Starting phenix.real_space_refine
on Tue Feb  3 18:57:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9x8x_66658/02_2026/9x8x_66658.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9x8x_66658/02_2026/9x8x_66658.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9x8x_66658/02_2026/9x8x_66658.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9x8x_66658/02_2026/9x8x_66658.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9x8x_66658/02_2026/9x8x_66658.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9x8x_66658/02_2026/9x8x_66658.cif"
  }
  resolution = 2.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.056
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      40      5.16       5
     C    4156      2.51       5
     N    1010      2.21       5
     O    1122      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6330
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 414, 3160
          Classifications: {'peptide': 414}
          Link IDs: {'PTRANS': 15, 'TRANS': 398}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 3160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 414, 3160
          Classifications: {'peptide': 414}
          Link IDs: {'PTRANS': 15, 'TRANS': 398}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 5
          Unusual residues: {'PO4': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 5
          Unusual residues: {'PO4': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.20, per 1000 atoms: 0.19
  Number of scatterers: 6330
  At special positions: 0
  Unit cell: (76.632, 94.76, 73.336, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      40     16.00
     P       2     15.00
     O    1122      8.00
     N    1010      7.00
     C    4156      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: 0.63
  Conformation dependent library (CDL) restraints added in 176.7 milliseconds
  

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1492

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 0 sheets defined
      74.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 19
    Processing helix  chain 'A' and resid 21 through 29
    Processing helix  chain 'A' and resid 29 through 42
      removed outlier: 3.561A  pdb=" N   VAL A  34 " --> pdb=" O   THR A  30 " (cutoff:3.500A)
      Proline residue:  A  36  - end of helix
      removed outlier: 3.589A  pdb=" N   GLU A  40 " --> pdb=" O   PRO A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 64
      removed outlier: 3.606A  pdb=" N   GLN A  56 " --> pdb=" O   ILE A  52 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE A  62 " --> pdb=" O   ALA A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 82
      removed outlier: 3.561A  pdb=" N   SER A  81 " --> pdb=" O   ARG A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 93
      removed outlier: 3.561A  pdb=" N   ASN A  91 " --> pdb=" O   VAL A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 115
      removed outlier: 3.842A  pdb=" N   GLY A 115 " --> pdb=" O   GLY A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 129
      removed outlier: 3.872A  pdb=" N   VAL A 124 " --> pdb=" O   PRO A 120 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   LYS A 127 " --> pdb=" O   LYS A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 142
    Processing helix  chain 'A' and resid 143 through 156
      Proline residue:  A 153  - end of helix
    Processing helix  chain 'A' and resid 164 through 185
      removed outlier: 3.894A  pdb=" N   PHE A 181 " --> pdb=" O   VAL A 177 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU A 182 " --> pdb=" O   VAL A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 221
    Processing helix  chain 'A' and resid 225 through 247
      removed outlier: 3.627A  pdb=" N   THR A 231 " --> pdb=" O   TRP A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 291
      removed outlier: 3.587A  pdb=" N   MET A 266 " --> pdb=" O   GLY A 262 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ILE A 278 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   GLY A 281 " --> pdb=" O   SER A 277 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LEU A 283 " --> pdb=" O   ALA A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 321
      removed outlier: 3.526A  pdb=" N   VAL A 313 " --> pdb=" O   ALA A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 349
      removed outlier: 3.536A  pdb=" N   ILE A 331 " --> pdb=" O   PRO A 327 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   PHE A 338 " --> pdb=" O   LEU A 334 " (cutoff:3.500A)
      Proline residue:  A 345  - end of helix
    Processing helix  chain 'A' and resid 351 through 357
      removed outlier: 3.622A  pdb=" N   GLU A 355 " --> pdb=" O   VAL A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 380
      removed outlier: 3.941A  pdb=" N   ASN A 374 " --> pdb=" O   GLY A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 391
    Processing helix  chain 'A' and resid 395 through 414
      removed outlier: 3.629A  pdb=" N   VAL A 399 " --> pdb=" O   THR A 395 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLU A 401 " --> pdb=" O   PHE A 397 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   PHE A 412 " --> pdb=" O   THR A 408 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 19
      removed outlier: 3.502A  pdb=" N   TYR C   9 " --> pdb=" O   GLY C   5 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   PHE C  14 " --> pdb=" O   ARG C  10 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA C  16 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 21 through 27
    Processing helix  chain 'C' and resid 29 through 34
      removed outlier: 3.597A  pdb=" N   VAL C  34 " --> pdb=" O   THR C  30 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 34 through 42
      removed outlier: 3.771A  pdb=" N   GLU C  40 " --> pdb=" O   PRO C  36 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLU C  41 " --> pdb=" O   SER C  37 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 62
      removed outlier: 3.671A  pdb=" N   GLN C  56 " --> pdb=" O   ILE C  52 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ILE C  62 " --> pdb=" O   ALA C  58 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 75 through 82
      removed outlier: 3.572A  pdb=" N   SER C  81 " --> pdb=" O   ARG C  77 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 83 through 93
      removed outlier: 3.601A  pdb=" N   ASN C  91 " --> pdb=" O   VAL C  87 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ILE C  92 " --> pdb=" O   GLY C  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 99 through 113
    Processing helix  chain 'C' and resid 118 through 129
      removed outlier: 3.903A  pdb=" N   VAL C 124 " --> pdb=" O   PRO C 120 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ARG C 126 " --> pdb=" O   GLY C 122 " (cutoff:3.500A)
      removed outlier: 4.986A  pdb=" N   LYS C 127 " --> pdb=" O   LYS C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 137 through 142
      removed outlier: 3.550A  pdb=" N   SER C 142 " --> pdb=" O   TRP C 138 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 143 through 156
      removed outlier: 3.661A  pdb=" N   GLY C 150 " --> pdb=" O   ASN C 146 " (cutoff:3.500A)
      Proline residue:  C 153  - end of helix
    Processing helix  chain 'C' and resid 157 through 161
      removed outlier: 3.681A  pdb=" N   GLN C 161 " --> pdb=" O   ILE C 158 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 164 through 185
      removed outlier: 3.750A  pdb=" N   LEU C 175 " --> pdb=" O   LEU C 171 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   CYS C 176 " --> pdb=" O   SER C 172 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   PHE C 181 " --> pdb=" O   VAL C 177 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 216 through 221
    Processing helix  chain 'C' and resid 230 through 246
    Processing helix  chain 'C' and resid 246 through 254
      removed outlier: 4.032A  pdb=" N   PHE C 250 " --> pdb=" O   TRP C 246 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU C 251 " --> pdb=" O   GLY C 247 " (cutoff:3.500A)
      removed outlier: 5.159A  pdb=" N   ILE C 252 " --> pdb=" O   GLN C 248 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 260 through 291
      removed outlier: 3.773A  pdb=" N   GLU C 270 " --> pdb=" O   MET C 266 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   VAL C 275 " --> pdb=" O   VAL C 271 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   GLY C 281 " --> pdb=" O   SER C 277 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU C 283 " --> pdb=" O   ALA C 279 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ALA C 287 " --> pdb=" O   LEU C 283 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 301 through 321
      removed outlier: 3.576A  pdb=" N   THR C 312 " --> pdb=" O   MET C 308 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   VAL C 313 " --> pdb=" O   ALA C 309 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 327 through 347
      removed outlier: 3.560A  pdb=" N   ILE C 331 " --> pdb=" O   PRO C 327 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   PHE C 338 " --> pdb=" O   LEU C 334 " (cutoff:3.500A)
      Proline residue:  C 345  - end of helix
    Processing helix  chain 'C' and resid 350 through 357
    Processing helix  chain 'C' and resid 368 through 380
      removed outlier: 3.962A  pdb=" N   ASN C 374 " --> pdb=" O   GLY C 370 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 381 through 391
      removed outlier: 3.624A  pdb=" N   ILE C 387 " --> pdb=" O   PRO C 383 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 395 through 411
      removed outlier: 3.623A  pdb=" N   VAL C 399 " --> pdb=" O   THR C 395 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLU C 401 " --> pdb=" O   PHE C 397 " (cutoff:3.500A)

