Starting phenix.real_space_refine
on Tue Feb 11 16:01:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gef_29968/02_2025/8gef_29968.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gef_29968/02_2025/8gef_29968.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gef_29968/02_2025/8gef_29968.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gef_29968/02_2025/8gef_29968.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gef_29968/02_2025/8gef_29968.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gef_29968/02_2025/8gef_29968.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.025
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      24      5.16       5
     C    4014      2.51       5
     N    1095      2.21       5
     O    1083      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6216
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 1835
          Classifications: {'peptide': 281}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 138}
          Link IDs: {'PTRANS': 6, 'TRANS': 274}
          Chain breaks: 7
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 500
          Unresolved non-hydrogen angles: 616
          Unresolved non-hydrogen dihedrals: 394
          Unresolved non-hydrogen chiralities: 32
          Planarities with less than four sites: {'GLN:plan1': 12, 'TYR:plan': 2, 'ASN:plan1': 8, 'ASP:plan': 16, 'PHE:plan': 1, 'GLU:plan': 21, 'ARG:plan': 17}
          Unresolved non-hydrogen planarities: 309
    Chain: "B"
      Number of atoms: 2131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2131
          Classifications: {'peptide': 329}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 124}
          Link IDs: {'PTRANS': 5, 'TRANS': 323}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 396
          Unresolved non-hydrogen angles: 498
          Unresolved non-hydrogen dihedrals: 304
          Unresolved non-hydrogen chiralities: 27
          Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 11, 'ASP:plan': 26, 'ASN%COO:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 13}
          Unresolved non-hydrogen planarities: 260
    Chain: "G"
      Number of atoms: 287
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 287
          Classifications: {'peptide': 50}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 4, 'TRANS': 45}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 106
          Unresolved non-hydrogen angles: 128
          Unresolved non-hydrogen dihedrals: 87
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 54
    Chain: "R"
      Number of atoms: 1948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 1948
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 99}
          Link IDs: {'PTRANS': 7, 'TRANS': 273}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 319
          Unresolved non-hydrogen angles: 403
          Unresolved non-hydrogen dihedrals: 253
          Unresolved non-hydrogen chiralities: 40
          Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 144
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.20, per 1000 atoms: 0.68
  Number of scatterers: 6216
  At special positions: 0
  Unit cell: (67.84, 97.52, 130.38, 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      24     16.00
     O    1083      8.00
     N    1095      7.00
     C    4014      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03

  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: 1.64
  Conformation dependent library (CDL) restraints added in 921.5 milliseconds
  

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1786

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 8 sheets defined
      50.5% alpha, 14.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.77
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 40
    Processing helix  chain 'A' and resid 52 through 61
      removed outlier: 3.796A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 108
    Processing helix  chain 'A' and resid 129 through 135
    Processing helix  chain 'A' and resid 159 through 165
      removed outlier: 3.718A  pdb=" N   TYR A 163 " --> pdb=" O   VAL A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 199
    Processing helix  chain 'A' and resid 234 through 238
    Processing helix  chain 'A' and resid 251 through 254
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 307 through 312
    Processing helix  chain 'A' and resid 313 through 316
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.504A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   GLY A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 390
    Processing helix  chain 'A' and resid 391 through 393
      No H-bonds generated for 'chain 'A' and resid 391 through 393'
    Processing helix  chain 'B' and resid 8 through 25
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.521A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 14 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'R' and resid 32 through 61
      removed outlier: 3.957A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 68 through 97
      removed outlier: 3.809A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
    Processing helix  chain 'R' and resid 137 through 145
      removed outlier: 4.083A  pdb=" N   GLN R 142 " --> pdb=" O   PRO R 138 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   SER R 143 " --> pdb=" O   PHE R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 4.456A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
    Processing helix  chain 'R' and resid 172 through 175
    Processing helix  chain 'R' and resid 181 through 187
    Processing helix  chain 'R' and resid 198 through 208
    Processing helix  chain 'R' and resid 208 through 237
    Processing helix  chain 'R' and resid 270 through 299
      removed outlier: 3.670A  pdb=" N   THR R 274 " --> pdb=" O   LYS R 270 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 4.326A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
    Processing helix  chain 'R' and resid 317 through 327
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 340
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213
      removed outlier: 6.735A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.566A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.312A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 7.794A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 8.116A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.910A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.061A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.678A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.062A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105
      removed outlier: 4.037A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.635A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 190 through 192
      removed outlier: 3.710A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.624A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277
      removed outlier: 4.088A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 5.794A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.005A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    385 hydrogen bonds defined for protein.
    1110 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: 1.95

