 ( 2055)

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

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

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 155
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   52 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7923 (p0)
REVERT: D   63 GLN cc_start: 0.7213 (tm-30) cc_final: 0.7001 (tm-30)
REVERT: D   67 ASP cc_start: 0.7231 (m-30) cc_final: 0.6769 (m-30)
REVERT: D  185 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8538 (mm)
REVERT: D  339 TYR cc_start: 0.7876 (m-80) cc_final: 0.7623 (m-80)
REVERT: D  341 ARG cc_start: 0.8418 (mmm160) cc_final: 0.8002 (mmm160)
REVERT: A  170 MET cc_start: 0.8008 (mmt) cc_final: 0.7642 (mmm)
REVERT: A  336 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8144 (mm)
REVERT: B   29 LEU cc_start: 0.7594 (mm) cc_final: 0.7115 (mm)
REVERT: B   68 MET cc_start: 0.8511 (ptm) cc_final: 0.7843 (tmm)
REVERT: B  244 TYR cc_start: 0.8652 (t80) cc_final: 0.8376 (t80)
REVERT: C  361 MET cc_start: 0.8130 (mmt) cc_final: 0.7794 (mmt)
REVERT: E  187 MET cc_start: 0.7666 (tmm) cc_final: 0.7420 (tmm)
REVERT: E  211 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8583 (pp)
REVERT: E  244 TYR cc_start: 0.8038 (t80) cc_final: 0.7146 (t80)
REVERT: E  247 GLU cc_start: 0.6771 (tp30) cc_final: 0.6379 (tp30)
  outliers start: 43
  outliers final: 26
  residues processed: 191
  average time/residue: 0.1102
  time to fit residues: 30.6028
Evaluate side-chains
  172 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 142
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   44 HIS
Chi-restraints excluded: chain D residue   52 ASP
Chi-restraints excluded: chain D residue  100 TYR
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  185 LEU
Chi-restraints excluded: chain D residue  258 VAL
Chi-restraints excluded: chain D residue  325 ILE
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue  102 SER
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  235 MET
Chi-restraints excluded: chain C residue  237 THR
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain C residue  330 SER
Chi-restraints excluded: chain C residue  344 ILE
Chi-restraints excluded: chain E residue   51 LYS
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue   79 LEU
Chi-restraints excluded: chain E residue   80 CYS
Chi-restraints excluded: chain E residue  166 PHE
Chi-restraints excluded: chain E residue  211 LEU
Chi-restraints excluded: chain E residue  341 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 53 optimal weight:    7.9990
   chunk 134 optimal weight:    8.9990
   chunk 76 optimal weight:    9.9990
   chunk 121 optimal weight:   10.0000
   chunk 51 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9990
   chunk 35 optimal weight:   20.0000
   chunk 15 optimal weight:    0.0370
   chunk 132 optimal weight:   20.0000
   chunk 85 optimal weight:    9.9990
   overall best weight:    3.6064

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

Flipped N/Q/H residues before XYZ refinement:
D  44 HIS
** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 174 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.136858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.106040 restraints weight = 26397.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.106453 restraints weight = 21911.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.107946 restraints weight = 16441.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.109067 restraints weight = 13377.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.108990 restraints weight = 12171.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3519
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3519 r_free = 0.3519    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3519 r_free = 0.3519    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3519
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.4428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12909  Z= 0.143
  Angle     :  0.560   8.611  17453  Z= 0.284
  Chirality :  0.039   0.142   1968
  Planarity :  0.005   0.087   2227
  Dihedral  :  3.854  26.328   1736
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 14.91 %
    Favored  : 82.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.03 (0.21), residues: 1592
  helix:  1.24 (0.16), residues: 1021
  sheet:  None (None), residues: 0
  loop : -0.21 (0.27), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 340 
 TYR   0.037   0.001   TYR D 260 
 PHE   0.038   0.002   PHE E  78 
 TRP   0.008   0.001   TRP E 202 
 HIS   0.011   0.001   HIS D  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (12909)
  covalent geometry    : angle       0.55956 (17453)
  hydrogen bonds       : bond        0.04581 (  719)
  hydrogen bonds       : angle       4.34130 ( 2055)