    368 hydrogen bonds defined for protein.
    1101 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.89

  Time building geometry restraints manager: 0.77 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 957
        1.32 -     1.44: 1929
        1.44 -     1.56: 3550
        1.56 -     1.69: 0
        1.69 -     1.81: 66
  Bond restraints: 6502
  Sorted by residual:
  bond pdb=" CA  SER A 223 "
       pdb=" C   SER A 223 "
    ideal  model  delta    sigma   weight residual
    1.525  1.482  0.043 1.13e-02 7.83e+03 1.42e+01
  bond pdb=" CA  TYR A 225 "
       pdb=" C   TYR A 225 "
    ideal  model  delta    sigma   weight residual
    1.522  1.475  0.047 1.32e-02 5.74e+03 1.25e+01
  bond pdb=" C   TYR A 225 "
       pdb=" N   LEU A 226 "
    ideal  model  delta    sigma   weight residual
    1.335  1.291  0.044 1.31e-02 5.83e+03 1.14e+01
  bond pdb=" C   GLY A 173 "
       pdb=" O   GLY A 173 "
    ideal  model  delta    sigma   weight residual
    1.234  1.197  0.037 1.19e-02 7.06e+03 9.83e+00
  bond pdb=" O3  PO4 A 501 "
       pdb=" P   PO4 A 501 "
    ideal  model  delta    sigma   weight residual
    1.569  1.509  0.060 2.00e-02 2.50e+03 9.02e+00
  ... (remaining 6497 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 8262
        1.67 -     3.33: 502
        3.33 -     5.00: 67
        5.00 -     6.66: 11
        6.66 -     8.33: 4
  Bond angle restraints: 8846
  Sorted by residual:
  angle pdb=" CA  VAL A 100 "
        pdb=" C   VAL A 100 "
        pdb=" N   PRO A 101 "
      ideal   model   delta    sigma   weight residual
     120.83  123.91   -3.08 5.90e-01 2.87e+00 2.73e+01
  angle pdb=" N   TYR A 225 "
        pdb=" CA  TYR A 225 "
        pdb=" C   TYR A 225 "
      ideal   model   delta    sigma   weight residual
     113.50  107.81    5.69 1.23e+00 6.61e-01 2.14e+01
  angle pdb=" N   VAL A 100 "
        pdb=" CA  VAL A 100 "
        pdb=" CB  VAL A 100 "
      ideal   model   delta    sigma   weight residual
     110.52  113.52   -3.00 6.70e-01 2.23e+00 2.01e+01
  angle pdb=" N   ILE A 368 "
        pdb=" CA  ILE A 368 "
        pdb=" C   ILE A 368 "
      ideal   model   delta    sigma   weight residual
     111.45  107.75    3.70 9.30e-01 1.16e+00 1.58e+01
  angle pdb=" N   TRP A 137 "
        pdb=" CA  TRP A 137 "
        pdb=" C   TRP A 137 "
      ideal   model   delta    sigma   weight residual
     113.88  109.19    4.69 1.23e+00 6.61e-01 1.45e+01
  ... (remaining 8841 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.70: 2983
       14.70 -    29.39: 465
       29.39 -    44.09: 174
       44.09 -    58.78: 59
       58.78 -    73.48: 9
  Dihedral angle restraints: 3690
    sinusoidal: 1342
      harmonic: 2348
  Sorted by residual:
  dihedral pdb=" CA  GLY A 247 "
           pdb=" C   GLY A 247 "
           pdb=" N   GLN A 248 "
           pdb=" CA  GLN A 248 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.56   19.44     0      5.00e+00 4.00e-02 1.51e+01
  dihedral pdb=" CA  ASN C  27 "
           pdb=" C   ASN C  27 "
           pdb=" N   ARG C  28 "
           pdb=" CA  ARG C  28 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.71   17.29     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CA  ASP A 193 "
           pdb=" CB  ASP A 193 "
           pdb=" CG  ASP A 193 "
           pdb=" OD1 ASP A 193 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.31   57.31     1      2.00e+01 2.50e-03 1.10e+01
  ... (remaining 3687 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 877
       0.062 -    0.123: 109
       0.123 -    0.185: 9
       0.185 -    0.247: 2
       0.247 -    0.308: 1
  Chirality restraints: 998
  Sorted by residual:
  chirality pdb=" CB  VAL C 351 "
            pdb=" CA  VAL C 351 "
            pdb=" CG1 VAL C 351 "
            pdb=" CG2 VAL C 351 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.31 2.00e-01 2.50e+01 2.38e+00
  chirality pdb=" CB  VAL A 351 "
            pdb=" CA  VAL A 351 "
            pdb=" CG1 VAL A 351 "
            pdb=" CG2 VAL A 351 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CA  ARG A  28 "
            pdb=" N   ARG A  28 "
            pdb=" C   ARG A  28 "
            pdb=" CB  ARG A  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.13e+00