  Time building geometry restraints manager: 1.78 seconds

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

  Histogram of bond lengths:
        1.22 -     1.46: 3717
        1.46 -     1.71: 2589
        1.71 -     1.96: 34
        1.96 -     2.20: 0
        2.20 -     2.45: 1
  Bond restraints: 6341
  Sorted by residual:
  bond pdb=" C   PRO A 328 "
       pdb=" N   GLU A 330 "
    ideal  model  delta    sigma   weight residual
    1.332  2.449 -1.116 1.40e-02 5.10e+03 6.36e+03
  bond pdb=" C   PRO A 332 "
       pdb=" N   ARG A 333 "
    ideal  model  delta    sigma   weight residual
    1.335  1.247  0.088 1.31e-02 5.83e+03 4.47e+01
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.602 -0.079 2.00e-02 2.50e+03 1.56e+01
  bond pdb=" CA  LEU B 168 "
       pdb=" C   LEU B 168 "
    ideal  model  delta    sigma   weight residual
    1.522  1.480  0.042 1.20e-02 6.94e+03 1.25e+01
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.448 -0.051 2.00e-02 2.50e+03 6.56e+00
  ... (remaining 6336 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     9.76: 8715
        9.76 -    19.51: 0
       19.51 -    29.27: 0
       29.27 -    39.03: 1
       39.03 -    48.79: 2
  Bond angle restraints: 8718
  Sorted by residual:
  angle pdb=" O   PRO A 328 "
        pdb=" C   PRO A 328 "
        pdb=" N   GLU A 330 "
      ideal   model   delta    sigma   weight residual
     122.64   84.01   38.63 1.35e+00 5.49e-01 8.19e+02
  angle pdb=" C   PRO A 328 "
        pdb=" N   GLU A 330 "
        pdb=" CA  GLU A 330 "
      ideal   model   delta    sigma   weight residual
     121.54  170.33  -48.79 1.91e+00 2.74e-01 6.52e+02
  angle pdb=" CA  PRO A 328 "
        pdb=" C   PRO A 328 "
        pdb=" N   GLU A 330 "
      ideal   model   delta    sigma   weight residual
     116.70  157.23  -40.53 2.07e+00 2.33e-01 3.83e+02
  angle pdb=" O   PRO A 332 "
        pdb=" C   PRO A 332 "
        pdb=" N   ARG A 333 "
      ideal   model   delta    sigma   weight residual
     122.23  115.52    6.71 1.20e+00 6.94e-01 3.13e+01
  angle pdb=" N   GLU A 327 "
        pdb=" CA  GLU A 327 "
        pdb=" C   GLU A 327 "
      ideal   model   delta    sigma   weight residual
     109.58  117.63   -8.05 1.63e+00 3.76e-01 2.44e+01
  ... (remaining 8713 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.39: 3374
       20.39 -    40.78: 210
       40.78 -    61.17: 18
       61.17 -    81.56: 1
       81.56 -   101.95: 3
  Dihedral angle restraints: 3606
    sinusoidal: 866
      harmonic: 2740
  Sorted by residual:
  dihedral pdb=" CA  PRO A 328 "
           pdb=" C   PRO A 328 "
           pdb=" N   GLU A 330 "
           pdb=" CA  GLU A 330 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -78.05 -101.95     0      5.00e+00 4.00e-02 4.16e+02
  dihedral pdb=" CAE G1I R 501 "
           pdb=" CAG G1I R 501 "
           pdb=" CAH G1I R 501 "
           pdb=" CAI G1I R 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      47.24  -48.83   96.07     1      3.00e+01 1.11e-03 1.18e+01
  dihedral pdb=" CA  MET R 171 "
           pdb=" C   MET R 171 "
           pdb=" N   HIS R 172 "
           pdb=" CA  HIS R 172 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.31  -16.69     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 3603 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 758
       0.034 -    0.068: 218
       0.068 -    0.101: 63
       0.101 -    0.135: 32
       0.135 -    0.169: 4
  Chirality restraints: 1075
  Sorted by residual:
  chirality pdb=" CA  CYS B 166 "
            pdb=" N   CYS B 166 "
            pdb=" C   CYS B 166 "
            pdb=" CB  CYS B 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.14e-01
  chirality pdb=" CB  VAL R 292 "
            pdb=" CA  VAL R 292 "
            pdb=" CG1 VAL R 292 "
            pdb=" CG2 VAL R 292 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.86e-01
  chirality pdb=" CB  THR R 118 "
            pdb=" CA  THR R 118 "
            pdb=" OG1 THR R 118 "
            pdb=" CG2 THR R 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.14 2.00e-01 2.50e+01 5.11e-01
  ... (remaining 1072 not shown)