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

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

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 152
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   52 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7988 (p0)
REVERT: D   67 ASP cc_start: 0.7352 (m-30) cc_final: 0.6880 (m-30)
REVERT: D  185 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8469 (mm)
REVERT: A  170 MET cc_start: 0.7805 (mmt) cc_final: 0.7491 (mmm)
REVERT: B   29 LEU cc_start: 0.7578 (mm) cc_final: 0.7234 (mm)
REVERT: B   68 MET cc_start: 0.8587 (ptm) cc_final: 0.7899 (tmm)
REVERT: B  139 HIS cc_start: 0.8716 (OUTLIER) cc_final: 0.6533 (t70)
REVERT: C  361 MET cc_start: 0.8204 (mmt) cc_final: 0.7813 (mmt)
REVERT: E  211 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8499 (pp)
REVERT: E  244 TYR cc_start: 0.8095 (t80) cc_final: 0.7334 (t80)
REVERT: E  247 GLU cc_start: 0.6955 (tp30) cc_final: 0.6450 (tp30)
  outliers start: 37
  outliers final: 27
  residues processed: 182
  average time/residue: 0.1019
  time to fit residues: 27.5482
Evaluate side-chains
  170 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 139
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   44 HIS
Chi-restraints excluded: chain D residue   52 ASP
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  100 TYR
Chi-restraints excluded: chain D residue  185 LEU
Chi-restraints excluded: chain D residue  258 VAL
Chi-restraints excluded: chain D residue  325 ILE
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  139 HIS
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue  102 SER
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  235 MET
Chi-restraints excluded: chain C residue  237 THR
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain C residue  330 SER
Chi-restraints excluded: chain C residue  344 ILE
Chi-restraints excluded: chain E residue   51 LYS
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue   79 LEU
Chi-restraints excluded: chain E residue   80 CYS
Chi-restraints excluded: chain E residue  166 PHE
Chi-restraints excluded: chain E residue  211 LEU
Chi-restraints excluded: chain E residue  341 ARG
Chi-restraints excluded: chain E residue  344 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 100 optimal weight:    9.9990
   chunk 122 optimal weight:    3.9990
   chunk 136 optimal weight:    8.9990
   chunk 150 optimal weight:   30.0000
   chunk 156 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 28 optimal weight:   30.0000
   chunk 74 optimal weight:   10.0000
   chunk 73 optimal weight:    9.9990
   chunk 94 optimal weight:   20.0000
   chunk 86 optimal weight:    4.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
D  44 HIS
D 186 GLN
** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 174 ASN
E 234 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.134375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.103031 restraints weight = 26645.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.103811 restraints weight = 21263.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.105046 restraints weight = 16257.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.105901 restraints weight = 14075.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.105875 restraints weight = 12785.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3471
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3471 r_free = 0.3471    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3471 r_free = 0.3471    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3471
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.4645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  12909  Z= 0.196
  Angle     :  0.617   6.989  17453  Z= 0.318
  Chirality :  0.041   0.156   1968
  Planarity :  0.005   0.074   2227
  Dihedral  :  4.025  27.920   1736
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 15.57 %
    Favored  : 81.14 %
  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:  0.88 (0.21), residues: 1592
  helix:  1.10 (0.16), residues: 1019
  sheet:  None (None), residues: 0
  loop : -0.23 (0.27), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 340 
 TYR   0.038   0.002   TYR D 260 
 PHE   0.064   0.002   PHE E  78 
 TRP   0.008   0.002   TRP E 196 
 HIS   0.011   0.001   HIS D  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 (12909)
  covalent geometry    : angle       0.61666 (17453)
  hydrogen bonds       : bond        0.05046 (  719)
  hydrogen bonds       : angle       4.48887 ( 2055)