  ... (remaining 995 not shown)

  Planarity restraints: 1084
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 249 "    0.012 2.00e-02 2.50e+03   2.37e-02 5.64e+00
        pdb=" C   PHE A 249 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   PHE A 249 "    0.015 2.00e-02 2.50e+03
        pdb=" N   PHE A 250 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 135 "    0.012 2.00e-02 2.50e+03   2.34e-02 5.50e+00
        pdb=" C   GLY A 135 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   GLY A 135 "    0.015 2.00e-02 2.50e+03
        pdb=" N   THR A 136 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 118 "   -0.037 5.00e-02 4.00e+02   5.62e-02 5.06e+00
        pdb=" N   PRO A 119 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO A 119 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 119 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1081 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 485
        2.74 -     3.28: 6389
        3.28 -     3.82: 10819
        3.82 -     4.36: 14214
        4.36 -     4.90: 22973
  Nonbonded interactions: 54880
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C   6 "
            pdb=" O   ARG C 197 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" ND2 ASN C  27 "
            pdb=" OG  SER C 172 "
     model   vdw
     2.230 3.120
  nonbonded pdb=" O   LEU A 382 "
            pdb=" OG1 THR A 386 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   TYR A  24 "
            pdb=" NE2 GLN A 114 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" O   LEU C 382 "
            pdb=" OG1 THR C 386 "
     model   vdw
     2.266 3.040
  ... (remaining 54875 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.130
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.550
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
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      :  0.005   0.060   6502  Z= 0.286
  Angle     :  0.879   8.327   8846  Z= 0.582
  Chirality :  0.043   0.308    998
  Planarity :  0.006   0.066   1084
  Dihedral  : 17.925  73.479   2198
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.76 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 30.63 %
    Favored  : 63.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.47 (0.25), residues: 820
  helix: -2.61 (0.17), residues: 692
  sheet:  None (None), residues: 0
  loop : -3.40 (0.49), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 415 
 TYR   0.011   0.001   TYR A  24 
 PHE   0.021   0.002   PHE C 134 
 TRP   0.021   0.001   TRP C 107 
 HIS   0.003   0.001   HIS C 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 6502)
  covalent geometry    : angle       0.87860 ( 8846)
  hydrogen bonds       : bond        0.26554 (  368)
  hydrogen bonds       : angle      10.10260 ( 1101)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 102
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A  329 LEU cc_start: 0.8419 (tp) cc_final: 0.8179 (tp)
REVERT: C    1 MET cc_start: 0.3674 (pmm) cc_final: 0.2673 (mtm)
REVERT: C  365 SER cc_start: 0.8597 (t) cc_final: 0.8285 (m)
  outliers start: 40
  outliers final: 31
  residues processed: 138
  average time/residue: 0.2950
  time to fit residues: 43.7114
Evaluate side-chains
  128 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 97
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 TYR
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue  107 TRP
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  294 SER
Chi-restraints excluded: chain A residue  295 ASN
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain C residue    6 TYR
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  144 SER
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  215 SER
Chi-restraints excluded: chain C residue  267 SER
Chi-restraints excluded: chain C residue  277 SER
Chi-restraints excluded: chain C residue  294 SER
Chi-restraints excluded: chain C residue  295 ASN
Chi-restraints excluded: chain C residue  392 SER
Chi-restraints excluded: chain C residue  407 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0670
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.6718