  Planarity restraints: 1111
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 328 "    0.031 2.00e-02 2.50e+03   3.65e-02 1.33e+01
        pdb=" C   PRO A 328 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   PRO A 328 "    0.014 2.00e-02 2.50e+03
        pdb=" N   GLU A 330 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 297 "   -0.006 2.00e-02 2.50e+03   8.22e-03 1.69e+00
        pdb=" CG  TRP B 297 "    0.021 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 297 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 297 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 297 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 297 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 297 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 297 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 297 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 297 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 326 "   -0.006 2.00e-02 2.50e+03   1.14e-02 1.31e+00
        pdb=" C   PRO A 326 "    0.020 2.00e-02 2.50e+03
        pdb=" O   PRO A 326 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   GLU A 327 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1108 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2027
        2.82 -     3.34: 5939
        3.34 -     3.86: 10232
        3.86 -     4.38: 10224
        4.38 -     4.90: 18745
  Nonbonded interactions: 47167
  Sorted by model distance:
  nonbonded pdb=" O   LYS B  57 "
            pdb=" OG  SER B  74 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" NH1 ARG A 385 "
            pdb=" OE1 GLN R 229 "
     model   vdw
     2.322 3.120
  nonbonded pdb=" O   HIS B  54 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" O   ASP B 186 "
            pdb=" N   CYS B 204 "
     model   vdw
     2.336 3.120
  nonbonded pdb=" OH  TYR R 209 "
            pdb=" O   PHE R 290 "
     model   vdw
     2.356 3.040
  ... (remaining 47162 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.450
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     18.150
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  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:2.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.014   1.116   6341  Z= 0.521
  Angle     :  0.957  48.785   8718  Z= 0.558
  Chirality :  0.040   0.169   1075
  Planarity :  0.003   0.037   1111
  Dihedral  : 13.648 101.948   1817
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 17.02 %
    Favored  : 81.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.13 (0.29), residues: 911
  helix:  3.07 (0.25), residues: 415
  sheet:  0.62 (0.43), residues: 160
  loop : -0.34 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 297 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.012   0.001   PHE A 340 
 TYR   0.013   0.001   TYR A 360 
 ARG   0.002   0.000   ARG B  49 

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.665 
Fit side-chains
REVERT: B  169 TRP cc_start: 0.8171 (m100) cc_final: 0.7909 (m100)
  outliers start: 6
  outliers final: 5
  residues processed: 72
  average time/residue: 0.1557
  time to fit residues: 15.6981
Evaluate side-chains
  66 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:    5.9990
   chunk 70 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   chunk 24 optimal weight:    0.0670
   chunk 47 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 72 optimal weight:    0.7980
   chunk 28 optimal weight:   20.0000
   chunk 44 optimal weight:    0.0000
   chunk 54 optimal weight:    2.9990
   chunk 84 optimal weight:    0.7980
   overall best weight:    0.4922

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

Flipped N/Q/H residues before XYZ refinement:
A 271 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.111021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.095550 restraints weight = 13200.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.097583 restraints weight = 7847.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.099064 restraints weight = 5425.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.0836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   6341  Z= 0.144
  Angle     :  0.439   5.321   8718  Z= 0.244
  Chirality :  0.039   0.162   1075
  Planarity :  0.003   0.028   1111
  Dihedral  :  4.441  37.708   1000
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 17.02 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.23 (0.29), residues: 913
  helix:  3.19 (0.25), residues: 413
  sheet:  0.65 (0.43), residues: 160
  loop : -0.30 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 297 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.010   0.001   PHE B 199 
 TYR   0.010   0.001   TYR R 199 
 ARG   0.003   0.000   ARG B  49 

