Starting phenix.real_space_refine
on Tue Mar 11 15:30:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gef_29968/03_2025/8gef_29968.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gef_29968/03_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_29968/03_2025/8gef_29968.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gef_29968/03_2025/8gef_29968.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gef_29968/03_2025/8gef_29968.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gef_29968/03_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.66, per 1000 atoms: 0.75
  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: 1.47
  Conformation dependent library (CDL) restraints added in 976.1 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: 0.85
  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: 1.98

  Time building geometry restraints manager: 1.76 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:             1.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.060
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  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:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.530
-------------------------------------------------------------------------------
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  : 0.668 
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: 0.1585
  time to fit residues: 15.9865
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  : 0.680 
-------------------------------------------------------------------------------
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 = 0.111022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.095547 restraints weight = 13200.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.097577 restraints weight = 7848.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.099090 restraints weight = 5428.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
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  :  4.442  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  : 0.685 
Fit side-chains
REVERT: R  296 HIS cc_start: 0.8386 (OUTLIER) cc_final: 0.8142 (p-80)
  outliers start: 12
  outliers final: 4
  residues processed: 86
  average time/residue: 0.1322
  time to fit residues: 16.5895
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  : 0.684 
-------------------------------------------------------------------------------
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:    0.0470
   chunk 53 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 12 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    1.4086

-------------------------------------------------------------------------------
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 = 0.3449 r_free = 0.3449 target = 0.107509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.092439 restraints weight = 13458.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.094381 restraints weight = 8221.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.095630 restraints weight = 5698.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.1099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6341  Z= 0.284
  Angle     :  0.494   5.795   8718  Z= 0.276
  Chirality :  0.040   0.168   1075
  Planarity :  0.003   0.029   1111
  Dihedral  :  4.597  40.662    995
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 18.91 %
    Favored  : 77.54 %
  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:  2.06 (0.29), residues: 913
  helix:  3.06 (0.25), residues: 427
  sheet:  0.65 (0.42), residues: 155
  loop : -0.61 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 169 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.022   0.002   PHE A 340 
 TYR   0.014   0.001   TYR R 199 
 ARG   0.003   0.000   ARG B  49 

*********************** 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: 15
    poor density    : 60
  time to evaluate  : 0.658 
Fit side-chains
REVERT: B  318 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8992 (tp)
REVERT: R  296 HIS cc_start: 0.8520 (OUTLIER) cc_final: 0.8288 (p-80)
  outliers start: 15
  outliers final: 10
  residues processed: 71
  average time/residue: 0.1353
  time to fit residues: 13.9425
Evaluate side-chains
  66 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 54
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 9 optimal weight:    0.0470
   chunk 83 optimal weight:    2.9990
   chunk 64 optimal weight:    0.0000
   chunk 27 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   chunk 1 optimal weight:    7.9990
   chunk 72 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   overall best weight:    0.5884

-------------------------------------------------------------------------------
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 = 0.3487 r_free = 0.3487 target = 0.109977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.094845 restraints weight = 13426.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.096741 restraints weight = 8094.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.098191 restraints weight = 5673.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.1174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6341  Z= 0.149
  Angle     :  0.424   5.398   8718  Z= 0.235
  Chirality :  0.039   0.145   1075
  Planarity :  0.003   0.028   1111
  Dihedral  :  4.326  39.392    995
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 21.75 %
    Favored  : 75.65 %
  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:  2.20 (0.29), residues: 913
  helix:  3.24 (0.25), residues: 420
  sheet:  0.52 (0.43), residues: 159
  loop : -0.46 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.018   0.001   PHE A 340 
 TYR   0.016   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: 11
    poor density    : 67
  time to evaluate  : 0.652 
Fit side-chains
  outliers start: 11
  outliers final: 7
  residues processed: 76
  average time/residue: 0.1348
  time to fit residues: 14.9730
Evaluate side-chains
  66 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
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  218 VAL
Chi-restraints excluded: chain R residue  321 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 5 optimal weight:   20.0000
   chunk 36 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   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:    1.3786