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

Flipped N/Q/H residues before XYZ refinement:
** A  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 ASN
C 354 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.163065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.123940 restraints weight = 6898.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 1.70
r_work: 0.3291 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3159 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.1230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6502  Z= 0.137
  Angle     :  0.619   8.859   8846  Z= 0.319
  Chirality :  0.039   0.299    998
  Planarity :  0.006   0.051   1084
  Dihedral  :  8.098  59.416    922
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 29.43 %
    Favored  : 65.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.14 (0.26), residues: 820
  helix: -1.64 (0.18), residues: 690
  sheet:  None (None), residues: 0
  loop : -3.38 (0.48), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 415 
 TYR   0.013   0.001   TYR A  24 
 PHE   0.008   0.001   PHE C 250 
 TRP   0.009   0.001   TRP C 107 
 HIS   0.003   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6502)
  covalent geometry    : angle       0.61916 ( 8846)
  hydrogen bonds       : bond        0.04631 (  368)
  hydrogen bonds       : angle       5.21345 ( 1101)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 101
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A   17 MET cc_start: 0.8464 (mtm) cc_final: 0.8016 (mtt)
REVERT: A   40 GLU cc_start: 0.8498 (tt0) cc_final: 0.7932 (tp30)
REVERT: A  107 TRP cc_start: 0.9014 (OUTLIER) cc_final: 0.7306 (m-90)
REVERT: A  143 THR cc_start: 0.7951 (OUTLIER) cc_final: 0.7657 (m)
REVERT: A  270 GLU cc_start: 0.8232 (mm-30) cc_final: 0.8013 (tp30)
REVERT: A  329 LEU cc_start: 0.8182 (tp) cc_final: 0.7954 (tp)
REVERT: A  365 SER cc_start: 0.8772 (t) cc_final: 0.8448 (m)
REVERT: A  415 ARG cc_start: 0.7145 (ttp-110) cc_final: 0.6718 (ttm110)
REVERT: C    1 MET cc_start: 0.3057 (pmm) cc_final: 0.2737 (mtm)
REVERT: C  107 TRP cc_start: 0.9000 (OUTLIER) cc_final: 0.7746 (m-90)
REVERT: C  298 ASN cc_start: 0.6374 (OUTLIER) cc_final: 0.6136 (m110)
REVERT: C  365 SER cc_start: 0.8641 (t) cc_final: 0.8327 (m)
  outliers start: 31
  outliers final: 9
  residues processed: 125
  average time/residue: 0.3059
  time to fit residues: 41.1823
Evaluate side-chains
  109 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue  107 TRP
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain C residue  107 TRP
Chi-restraints excluded: chain C residue  199 LEU
Chi-restraints excluded: chain C residue  298 ASN
Chi-restraints excluded: chain C residue  407 SER
Chi-restraints excluded: chain C residue  424 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   chunk 50 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 31 optimal weight:    6.9990
   chunk 15 optimal weight:    0.0770
   chunk 19 optimal weight:    9.9990
   chunk 55 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.7338