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.656 
Fit side-chains
REVERT: R  296 HIS cc_start: 0.8384 (OUTLIER) cc_final: 0.8141 (p-80)
  outliers start: 12
  outliers final: 4
  residues processed: 86
  average time/residue: 0.1319
  time to fit residues: 16.4991
Evaluate side-chains
  65 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   chunk 23 optimal weight:    0.0370
   chunk 53 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 12 optimal weight:    6.9990
   chunk 48 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    1.8066

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.105986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.090985 restraints weight = 13590.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.092907 restraints weight = 8334.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.093895 restraints weight = 5817.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.1216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6341  Z= 0.354
  Angle     :  0.535   5.946   8718  Z= 0.299
  Chirality :  0.042   0.174   1075
  Planarity :  0.003   0.030   1111
  Dihedral  :  4.834  42.001    995
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 18.68 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.89 (0.29), residues: 913
  helix:  2.99 (0.25), residues: 426
  sheet:  0.36 (0.42), residues: 160
  loop : -0.68 (0.33), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 169 
 HIS   0.007   0.001   HIS B 142 
 PHE   0.023   0.002   PHE B 235 
 TYR   0.016   0.002   TYR R 199 
 ARG   0.002   0.000   ARG A 336 

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.727 
Fit side-chains
   revert: symmetry clash
REVERT: B  318 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.9008 (tp)
REVERT: R  296 HIS cc_start: 0.8566 (OUTLIER) cc_final: 0.8340 (p-80)
  outliers start: 17
  outliers final: 11
  residues processed: 72
  average time/residue: 0.1572
  time to fit residues: 16.0658
Evaluate side-chains
  67 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  157 VAL
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  321 PHE
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 9 optimal weight:    0.0270
   chunk 83 optimal weight:    0.9990
   chunk 64 optimal weight:    6.9990
   chunk 27 optimal weight:    0.7980
   chunk 71 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 72 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   overall best weight:    0.6238

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.109402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.094259 restraints weight = 13470.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.096179 restraints weight = 8115.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.097616 restraints weight = 5653.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.1217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6341  Z= 0.160
  Angle     :  0.431   5.426   8718  Z= 0.240
  Chirality :  0.039   0.151   1075
  Planarity :  0.003   0.029   1111
  Dihedral  :  4.433  40.032    995
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 21.75 %
    Favored  : 75.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.29), residues: 913
  helix:  3.11 (0.25), residues: 422
  sheet:  0.46 (0.43), residues: 159
  loop : -0.45 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.012   0.001   PHE B 199 
 TYR   0.015   0.001   TYR R 174 
 ARG   0.002   0.000   ARG B  49 

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.724 
Fit side-chains
REVERT: A  340 PHE cc_start: 0.8511 (t80) cc_final: 0.8301 (t80)
  outliers start: 12
  outliers final: 9
  residues processed: 76
  average time/residue: 0.1423
  time to fit residues: 15.7820
Evaluate side-chains
  66 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  321 PHE
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 5 optimal weight:   20.0000
   chunk 36 optimal weight:    3.9990
   chunk 53 optimal weight:    0.4980
   chunk 16 optimal weight:    0.8980
   chunk 73 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   chunk 89 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.106604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.091349 restraints weight = 13672.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.093311 restraints weight = 8339.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.094545 restraints weight = 5802.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6341  Z= 0.287
  Angle     :  0.495   5.839   8718  Z= 0.275
  Chirality :  0.040   0.161   1075
  Planarity :  0.003   0.029   1111
  Dihedral  :  4.719  42.046    995
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 23.40 %
    Favored  : 72.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.29), residues: 913
  helix:  3.11 (0.25), residues: 421
  sheet: -0.02 (0.42), residues: 166
  loop : -0.69 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 169 
 HIS   0.006   0.001   HIS B 142 
 PHE   0.020   0.001   PHE B 235 
 TYR   0.017   0.001   TYR R 174 
 ARG   0.002   0.000   ARG A 336 