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

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

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 141
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   52 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.7974 (p0)
REVERT: D   67 ASP cc_start: 0.7325 (m-30) cc_final: 0.7089 (m-30)
REVERT: D  185 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8548 (mm)
REVERT: A  169 MET cc_start: 0.9108 (ttt) cc_final: 0.8881 (ttm)
REVERT: B   29 LEU cc_start: 0.7703 (mm) cc_final: 0.7327 (mm)
REVERT: B   68 MET cc_start: 0.8604 (ptm) cc_final: 0.8037 (tmm)
REVERT: B  139 HIS cc_start: 0.8808 (OUTLIER) cc_final: 0.6724 (t70)
REVERT: B  249 MET cc_start: 0.7938 (mmm) cc_final: 0.7646 (mmm)
REVERT: E  244 TYR cc_start: 0.8067 (t80) cc_final: 0.7760 (t80)
REVERT: E  247 GLU cc_start: 0.6781 (tp30) cc_final: 0.6347 (tp30)
  outliers start: 45
  outliers final: 36
  residues processed: 178
  average time/residue: 0.0924
  time to fit residues: 24.9498
Evaluate side-chains
  177 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 138
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   44 HIS
Chi-restraints excluded: chain D residue   52 ASP
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue   75 SER
Chi-restraints excluded: chain D residue  100 TYR
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  185 LEU
Chi-restraints excluded: chain D residue  207 VAL
Chi-restraints excluded: chain D residue  258 VAL
Chi-restraints excluded: chain D residue  262 ILE
Chi-restraints excluded: chain D residue  325 ILE
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain B residue   83 ILE
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  139 HIS
Chi-restraints excluded: chain B residue  170 MET
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue  102 SER
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  235 MET
Chi-restraints excluded: chain C residue  237 THR
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain C residue  330 SER
Chi-restraints excluded: chain C residue  344 ILE
Chi-restraints excluded: chain E residue   51 LYS
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue   80 CYS
Chi-restraints excluded: chain E residue  166 PHE
Chi-restraints excluded: chain E residue  341 ARG
Chi-restraints excluded: chain E residue  344 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 32 optimal weight:   10.0000
   chunk 60 optimal weight:    0.0570
   chunk 77 optimal weight:    8.9990
   chunk 126 optimal weight:   30.0000
   chunk 61 optimal weight:    0.3980
   chunk 22 optimal weight:    5.9990
   chunk 55 optimal weight:    6.9990
   chunk 64 optimal weight:   20.0000
   chunk 66 optimal weight:   20.0000
   chunk 70 optimal weight:    5.9990
   chunk 89 optimal weight:    9.9990
   overall best weight:    3.8904

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

Flipped N/Q/H residues before XYZ refinement:
D  44 HIS
** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 174 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.136024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.105226 restraints weight = 26382.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.105695 restraints weight = 22426.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.107459 restraints weight = 16500.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.108222 restraints weight = 13187.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.108344 restraints weight = 12328.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3508
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3508 r_free = 0.3508    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3508 r_free = 0.3508    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3508
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.4808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12909  Z= 0.149
  Angle     :  0.588   8.323  17453  Z= 0.299
  Chirality :  0.040   0.272   1968
  Planarity :  0.005   0.084   2227
  Dihedral  :  3.918  26.910   1736
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 16.30 %
    Favored  : 80.63 %
  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:  0.98 (0.21), residues: 1592
  helix:  1.18 (0.16), residues: 1019
  sheet:  None (None), residues: 0
  loop : -0.17 (0.27), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B 362 
 TYR   0.040   0.001   TYR D 260 
 PHE   0.055   0.002   PHE E  78 
 TRP   0.010   0.001   TRP E 202 
 HIS   0.008   0.001   HIS D  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (12909)
  covalent geometry    : angle       0.58792 (17453)
  hydrogen bonds       : bond        0.04557 (  719)
  hydrogen bonds       : angle       4.33480 ( 2055)