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

Flipped N/Q/H residues before XYZ refinement:
C 354 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.152794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.110638 restraints weight = 7041.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3075 rms_B_bonded: 1.76
r_work: 0.2944 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2809 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.1639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6502  Z= 0.129
  Angle     :  0.572  12.573   8846  Z= 0.292
  Chirality :  0.039   0.320    998
  Planarity :  0.005   0.051   1084
  Dihedral  :  6.368  58.934    891
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 29.73 %
    Favored  : 67.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.21 (0.28), residues: 820
  helix: -1.01 (0.19), residues: 684
  sheet:  None (None), residues: 0
  loop : -2.96 (0.49), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 300 
 TYR   0.012   0.001   TYR C  24 
 PHE   0.013   0.001   PHE A 134 
 TRP   0.008   0.001   TRP C 107 
 HIS   0.001   0.000   HIS C 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6502)
  covalent geometry    : angle       0.57214 ( 8846)
  hydrogen bonds       : bond        0.03753 (  368)
  hydrogen bonds       : angle       4.73256 ( 1101)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A   17 MET cc_start: 0.8362 (mtm) cc_final: 0.7881 (mtt)
REVERT: A  107 TRP cc_start: 0.8993 (OUTLIER) cc_final: 0.7504 (m-90)
REVERT: A  365 SER cc_start: 0.8683 (t) cc_final: 0.8391 (m)
REVERT: A  415 ARG cc_start: 0.6959 (ttp-110) cc_final: 0.6455 (ttm110)
REVERT: C  365 SER cc_start: 0.8581 (t) cc_final: 0.8283 (m)
  outliers start: 18
  outliers final: 8
  residues processed: 108
  average time/residue: 0.2893
  time to fit residues: 33.5585
Evaluate side-chains
  100 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 TRP
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain C residue    6 TYR
Chi-restraints excluded: chain C residue  107 TRP
Chi-restraints excluded: chain C residue  199 LEU
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  407 SER
Chi-restraints excluded: chain C residue  424 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    8.9990
   chunk 71 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 75 optimal weight:    0.0370
   chunk 8 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0000
   chunk 40 optimal weight:    7.9990
   overall best weight:    1.0066

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

Flipped N/Q/H residues before XYZ refinement:
A 374 ASN
C 354 ASN
C 374 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.148778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.105667 restraints weight = 7070.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 1.75
r_work: 0.2919 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2785 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6502  Z= 0.137
  Angle     :  0.557  13.191   8846  Z= 0.281
  Chirality :  0.040   0.301    998
  Planarity :  0.005   0.050   1084
  Dihedral  :  6.080  58.172    886
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 27.93 %
    Favored  : 68.47 %
  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: -1.63 (0.28), residues: 820
  helix: -0.61 (0.19), residues: 682
  sheet:  None (None), residues: 0
  loop : -2.78 (0.48), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 418 
 TYR   0.014   0.001   TYR C  24 
 PHE   0.012   0.001   PHE A 134 
 TRP   0.009   0.001   TRP C 107 
 HIS   0.002   0.000   HIS C 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6502)
  covalent geometry    : angle       0.55672 ( 8846)
  hydrogen bonds       : bond        0.03598 (  368)
  hydrogen bonds       : angle       4.46990 ( 1101)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A   17 MET cc_start: 0.8342 (mtm) cc_final: 0.7804 (mtt)
REVERT: A  107 TRP cc_start: 0.8974 (OUTLIER) cc_final: 0.7327 (m-90)
REVERT: A  143 THR cc_start: 0.7529 (OUTLIER) cc_final: 0.7313 (m)
REVERT: A  300 ARG cc_start: 0.6466 (OUTLIER) cc_final: 0.5007 (mtp180)
REVERT: A  365 SER cc_start: 0.8638 (t) cc_final: 0.8332 (m)
REVERT: A  415 ARG cc_start: 0.6873 (ttp-110) cc_final: 0.6355 (ttm110)
REVERT: A  420 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.6728 (mptt)
REVERT: C  365 SER cc_start: 0.8509 (t) cc_final: 0.8190 (m)
  outliers start: 24
  outliers final: 11
  residues processed: 117
  average time/residue: 0.2958
  time to fit residues: 37.2296
Evaluate side-chains
  109 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue  107 TRP
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  326 SER
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  420 LYS
Chi-restraints excluded: chain C residue    6 TYR
Chi-restraints excluded: chain C residue  107 TRP
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  326 SER
Chi-restraints excluded: chain C residue  407 SER
Chi-restraints excluded: chain C residue  424 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 28 optimal weight:    9.9990
   chunk 38 optimal weight:    0.9990
   chunk 33 optimal weight:    0.2980
   chunk 72 optimal weight:    7.9990
   chunk 67 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 80 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 13 optimal weight:    0.3980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
A 374 ASN
C 354 ASN
C 374 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.146803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.102801 restraints weight = 7203.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3040 rms_B_bonded: 1.79
r_work: 0.2910 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2774 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6502  Z= 0.130
  Angle     :  0.545  12.486   8846  Z= 0.276
  Chirality :  0.040   0.276    998
  Planarity :  0.005   0.049   1084
  Dihedral  :  5.505  57.721    884
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 28.08 %
    Favored  : 68.32 %
  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: -1.25 (0.29), residues: 820
  helix: -0.36 (0.20), residues: 682
  sheet:  None (None), residues: 0
  loop : -2.58 (0.48), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 418 
 TYR   0.012   0.001   TYR C  24 
 PHE   0.010   0.001   PHE A 134 
 TRP   0.009   0.001   TRP C 107 
 HIS   0.002   0.000   HIS C 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6502)
  covalent geometry    : angle       0.54456 ( 8846)
  hydrogen bonds       : bond        0.03452 (  368)
  hydrogen bonds       : angle       4.34493 ( 1101)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A   17 MET cc_start: 0.8293 (mtm) cc_final: 0.7798 (mtt)
REVERT: A  107 TRP cc_start: 0.8986 (OUTLIER) cc_final: 0.7379 (m-90)
REVERT: A  300 ARG cc_start: 0.6449 (OUTLIER) cc_final: 0.5016 (mtp180)
REVERT: A  365 SER cc_start: 0.8655 (t) cc_final: 0.8288 (m)
REVERT: A  415 ARG cc_start: 0.6792 (ttp-110) cc_final: 0.6291 (ttm110)
REVERT: A  420 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.6677 (mptt)
REVERT: C  365 SER cc_start: 0.8549 (t) cc_final: 0.8164 (m)
REVERT: C  420 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.6744 (mptt)
  outliers start: 24
  outliers final: 11
  residues processed: 114
  average time/residue: 0.3161
  time to fit residues: 38.8299
Evaluate side-chains
  107 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue  107 TRP
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  326 SER
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  420 LYS
Chi-restraints excluded: chain C residue    6 TYR
Chi-restraints excluded: chain C residue  107 TRP
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  326 SER
Chi-restraints excluded: chain C residue  407 SER
Chi-restraints excluded: chain C residue  420 LYS
Chi-restraints excluded: chain C residue  424 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 31 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0370
   chunk 14 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 76 optimal weight:    5.9990
   chunk 79 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0000
   overall best weight:    0.5062