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 61
  time to evaluate  : 0.668 
Fit side-chains
REVERT: R  275 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8696 (mm)
REVERT: R  296 HIS cc_start: 0.8597 (OUTLIER) cc_final: 0.8275 (p-80)
  outliers start: 17
  outliers final: 13
  residues processed: 75
  average time/residue: 0.1566
  time to fit residues: 16.4955
Evaluate side-chains
  70 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 55
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue  157 VAL
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  321 PHE
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 10 optimal weight:    0.5980
   chunk 8 optimal weight:   50.0000
   chunk 42 optimal weight:    0.0970
   chunk 24 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.108971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.093903 restraints weight = 13404.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.095852 restraints weight = 8110.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.097061 restraints weight = 5634.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.1434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6341  Z= 0.166
  Angle     :  0.432   5.461   8718  Z= 0.239
  Chirality :  0.039   0.157   1075
  Planarity :  0.003   0.028   1111
  Dihedral  :  4.445  40.325    995
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 23.64 %
    Favored  : 72.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.29), residues: 913
  helix:  3.18 (0.25), residues: 422
  sheet: -0.10 (0.41), residues: 174
  loop : -0.60 (0.34), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.012   0.001   PHE B 199 
 TYR   0.019   0.001   TYR R 174 
 ARG   0.001   0.000   ARG B  49 

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.623 
Fit side-chains
REVERT: R  275 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8721 (mm)
REVERT: R  296 HIS cc_start: 0.8456 (OUTLIER) cc_final: 0.7862 (p-80)
  outliers start: 17
  outliers final: 11
  residues processed: 80
  average time/residue: 0.1431
  time to fit residues: 16.4425
Evaluate side-chains
  70 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain R residue   55 ILE
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  321 PHE
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 8 optimal weight:   50.0000
   chunk 83 optimal weight:    4.9990
   chunk 62 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 77 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.108635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.093381 restraints weight = 13438.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.095384 restraints weight = 8128.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.096773 restraints weight = 5623.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.1505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6341  Z= 0.188
  Angle     :  0.442   5.921   8718  Z= 0.244
  Chirality :  0.039   0.175   1075
  Planarity :  0.003   0.034   1111
  Dihedral  :  4.439  40.474    995
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 23.17 %
    Favored  : 72.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.29), residues: 913
  helix:  3.23 (0.25), residues: 416
  sheet: -0.11 (0.41), residues: 174
  loop : -0.49 (0.34), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.014   0.001   PHE B 235 
 TYR   0.022   0.001   TYR R 174 
 ARG   0.001   0.000   ARG B  49 

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 61
  time to evaluate  : 0.667 
Fit side-chains
REVERT: R  275 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8828 (mm)
REVERT: R  296 HIS cc_start: 0.8423 (OUTLIER) cc_final: 0.7852 (p-80)
  outliers start: 20
  outliers final: 17
  residues processed: 78
  average time/residue: 0.1369
  time to fit residues: 15.4994
Evaluate side-chains
  77 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 58
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain R residue   55 ILE
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  129 VAL
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  321 PHE
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 6 optimal weight:    7.9990
   chunk 3 optimal weight:    4.9990
   chunk 48 optimal weight:    0.5980
   chunk 57 optimal weight:    0.7980
   chunk 73 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 60 optimal weight:   10.0000
   chunk 91 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    0.7982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.108908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.093823 restraints weight = 13421.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.095841 restraints weight = 8130.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.097082 restraints weight = 5598.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.1544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6341  Z= 0.181
  Angle     :  0.434   5.532   8718  Z= 0.239
  Chirality :  0.039   0.172   1075
  Planarity :  0.003   0.034   1111
  Dihedral  :  4.379  39.886    995
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 22.93 %
    Favored  : 71.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.29), residues: 913
  helix:  3.27 (0.25), residues: 416
  sheet: -0.12 (0.41), residues: 174
  loop : -0.47 (0.34), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.014   0.001   PHE B 235 
 TYR   0.022   0.001   TYR R 174 
 ARG   0.001   0.000   ARG B  49 