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

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

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 144
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   52 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7992 (p0)
REVERT: D  185 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8485 (mm)
REVERT: A  169 MET cc_start: 0.9028 (ttt) cc_final: 0.8802 (ttm)
REVERT: A  229 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8197 (p)
REVERT: B   29 LEU cc_start: 0.7650 (mm) cc_final: 0.7282 (mm)
REVERT: B   68 MET cc_start: 0.8503 (ptm) cc_final: 0.7975 (tmm)
REVERT: B  139 HIS cc_start: 0.8731 (OUTLIER) cc_final: 0.6592 (t70)
REVERT: B  249 MET cc_start: 0.7944 (mmm) cc_final: 0.7681 (mmm)
REVERT: C  229 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8485 (t)
REVERT: E  211 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8419 (pp)
REVERT: E  244 TYR cc_start: 0.8190 (t80) cc_final: 0.7318 (t80)
  outliers start: 42
  outliers final: 33
  residues processed: 180
  average time/residue: 0.0924
  time to fit residues: 25.4017
Evaluate side-chains
  172 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 133
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   44 HIS
Chi-restraints excluded: chain D residue   52 ASP
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue   75 SER
Chi-restraints excluded: chain D residue  100 TYR
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  185 LEU
Chi-restraints excluded: chain D residue  207 VAL
Chi-restraints excluded: chain D residue  258 VAL
Chi-restraints excluded: chain D residue  325 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  139 HIS
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue  102 SER
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  235 MET
Chi-restraints excluded: chain C residue  237 THR
Chi-restraints excluded: chain C residue  252 THR
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain C residue  330 SER
Chi-restraints excluded: chain C residue  344 ILE
Chi-restraints excluded: chain E residue   51 LYS
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue   80 CYS
Chi-restraints excluded: chain E residue  166 PHE
Chi-restraints excluded: chain E residue  211 LEU
Chi-restraints excluded: chain E residue  341 ARG
Chi-restraints excluded: chain E residue  344 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 35 optimal weight:   20.0000
   chunk 74 optimal weight:    9.9990
   chunk 112 optimal weight:    6.9990
   chunk 135 optimal weight:   50.0000
   chunk 5 optimal weight:    7.9990
   chunk 91 optimal weight:    9.9990
   chunk 69 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 104 optimal weight:   30.0000
   chunk 83 optimal weight:    8.9990
   chunk 70 optimal weight:    9.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
D  44 HIS
** C  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 174 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.134235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.102633 restraints weight = 26202.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.103285 restraints weight = 22312.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.104287 restraints weight = 17193.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.105397 restraints weight = 14501.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.105330 restraints weight = 12942.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3458
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3458 r_free = 0.3458    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3458 r_free = 0.3458    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3458
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.4909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065  12909  Z= 0.198
  Angle     :  0.635   7.701  17453  Z= 0.327
  Chirality :  0.041   0.217   1968
  Planarity :  0.005   0.050   2227
  Dihedral  :  4.071  27.930   1736
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 16.89 %
    Favored  : 79.82 %
  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:  0.85 (0.21), residues: 1592
  helix:  1.05 (0.16), residues: 1020
  sheet:  None (None), residues: 0
  loop : -0.17 (0.27), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 362 
 TYR   0.051   0.002   TYR E 260 
 PHE   0.050   0.002   PHE E  78 
 TRP   0.011   0.002   TRP E 196 
 HIS   0.008   0.001   HIS D  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 (12909)
  covalent geometry    : angle       0.63483 (17453)
  hydrogen bonds       : bond        0.04994 (  719)
  hydrogen bonds       : angle       4.51891 ( 2055)

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

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

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 139
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   52 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.8029 (p0)
REVERT: D  185 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8507 (mm)
REVERT: D  370 ASN cc_start: 0.8588 (t0) cc_final: 0.7238 (p0)
REVERT: A  169 MET cc_start: 0.9110 (ttt) cc_final: 0.8888 (ttm)
REVERT: A  229 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8189 (p)
REVERT: B   29 LEU cc_start: 0.7727 (mm) cc_final: 0.7362 (mm)
REVERT: B   68 MET cc_start: 0.8638 (ptm) cc_final: 0.8093 (tmm)
REVERT: E  211 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8385 (pp)
REVERT: E  235 MET cc_start: 0.8902 (mmm) cc_final: 0.8553 (mmm)
  outliers start: 45
  outliers final: 40
  residues processed: 177
  average time/residue: 0.0927
  time to fit residues: 25.3456
Evaluate side-chains
  178 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 134
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   44 HIS
Chi-restraints excluded: chain D residue   52 ASP
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue   75 SER
Chi-restraints excluded: chain D residue  100 TYR
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  185 LEU
Chi-restraints excluded: chain D residue  207 VAL
Chi-restraints excluded: chain D residue  252 THR
Chi-restraints excluded: chain D residue  258 VAL
Chi-restraints excluded: chain D residue  262 ILE
Chi-restraints excluded: chain D residue  325 ILE
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  139 HIS
Chi-restraints excluded: chain B residue  170 MET
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue  102 SER
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  207 VAL
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  235 MET
Chi-restraints excluded: chain C residue  237 THR
Chi-restraints excluded: chain C residue  252 THR
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain C residue  330 SER
Chi-restraints excluded: chain C residue  344 ILE
Chi-restraints excluded: chain E residue   51 LYS
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue   80 CYS
Chi-restraints excluded: chain E residue  166 PHE
Chi-restraints excluded: chain E residue  211 LEU
Chi-restraints excluded: chain E residue  341 ARG
Chi-restraints excluded: chain E residue  344 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 117 optimal weight:    0.9990
   chunk 27 optimal weight:    9.9990
   chunk 135 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:   30.0000
   chunk 66 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9990
   chunk 137 optimal weight:   40.0000
   chunk 54 optimal weight:    9.9990
   chunk 83 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
D  44 HIS
** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 174 ASN
E 198 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.139409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.111197 restraints weight = 26139.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.110938 restraints weight = 21426.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.112252 restraints weight = 16840.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.112612 restraints weight = 14682.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.112782 restraints weight = 13801.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3576
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3576 r_free = 0.3576    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3576 r_free = 0.3576    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3576
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.5100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  12909  Z= 0.115
  Angle     :  0.585   8.906  17453  Z= 0.294
  Chirality :  0.039   0.184   1968
  Planarity :  0.004   0.047   2227
  Dihedral  :  3.755  23.766   1736
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 18.42 %
    Favored  : 79.53 %
  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:  1.21 (0.21), residues: 1592
  helix:  1.31 (0.16), residues: 1022
  sheet:  None (None), residues: 0
  loop :  0.01 (0.28), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 362 
 TYR   0.045   0.001   TYR E 260 
 PHE   0.047   0.002   PHE E  78 
 TRP   0.015   0.001   TRP E 202 
 HIS   0.013   0.001   HIS D  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 (12909)
  covalent geometry    : angle       0.58531 (17453)
  hydrogen bonds       : bond        0.03900 (  719)
  hydrogen bonds       : angle       4.18755 ( 2055)