-------------------------------------------------------------------------------
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 = 0.3446 r_free = 0.3446 target = 0.107312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.091961 restraints weight = 13650.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.093937 restraints weight = 8280.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.095176 restraints weight = 5737.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6341  Z= 0.275
  Angle     :  0.483   5.805   8718  Z= 0.268
  Chirality :  0.040   0.163   1075
  Planarity :  0.003   0.029   1111
  Dihedral  :  4.600  41.558    995
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 22.93 %
    Favored  : 73.29 %
  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:  1.94 (0.29), residues: 913
  helix:  3.18 (0.25), residues: 421
  sheet:  0.07 (0.42), residues: 166
  loop : -0.64 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 169 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.019   0.001   PHE B 235 
 TYR   0.017   0.001   TYR R 174 
 ARG   0.001   0.000   ARG B  49 

*********************** 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: 16
    poor density    : 62
  time to evaluate  : 0.647 
Fit side-chains
REVERT: R  275 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8677 (mm)
REVERT: R  296 HIS cc_start: 0.8552 (OUTLIER) cc_final: 0.8185 (p-80)
  outliers start: 16
  outliers final: 13
  residues processed: 75
  average time/residue: 0.1524
  time to fit residues: 16.1020
Evaluate side-chains
  71 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 56
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
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  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 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:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 42 optimal weight:    0.6980
   chunk 24 optimal weight:    6.9990
   chunk 23 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.3459 r_free = 0.3459 target = 0.108113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.092915 restraints weight = 13466.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.094878 restraints weight = 8126.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.096231 restraints weight = 5649.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.1422

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= 0.219
  Angle     :  0.455   5.646   8718  Z= 0.252
  Chirality :  0.039   0.166   1075
  Planarity :  0.003   0.029   1111
  Dihedral  :  4.544  41.015    995
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 22.70 %
    Favored  : 74.00 %
  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:  1.87 (0.29), residues: 913
  helix:  3.17 (0.25), residues: 421
  sheet: -0.14 (0.41), residues: 174
  loop : -0.67 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.016   0.001   PHE B 235 
 TYR   0.020   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
  76 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.657 
Fit side-chains
REVERT: R  275 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8699 (mm)
REVERT: R  296 HIS cc_start: 0.8538 (OUTLIER) cc_final: 0.8097 (p-80)
  outliers start: 14
  outliers final: 11
  residues processed: 73
  average time/residue: 0.1380
  time to fit residues: 14.7176
Evaluate side-chains
  68 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 0.650 
-------------------------------------------------------------------------------
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 8 optimal weight:   50.0000
   chunk 83 optimal weight:    0.2980
   chunk 62 optimal weight:    0.0980
   chunk 87 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0060
   overall best weight:    0.4196

-------------------------------------------------------------------------------
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 = 0.3498 r_free = 0.3498 target = 0.110748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.095709 restraints weight = 13338.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.097617 restraints weight = 7990.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.099069 restraints weight = 5562.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.1528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6341  Z= 0.132
  Angle     :  0.419   6.166   8718  Z= 0.230
  Chirality :  0.039   0.168   1075
  Planarity :  0.002   0.027   1111
  Dihedral  :  4.228  39.356    995
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 24.35 %
    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:  2.06 (0.29), residues: 913
  helix:  3.32 (0.25), residues: 414
  sheet:  0.04 (0.41), residues: 172
  loop : -0.51 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.014   0.001   PHE A 340 
 TYR   0.021   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
  87 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.768 
Fit side-chains
REVERT: A  385 ARG cc_start: 0.8671 (mtm-85) cc_final: 0.8447 (ttp-110)
REVERT: R  275 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8666 (mm)
REVERT: R  296 HIS cc_start: 0.8314 (OUTLIER) cc_final: 0.7646 (p-80)
  outliers start: 14
  outliers final: 9
  residues processed: 86
  average time/residue: 0.1541
  time to fit residues: 18.7489
Evaluate side-chains
  70 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
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  159 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
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:    8.9990
   chunk 3 optimal weight:    3.9990
   chunk 48 optimal weight:    0.3980
   chunk 57 optimal weight:    7.9990
   chunk 73 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 60 optimal weight:   10.0000
   chunk 91 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    1.4382

-------------------------------------------------------------------------------
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 = 0.3448 r_free = 0.3448 target = 0.107388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.092197 restraints weight = 13524.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.094096 restraints weight = 8217.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.095330 restraints weight = 5714.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.1617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6341  Z= 0.283
  Angle     :  0.485   6.034   8718  Z= 0.268
  Chirality :  0.040   0.180   1075
  Planarity :  0.003   0.037   1111
  Dihedral  :  4.570  41.297    995
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 23.17 %
    Favored  : 72.81 %
  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:  3.19 (0.25), residues: 421
  sheet: -0.16 (0.41), residues: 174
  loop : -0.62 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 169 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.020   0.001   PHE B 235 
 TYR   0.013   0.001   TYR R 199 
 ARG   0.002   0.000   ARG A 336 