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 59
  time to evaluate  : 0.639 
Fit side-chains
REVERT: R  275 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8823 (mm)
REVERT: R  296 HIS cc_start: 0.8395 (OUTLIER) cc_final: 0.7829 (p-80)
  outliers start: 22
  outliers final: 18
  residues processed: 77
  average time/residue: 0.1411
  time to fit residues: 15.7495
Evaluate side-chains
  77 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 57
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   99 TRP
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain R residue   55 ILE
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  129 VAL
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  321 PHE
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 24 optimal weight:    0.2980
   chunk 61 optimal weight:    7.9990
   chunk 42 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.109187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.093999 restraints weight = 13523.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.095959 restraints weight = 8168.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.097214 restraints weight = 5681.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.1586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6341  Z= 0.172
  Angle     :  0.432   5.485   8718  Z= 0.239
  Chirality :  0.039   0.178   1075
  Planarity :  0.003   0.032   1111
  Dihedral  :  4.337  39.850    995
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 23.64 %
    Favored  : 71.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.29), residues: 913
  helix:  3.31 (0.25), residues: 415
  sheet: -0.11 (0.41), residues: 174
  loop : -0.46 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.014   0.001   PHE B 235 
 TYR   0.023   0.001   TYR R 174 
 ARG   0.001   0.000   ARG B  49 

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 65
  time to evaluate  : 0.654 
Fit side-chains
REVERT: R  275 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8808 (mm)
REVERT: R  296 HIS cc_start: 0.8395 (OUTLIER) cc_final: 0.7741 (p-80)
  outliers start: 21
  outliers final: 18
  residues processed: 83
  average time/residue: 0.1519
  time to fit residues: 17.7679
Evaluate side-chains
  79 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 59
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain R residue   55 ILE
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  129 VAL
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  321 PHE
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 6 optimal weight:    6.9990
   chunk 59 optimal weight:    5.9990
   chunk 61 optimal weight:    8.9990
   chunk 49 optimal weight:    0.3980
   chunk 62 optimal weight:    0.7980
   chunk 75 optimal weight:    0.3980
   overall best weight:    0.8982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.108878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.093731 restraints weight = 13629.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.095703 restraints weight = 8244.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.096954 restraints weight = 5696.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6341  Z= 0.196
  Angle     :  0.447   6.270   8718  Z= 0.246
  Chirality :  0.039   0.143   1075
  Planarity :  0.003   0.033   1111
  Dihedral  :  4.378  40.192    995
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 23.17 %
    Favored  : 72.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.29), residues: 913
  helix:  3.28 (0.25), residues: 416
  sheet: -0.13 (0.41), residues: 174
  loop : -0.47 (0.34), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 169 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.015   0.001   PHE B 235 
 TYR   0.025   0.001   TYR R 174 
 ARG   0.001   0.000   ARG B  49 

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 59
  time to evaluate  : 0.690 
Fit side-chains
REVERT: R  275 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8833 (mm)
REVERT: R  296 HIS cc_start: 0.8400 (OUTLIER) cc_final: 0.7732 (p-80)
  outliers start: 20
  outliers final: 18
  residues processed: 75
  average time/residue: 0.1366
  time to fit residues: 15.1422
Evaluate side-chains
  79 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 59
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   99 TRP
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain R residue   55 ILE
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  129 VAL
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  321 PHE
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0000
   chunk 43 optimal weight:    4.9990
   chunk 2 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    0.6786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.109390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.094209 restraints weight = 13709.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.096163 restraints weight = 8216.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.097547 restraints weight = 5693.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.1668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6341  Z= 0.164
  Angle     :  0.434   6.068   8718  Z= 0.238
  Chirality :  0.039   0.180   1075
  Planarity :  0.003   0.032   1111
  Dihedral  :  4.292  39.367    995
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 24.11 %
    Favored  : 71.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.07 (0.29), residues: 913
  helix:  3.32 (0.25), residues: 415
  sheet:  0.01 (0.41), residues: 172
  loop : -0.47 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 169 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.013   0.001   PHE B 235 
 TYR   0.026   0.001   TYR R 174 
 ARG   0.001   0.000   ARG R 175 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1819.20 seconds
wall clock time: 33 minutes 19.88 seconds (1999.88 seconds total)