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

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

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 164
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  153 SER cc_start: 0.7606 (p) cc_final: 0.7221 (t)
REVERT: D  341 ARG cc_start: 0.8351 (mmm160) cc_final: 0.8040 (mmm160)
REVERT: D  370 ASN cc_start: 0.8462 (t0) cc_final: 0.7281 (p0)
REVERT: A  169 MET cc_start: 0.8829 (ttt) cc_final: 0.8594 (ttm)
REVERT: A  223 MET cc_start: 0.6754 (mmp) cc_final: 0.6434 (mtm)
REVERT: A  229 VAL cc_start: 0.8324 (OUTLIER) cc_final: 0.8085 (p)
REVERT: B   29 LEU cc_start: 0.7554 (mm) cc_final: 0.7133 (mm)
REVERT: B   68 MET cc_start: 0.8214 (ptm) cc_final: 0.7802 (tmm)
REVERT: B  361 MET cc_start: 0.8629 (mmp) cc_final: 0.8322 (mmp)
REVERT: E  211 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8482 (pp)
REVERT: E  235 MET cc_start: 0.8836 (mmm) cc_final: 0.8573 (mmm)
  outliers start: 28
  outliers final: 19
  residues processed: 187
  average time/residue: 0.0966
  time to fit residues: 27.3777
Evaluate side-chains
  166 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 145
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   44 HIS
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  100 TYR
Chi-restraints excluded: chain D residue  252 THR
Chi-restraints excluded: chain D residue  258 VAL
Chi-restraints excluded: chain D residue  325 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue  102 SER
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain C residue  330 SER
Chi-restraints excluded: chain C residue  344 ILE
Chi-restraints excluded: chain E residue   80 CYS
Chi-restraints excluded: chain E residue  166 PHE
Chi-restraints excluded: chain E residue  211 LEU
Chi-restraints excluded: chain E residue  341 ARG
Chi-restraints excluded: chain E residue  344 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 89 optimal weight:   10.0000
   chunk 109 optimal weight:    7.9990
   chunk 77 optimal weight:    6.9990
   chunk 129 optimal weight:   50.0000
   chunk 117 optimal weight:    8.9990
   chunk 156 optimal weight:   20.0000
   chunk 21 optimal weight:   10.0000
   chunk 106 optimal weight:   10.0000
   chunk 55 optimal weight:    2.9990
   chunk 67 optimal weight:    9.9990
   chunk 15 optimal weight:    0.4980
   overall best weight:    5.4988