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

Flipped N/Q/H residues before XYZ refinement:
A 374 ASN
C 354 ASN
C 374 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.148770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.104936 restraints weight = 7129.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3077 rms_B_bonded: 1.74
r_work: 0.2949 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2812 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.2174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6502  Z= 0.106
  Angle     :  0.517  12.459   8846  Z= 0.262
  Chirality :  0.038   0.264    998
  Planarity :  0.005   0.049   1084
  Dihedral  :  5.109  56.810    883
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 27.78 %
    Favored  : 68.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.93 (0.29), residues: 820
  helix: -0.11 (0.20), residues: 684
  sheet:  None (None), residues: 0
  loop : -2.69 (0.48), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 418 
 TYR   0.010   0.001   TYR C  24 
 PHE   0.011   0.001   PHE C 340 
 TRP   0.008   0.001   TRP C 107 
 HIS   0.002   0.000   HIS C 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 6502)
  covalent geometry    : angle       0.51702 ( 8846)
  hydrogen bonds       : bond        0.03148 (  368)
  hydrogen bonds       : angle       4.17046 ( 1101)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A   17 MET cc_start: 0.8216 (mtm) cc_final: 0.7727 (mtp)
REVERT: A  107 TRP cc_start: 0.8943 (OUTLIER) cc_final: 0.7433 (m-90)
REVERT: A  143 THR cc_start: 0.7478 (OUTLIER) cc_final: 0.7262 (m)
REVERT: A  365 SER cc_start: 0.8607 (t) cc_final: 0.8232 (m)
REVERT: A  415 ARG cc_start: 0.6627 (ttp-110) cc_final: 0.6216 (ttm110)
REVERT: A  420 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.6655 (mptt)
REVERT: C  107 TRP cc_start: 0.8942 (OUTLIER) cc_final: 0.7446 (m-90)
REVERT: C  197 ARG cc_start: 0.5927 (ttp80) cc_final: 0.5712 (ttp80)
REVERT: C  278 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.6967 (mp)
REVERT: C  329 LEU cc_start: 0.8017 (tp) cc_final: 0.7727 (mm)
REVERT: C  365 SER cc_start: 0.8503 (t) cc_final: 0.8118 (m)
REVERT: C  420 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.6677 (mptt)
  outliers start: 24
  outliers final: 8
  residues processed: 114
  average time/residue: 0.3272
  time to fit residues: 40.0516
Evaluate side-chains
  105 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue  107 TRP
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  326 SER
Chi-restraints excluded: chain A residue  420 LYS
Chi-restraints excluded: chain C residue  107 TRP
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  278 ILE
Chi-restraints excluded: chain C residue  326 SER
Chi-restraints excluded: chain C residue  407 SER
Chi-restraints excluded: chain C residue  420 LYS
Chi-restraints excluded: chain C residue  424 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    3.9990
   chunk 48 optimal weight:    0.0040
   chunk 45 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 75 optimal weight:    7.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    0.9998

