Starting phenix.real_space_refine
on Tue Mar 11 16:20:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gdz_29951/03_2025/8gdz_29951.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gdz_29951/03_2025/8gdz_29951.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gdz_29951/03_2025/8gdz_29951.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gdz_29951/03_2025/8gdz_29951.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gdz_29951/03_2025/8gdz_29951.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gdz_29951/03_2025/8gdz_29951.cif"
  }
  resolution = 3.5
  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=   0.033
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      37      5.16       5
     C    4079      2.51       5
     N    1102      2.21       5
     O    1102      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6320
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1644
          Classifications: {'peptide': 232}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 80}
          Link IDs: {'PTRANS': 6, 'TRANS': 225}
          Chain breaks: 3
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 292
          Unresolved non-hydrogen angles: 353
          Unresolved non-hydrogen dihedrals: 235
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 5, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 10}
          Unresolved non-hydrogen planarities: 192
    Chain: "B"
      Number of atoms: 2308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2308
          Classifications: {'peptide': 333}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 80}
          Link IDs: {'PTRANS': 5, 'TRANS': 327}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 253
          Unresolved non-hydrogen angles: 316
          Unresolved non-hydrogen dihedrals: 192
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 19, 'ASN:plan1': 6, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 10}
          Unresolved non-hydrogen planarities: 170
    Chain: "G"
      Number of atoms: 336
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 336
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 74
          Unresolved non-hydrogen angles: 87
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 40
    Chain: "R"
      Number of atoms: 2017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2017
          Classifications: {'peptide': 286}
          Incomplete info: {'truncation_to_alanine': 84}
          Link IDs: {'PTRANS': 7, 'TRANS': 278}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 295
          Unresolved non-hydrogen angles: 368
          Unresolved non-hydrogen dihedrals: 236
          Unresolved non-hydrogen chiralities: 30
          Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 145
    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: 4.87, per 1000 atoms: 0.77
  Number of scatterers: 6320
  At special positions: 0
  Unit cell: (68.9, 97.52, 129.32, 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      37     16.00
     O    1102      8.00
     N    1102      7.00
     C    4079      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 184 " - pdb=" SG  CYS R 190 " 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: 1.75
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1714

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 8 sheets defined
      49.6% alpha, 16.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 40
      removed outlier: 4.412A  pdb=" N   LYS A  17 " --> pdb=" O   ARG A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 51
    Processing helix  chain 'A' and resid 52 through 61
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.541A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    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
      removed outlier: 3.507A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.587A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 5 through 26
      removed outlier: 3.560A  pdb=" N   GLU B  10 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.637A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'B' and resid 280 through 282
      No H-bonds generated for 'chain 'B' and resid 280 through 282'
    Processing helix  chain 'G' and resid 11 through 23
      removed outlier: 3.748A  pdb=" N   GLN G  18 " --> pdb=" O   LYS G  14 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'R' and resid 30 through 61
      removed outlier: 3.535A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 97
      removed outlier: 4.274A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.250A  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 140 through 145
      removed outlier: 3.647A  pdb=" N   LEU R 145 " --> pdb=" O   TYR R 141 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 3.503A  pdb=" N   SER R 161 " --> pdb=" O   VAL R 157 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
      removed outlier: 3.686A  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 178 through 187
      removed outlier: 4.037A  pdb=" N   ALA R 186 " --> pdb=" O   ILE R 182 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   GLU R 187 " --> pdb=" O   ASN R 183 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 196 through 238
      removed outlier: 5.059A  pdb=" N   VAL R 210 " --> pdb=" O   VAL R 206 " (cutoff:3.500A)
      Proline residue:  R 211  - end of helix
    Processing helix  chain 'R' and resid 269 through 299
      removed outlier: 3.930A  pdb=" N   THR R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   CYS R 285 " --> pdb=" O   THR R 281 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
    Processing helix  chain 'R' and resid 304 through 327
      removed outlier: 3.791A  pdb=" N   TYR R 308 " --> pdb=" O   ARG R 304 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   SER R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   GLY R 320 " --> pdb=" O   TYR R 316 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   PHE R 321 " --> pdb=" O   VAL R 317 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ASN R 322 " --> pdb=" O   ASN R 318 " (cutoff:3.500A)
      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 208 through 214
      removed outlier: 7.002A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.013A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.635A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.012A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.193A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.238A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.254A  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 61
      removed outlier: 4.078A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105
      removed outlier: 5.455A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.678A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.728A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.718A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 8.024A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.099A  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: 3.858A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.113A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.929A  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 278
      removed outlier: 3.556A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    376 hydrogen bonds defined for protein.
    1086 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.13