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

Flipped N/Q/H residues before XYZ refinement:
D  44 HIS
A 178 HIS
** C  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 174 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.135159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.105570 restraints weight = 26834.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.105758 restraints weight = 21663.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.106851 restraints weight = 19158.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.107735 restraints weight = 14756.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.107972 restraints weight = 13209.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3504
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3504 r_free = 0.3504    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3504 r_free = 0.3504    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3504
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.5139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  12909  Z= 0.191
  Angle     :  0.674  11.695  17453  Z= 0.344
  Chirality :  0.042   0.237   1968
  Planarity :  0.005   0.052   2227
  Dihedral  :  3.918  19.225   1735
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 19.01 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.94 (0.21), residues: 1592
  helix:  1.08 (0.16), residues: 1021
  sheet:  None (None), residues: 0
  loop : -0.06 (0.28), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 362 
 TYR   0.046   0.002   TYR E 260 
 PHE   0.082   0.002   PHE E  78 
 TRP   0.024   0.002   TRP E 196 
 HIS   0.011   0.001   HIS D 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 (12909)
  covalent geometry    : angle       0.67389 (17453)
  hydrogen bonds       : bond        0.04798 (  719)
  hydrogen bonds       : angle       4.48362 ( 2055)

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

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

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 139
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  370 ASN cc_start: 0.8602 (t0) cc_final: 0.7293 (p0)
REVERT: A  229 VAL cc_start: 0.8404 (OUTLIER) cc_final: 0.8121 (p)
REVERT: B   29 LEU cc_start: 0.7566 (mm) cc_final: 0.7226 (mm)
REVERT: B   68 MET cc_start: 0.8523 (ptm) cc_final: 0.8019 (tmm)
REVERT: B  361 MET cc_start: 0.8708 (mmp) cc_final: 0.8415 (mmp)
  outliers start: 25
  outliers final: 21
  residues processed: 158
  average time/residue: 0.0829
  time to fit residues: 20.7886
Evaluate side-chains
  156 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 134
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   44 HIS
Chi-restraints excluded: chain D residue  100 TYR
Chi-restraints excluded: chain D residue  252 THR
Chi-restraints excluded: chain D residue  258 VAL
Chi-restraints excluded: chain D residue  325 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  170 MET
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue  102 SER
Chi-restraints excluded: chain C residue  235 MET
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain C residue  330 SER
Chi-restraints excluded: chain C residue  344 ILE
Chi-restraints excluded: chain E residue   51 LYS
Chi-restraints excluded: chain E residue  166 PHE
Chi-restraints excluded: chain E residue  211 LEU
Chi-restraints excluded: chain E residue  344 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 70 optimal weight:    0.0570
   chunk 33 optimal weight:    5.9990
   chunk 124 optimal weight:   20.0000
   chunk 95 optimal weight:    6.9990
   chunk 20 optimal weight:   10.0000
   chunk 80 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 15 optimal weight:    7.9990
   chunk 11 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 101 optimal weight:    0.9990
   overall best weight:    2.6106

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

Flipped N/Q/H residues before XYZ refinement:
D  44 HIS
C  87 HIS
** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 174 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.137761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.107014 restraints weight = 26867.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.107650 restraints weight = 21349.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.109338 restraints weight = 16171.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.109939 restraints weight = 13586.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.110223 restraints weight = 12383.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3536
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3536 r_free = 0.3536    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3536 r_free = 0.3536    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3536
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.5240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12909  Z= 0.135
  Angle     :  0.634  10.924  17453  Z= 0.321
  Chirality :  0.040   0.205   1968
  Planarity :  0.004   0.052   2227
  Dihedral  :  3.834  23.193   1735
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 19.96 %
    Favored  : 78.73 %
  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:  1.02 (0.21), residues: 1592
  helix:  1.12 (0.16), residues: 1022
  sheet:  None (None), residues: 0
  loop :  0.01 (0.28), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 362 
 TYR   0.044   0.001   TYR E 260 
 PHE   0.078   0.002   PHE E  78 
 TRP   0.022   0.002   TRP E 196 
 HIS   0.012   0.001   HIS D 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (12909)
  covalent geometry    : angle       0.63376 (17453)
  hydrogen bonds       : bond        0.04266 (  719)
  hydrogen bonds       : angle       4.34344 ( 2055)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1741.88 seconds
wall clock time: 30 minutes 59.69 seconds (1859.69 seconds total)