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

Flipped N/Q/H residues before XYZ refinement:
A 374 ASN
C 366 HIS
C 374 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.155541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.114070 restraints weight = 6993.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 1.73
r_work: 0.3205 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.2192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6502  Z= 0.132
  Angle     :  0.531  11.654   8846  Z= 0.268
  Chirality :  0.040   0.249    998
  Planarity :  0.005   0.049   1084
  Dihedral  :  5.073  57.278    883
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 28.08 %
    Favored  : 68.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.74 (0.29), residues: 820
  helix:  0.00 (0.20), residues: 682
  sheet:  None (None), residues: 0
  loop : -2.45 (0.49), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 126 
 TYR   0.012   0.001   TYR C  24 
 PHE   0.011   0.001   PHE C 340 
 TRP   0.009   0.001   TRP C 107 
 HIS   0.001   0.000   HIS C 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6502)
  covalent geometry    : angle       0.53144 ( 8846)
  hydrogen bonds       : bond        0.03380 (  368)
  hydrogen bonds       : angle       4.18185 ( 1101)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.207 
Fit side-chains
REVERT: A   17 MET cc_start: 0.8301 (mtm) cc_final: 0.7875 (mtp)
REVERT: A  107 TRP cc_start: 0.9006 (OUTLIER) cc_final: 0.7401 (m-90)
REVERT: A  143 THR cc_start: 0.7805 (OUTLIER) cc_final: 0.7581 (m)
REVERT: A  365 SER cc_start: 0.8649 (t) cc_final: 0.8290 (m)
REVERT: A  420 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.6810 (mptt)
REVERT: C  197 ARG cc_start: 0.5916 (ttp80) cc_final: 0.5684 (ttp80)
REVERT: C  278 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7086 (mp)
REVERT: C  329 LEU cc_start: 0.8149 (tp) cc_final: 0.7863 (mm)
REVERT: C  420 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.6794 (mptt)
  outliers start: 22
  outliers final: 11
  residues processed: 108
  average time/residue: 0.3154
  time to fit residues: 36.7143
Evaluate side-chains
  102 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue  107 TRP
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  326 SER
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  420 LYS
Chi-restraints excluded: chain C residue    6 TYR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  107 TRP
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  278 ILE
Chi-restraints excluded: chain C residue  326 SER
Chi-restraints excluded: chain C residue  420 LYS
Chi-restraints excluded: chain C residue  424 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 78 optimal weight:    0.8980
   chunk 24 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 52 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 374 ASN
C 354 ASN
C 374 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.155880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.114289 restraints weight = 6999.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 1.74
r_work: 0.3173 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6502  Z= 0.125
  Angle     :  0.547  11.958   8846  Z= 0.272
  Chirality :  0.040   0.310    998
  Planarity :  0.005   0.049   1084
  Dihedral  :  4.991  57.083    882
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 28.68 %
    Favored  : 68.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.29), residues: 820
  helix:  0.11 (0.20), residues: 682
  sheet:  None (None), residues: 0
  loop : -2.41 (0.50), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 126 
 TYR   0.011   0.001   TYR C  24 
 PHE   0.011   0.001   PHE C 340 
 TRP   0.009   0.001   TRP C 107 
 HIS   0.002   0.000   HIS C 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 6502)
  covalent geometry    : angle       0.54743 ( 8846)
  hydrogen bonds       : bond        0.03287 (  368)
  hydrogen bonds       : angle       4.12156 ( 1101)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A   17 MET cc_start: 0.8290 (mtm) cc_final: 0.7866 (mtp)
REVERT: A  107 TRP cc_start: 0.8998 (OUTLIER) cc_final: 0.7423 (m-90)
REVERT: A  365 SER cc_start: 0.8620 (t) cc_final: 0.8265 (m)
REVERT: A  420 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.6797 (mptt)
REVERT: C  278 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7036 (mp)
REVERT: C  329 LEU cc_start: 0.8155 (tp) cc_final: 0.7868 (mm)
REVERT: C  420 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.6764 (mptt)
  outliers start: 16
  outliers final: 9
  residues processed: 101
  average time/residue: 0.3059
  time to fit residues: 33.3908
Evaluate side-chains
  97 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue  107 TRP
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  326 SER
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  420 LYS
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  107 TRP
Chi-restraints excluded: chain C residue  278 ILE
Chi-restraints excluded: chain C residue  326 SER
Chi-restraints excluded: chain C residue  420 LYS
Chi-restraints excluded: chain C residue  424 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 64 optimal weight:    0.0980
   chunk 40 optimal weight:    6.9990
   chunk 20 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 34 optimal weight:    0.2980
   chunk 60 optimal weight:    0.6980
   chunk 43 optimal weight:    0.6980
   chunk 66 optimal weight:    0.5980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 374 ASN
C 374 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.153806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.110425 restraints weight = 7015.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 1.82
r_work: 0.3219 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3084 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.2375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6502  Z= 0.103
  Angle     :  0.523  10.059   8846  Z= 0.262
  Chirality :  0.039   0.239    998
  Planarity :  0.005   0.049   1084
  Dihedral  :  4.873  56.301    882
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 28.83 %
    Favored  : 68.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.29), residues: 820
  helix:  0.35 (0.20), residues: 682
  sheet:  None (None), residues: 0
  loop : -2.38 (0.50), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 126 
 TYR   0.010   0.001   TYR A  24 
 PHE   0.012   0.001   PHE C 340 
 TRP   0.008   0.001   TRP C 107 
 HIS   0.002   0.000   HIS C 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 6502)
  covalent geometry    : angle       0.52261 ( 8846)
  hydrogen bonds       : bond        0.03032 (  368)
  hydrogen bonds       : angle       4.00752 ( 1101)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A   17 MET cc_start: 0.8202 (mtm) cc_final: 0.7831 (mtt)
REVERT: A  107 TRP cc_start: 0.8960 (OUTLIER) cc_final: 0.7502 (m-90)
REVERT: A  143 THR cc_start: 0.7698 (OUTLIER) cc_final: 0.7459 (m)
REVERT: A  329 LEU cc_start: 0.8162 (tp) cc_final: 0.7850 (mm)
REVERT: A  420 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.6757 (mptt)
REVERT: C   10 ARG cc_start: 0.6808 (ttp80) cc_final: 0.6384 (ttm110)
REVERT: C  278 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7001 (mp)
REVERT: C  329 LEU cc_start: 0.8132 (tp) cc_final: 0.7838 (mm)
REVERT: C  420 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.6753 (mptt)
  outliers start: 17
  outliers final: 11
  residues processed: 109
  average time/residue: 0.3716
  time to fit residues: 43.3167
Evaluate side-chains
  110 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue  107 TRP
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  326 SER
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  420 LYS
Chi-restraints excluded: chain C residue    6 TYR
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  107 TRP
Chi-restraints excluded: chain C residue  278 ILE
Chi-restraints excluded: chain C residue  326 SER
Chi-restraints excluded: chain C residue  420 LYS
Chi-restraints excluded: chain C residue  424 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 41 optimal weight:   10.0000
   chunk 24 optimal weight:    0.0770
   chunk 67 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.7140