*********************** 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
  76 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 59
  time to evaluate  : 0.697 
Fit side-chains
REVERT: R  275 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8721 (mm)
REVERT: R  296 HIS cc_start: 0.8503 (OUTLIER) cc_final: 0.8016 (p-80)
  outliers start: 17
  outliers final: 15
  residues processed: 73
  average time/residue: 0.1524
  time to fit residues: 15.9198
Evaluate side-chains
  73 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 56
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
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 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   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  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:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 61 optimal weight:    0.1980
   chunk 42 optimal weight:    0.7980
   chunk 36 optimal weight:    0.0070
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.5598

-------------------------------------------------------------------------------
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 = 0.3477 r_free = 0.3477 target = 0.109361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.094276 restraints weight = 13482.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.096181 restraints weight = 8079.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.097587 restraints weight = 5626.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
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      :  0.002   0.027   6341  Z= 0.153
  Angle     :  0.438   5.777   8718  Z= 0.240
  Chirality :  0.039   0.138   1075
  Planarity :  0.003   0.033   1111
  Dihedral  :  4.349  39.964    995
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 24.35 %
    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:  2.10 (0.29), residues: 913
  helix:  3.39 (0.25), residues: 408
  sheet: -0.01 (0.41), residues: 172
  loop : -0.43 (0.34), residues: 333

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   0.012   0.001   PHE B 235 
 TYR   0.010   0.001   TYR R 199 
 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
  71 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 56
  time to evaluate  : 0.714 
Fit side-chains
REVERT: R  275 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8733 (mm)
REVERT: R  296 HIS cc_start: 0.8383 (OUTLIER) cc_final: 0.7725 (p-80)
  outliers start: 15
  outliers final: 12
  residues processed: 68
  average time/residue: 0.1281
  time to fit residues: 12.9582
Evaluate side-chains
  70 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
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   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 B residue  315 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 16 optimal weight:    0.4980
   chunk 35 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 59 optimal weight:    6.9990
   chunk 61 optimal weight:    7.9990
   chunk 49 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   overall best weight:    1.0386

-------------------------------------------------------------------------------
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 = 0.3463 r_free = 0.3463 target = 0.108308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.093154 restraints weight = 13614.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.095071 restraints weight = 8202.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.096306 restraints weight = 5692.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.1663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6341  Z= 0.219
  Angle     :  0.459   5.738   8718  Z= 0.252
  Chirality :  0.039   0.188   1075
  Planarity :  0.003   0.032   1111
  Dihedral  :  4.443  40.497    995
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 25.06 %
    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:  2.05 (0.29), residues: 913
  helix:  3.39 (0.25), residues: 408
  sheet: -0.12 (0.41), residues: 174
  loop : -0.45 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 169 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.017   0.001   PHE B 235 
 TYR   0.012   0.001   TYR R 199 
 ARG   0.001   0.000   ARG A 336 

********************** 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
  72 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 57
  time to evaluate  : 0.670 
Fit side-chains
REVERT: R  275 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8752 (mm)
REVERT: R  296 HIS cc_start: 0.8427 (OUTLIER) cc_final: 0.7859 (p-80)
  outliers start: 15
  outliers final: 13
  residues processed: 70
  average time/residue: 0.1298
  time to fit residues: 13.5522
Evaluate side-chains
  71 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 56
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
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 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 B residue  315 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 87 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3476 r_free = 0.3476 target = 0.109219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.093955 restraints weight = 13672.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.095921 restraints weight = 8233.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.097167 restraints weight = 5683.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.1700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6341  Z= 0.168
  Angle     :  0.438   5.576   8718  Z= 0.241
  Chirality :  0.039   0.144   1075
  Planarity :  0.003   0.031   1111
  Dihedral  :  4.318  39.784    995
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 25.53 %
    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:  2.10 (0.29), residues: 913
  helix:  3.38 (0.25), residues: 408
  sheet: -0.09 (0.40), residues: 179
  loop : -0.35 (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   0.014   0.001   TYR R 174 
 ARG   0.001   0.000   ARG A 374 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1880.33 seconds
wall clock time: 33 minutes 12.10 seconds (1992.10 seconds total)