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

Flipped N/Q/H residues before XYZ refinement:
A 374 ASN
C 374 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.150142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.105292 restraints weight = 6935.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 1.84
r_work: 0.2931 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2797 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6502  Z= 0.115
  Angle     :  0.533   9.316   8846  Z= 0.265
  Chirality :  0.039   0.235    998
  Planarity :  0.005   0.049   1084
  Dihedral  :  4.885  56.508    882
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 28.68 %
    Favored  : 68.77 %
  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: -0.15 (0.29), residues: 820
  helix:  0.42 (0.20), residues: 682
  sheet:  None (None), residues: 0
  loop : -2.32 (0.49), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG C 300 
 TYR   0.010   0.001   TYR A  24 
 PHE   0.012   0.001   PHE C 340 
 TRP   0.008   0.001   TRP C 107 
 HIS   0.001   0.000   HIS C 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 6502)
  covalent geometry    : angle       0.53267 ( 8846)
  hydrogen bonds       : bond        0.03174 (  368)
  hydrogen bonds       : angle       4.01523 ( 1101)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A   17 MET cc_start: 0.8242 (mtm) cc_final: 0.7774 (mtp)
REVERT: A  107 TRP cc_start: 0.8968 (OUTLIER) cc_final: 0.7452 (m-90)
REVERT: A  143 THR cc_start: 0.7514 (OUTLIER) cc_final: 0.7292 (m)
REVERT: A  329 LEU cc_start: 0.8096 (tp) cc_final: 0.7779 (mm)
REVERT: A  420 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.6681 (mptt)
REVERT: C   10 ARG cc_start: 0.6747 (ttp80) cc_final: 0.6335 (ttm110)
REVERT: C  166 ARG cc_start: 0.8510 (mtp85) cc_final: 0.8276 (mtt-85)
REVERT: C  254 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7841 (mt-10)
REVERT: C  278 ILE cc_start: 0.7510 (OUTLIER) cc_final: 0.6860 (mp)
REVERT: C  329 LEU cc_start: 0.8066 (tp) cc_final: 0.7771 (mm)
REVERT: C  420 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.6679 (mptt)
  outliers start: 17
  outliers final: 11
  residues processed: 109
  average time/residue: 0.3733
  time to fit residues: 43.1533
Evaluate side-chains
  112 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue  107 TRP
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  326 SER
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  420 LYS
Chi-restraints excluded: chain C residue    6 TYR
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  107 TRP
Chi-restraints excluded: chain C residue  278 ILE
Chi-restraints excluded: chain C residue  326 SER
Chi-restraints excluded: chain C residue  420 LYS
Chi-restraints excluded: chain C residue  424 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 13 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 80 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0000
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    0.4980
   chunk 19 optimal weight:    0.0000
   chunk 60 optimal weight:    3.9990
   chunk 66 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 374 ASN
C 374 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.150741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.106711 restraints weight = 7038.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3109 rms_B_bonded: 1.74
r_work: 0.2977 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2843 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.2588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6502  Z= 0.099
  Angle     :  0.520   8.945   8846  Z= 0.260
  Chirality :  0.039   0.215    998
  Planarity :  0.005   0.049   1084
  Dihedral  :  4.789  55.881    882
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 28.83 %
    Favored  : 68.77 %
  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:  0.19 (0.30), residues: 820
  helix:  0.67 (0.20), residues: 676
  sheet:  None (None), residues: 0
  loop : -2.19 (0.50), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 126 
 TYR   0.009   0.001   TYR A  24 
 PHE   0.012   0.001   PHE C 340 
 TRP   0.008   0.001   TRP C 107 
 HIS   0.002   0.000   HIS C 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 6502)
  covalent geometry    : angle       0.51988 ( 8846)
  hydrogen bonds       : bond        0.02938 (  368)
  hydrogen bonds       : angle       3.91094 ( 1101)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1875.24 seconds
wall clock time: 32 minutes 43.05 seconds (1963.05 seconds total)