  Time building geometry restraints manager: 2.08 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2051
        1.34 -     1.46: 1604
        1.46 -     1.58: 2753
        1.58 -     1.70: 0
        1.70 -     1.82: 50
  Bond restraints: 6458
  Sorted by residual:
  bond pdb=" CA  ARG A 231 "
       pdb=" C   ARG A 231 "
    ideal  model  delta    sigma   weight residual
    1.524  1.460  0.063 1.26e-02 6.30e+03 2.51e+01
  bond pdb=" CA  ARG A 232 "
       pdb=" C   ARG A 232 "
    ideal  model  delta    sigma   weight residual
    1.521  1.463  0.058 1.17e-02 7.31e+03 2.50e+01
  bond pdb=" N   ARG A 232 "
       pdb=" CA  ARG A 232 "
    ideal  model  delta    sigma   weight residual
    1.458  1.415  0.043 1.19e-02 7.06e+03 1.28e+01
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.450 -0.053 2.00e-02 2.50e+03 7.08e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.438 -0.044 2.00e-02 2.50e+03 4.94e+00
  ... (remaining 6453 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.11: 8784
        2.11 -     4.23: 57
        4.23 -     6.34: 12
        6.34 -     8.46: 2
        8.46 -    10.57: 1
  Bond angle restraints: 8856
  Sorted by residual:
  angle pdb=" N   ARG A 231 "
        pdb=" CA  ARG A 231 "
        pdb=" C   ARG A 231 "
      ideal   model   delta    sigma   weight residual
     110.23   99.66   10.57 1.45e+00 4.76e-01 5.32e+01
  angle pdb=" C   ARG A 232 "
        pdb=" N   LYS A 233 "
        pdb=" CA  LYS A 233 "
      ideal   model   delta    sigma   weight residual
     122.54  116.22    6.32 1.65e+00 3.67e-01 1.47e+01
  angle pdb=" C   ARG A 231 "
        pdb=" N   ARG A 232 "
        pdb=" CA  ARG A 232 "
      ideal   model   delta    sigma   weight residual
     123.00  117.91    5.09 1.41e+00 5.03e-01 1.30e+01
  angle pdb=" CA  LEU G  15 "
        pdb=" CB  LEU G  15 "
        pdb=" CG  LEU G  15 "
      ideal   model   delta    sigma   weight residual
     116.30  124.07   -7.77 3.50e+00 8.16e-02 4.93e+00
  angle pdb=" N   GLU B 226 "
        pdb=" CA  GLU B 226 "
        pdb=" C   GLU B 226 "
      ideal   model   delta    sigma   weight residual
     113.88  111.24    2.64 1.23e+00 6.61e-01 4.59e+00
  ... (remaining 8851 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 3425
       17.69 -    35.37: 224
       35.37 -    53.06: 39
       53.06 -    70.75: 8
       70.75 -    88.43: 4
  Dihedral angle restraints: 3700
    sinusoidal: 1063
      harmonic: 2637
  Sorted by residual:
  dihedral pdb=" CB  CYS R 184 "
           pdb=" SG  CYS R 184 "
           pdb=" SG  CYS R 190 "
           pdb=" CB  CYS R 190 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00    2.43  -88.43     1      1.00e+01 1.00e-02 9.34e+01
  dihedral pdb=" C   ARG A 231 "
           pdb=" N   ARG A 231 "
           pdb=" CA  ARG A 231 "
           pdb=" CB  ARG A 231 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -114.16   -8.44     0      2.50e+00 1.60e-01 1.14e+01
  dihedral pdb=" CG  ARG A 385 "
           pdb=" CD  ARG A 385 "
           pdb=" NE  ARG A 385 "
           pdb=" CZ  ARG A 385 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -136.01  -43.99     2      1.50e+01 4.44e-03 1.03e+01
  ... (remaining 3697 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 692
       0.032 -    0.063: 264
       0.063 -    0.095: 80
       0.095 -    0.126: 33
       0.126 -    0.158: 3
  Chirality restraints: 1072
  Sorted by residual:
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.56   -0.16 2.00e-01 2.50e+01 6.21e-01
  chirality pdb=" CA  ILE B 232 "
            pdb=" N   ILE B 232 "
            pdb=" C   ILE B 232 "
            pdb=" CB  ILE B 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.34e-01
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.00e-01
  ... (remaining 1069 not shown)

  Planarity restraints: 1121
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "    0.029 5.00e-02 4.00e+02   4.39e-02 3.09e+00
        pdb=" N   PRO G  49 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.026 5.00e-02 4.00e+02   3.89e-02 2.42e+00
        pdb=" N   PRO B 236 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 205 "    0.007 2.00e-02 2.50e+03   1.41e-02 1.98e+00
        pdb=" C   ILE R 205 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   ILE R 205 "    0.009 2.00e-02 2.50e+03
        pdb=" N   VAL R 206 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1118 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1633
        2.80 -     3.32: 6136
        3.32 -     3.85: 10506
        3.85 -     4.37: 11298
        4.37 -     4.90: 20569
  Nonbonded interactions: 50142
  Sorted by model distance:
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   ALA R 119 "
            pdb=" OG1 THR R 123 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAL G1I R 501 "
     model   vdw
     2.351 3.040
  nonbonded pdb=" OD2 ASP B 212 "
            pdb=" NH2 ARG B 219 "
     model   vdw
     2.363 3.120
  ... (remaining 50137 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:             1.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.460
  Find NCS groups from input model:        0.090
  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:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
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      :  0.003   0.063   6458  Z= 0.232
  Angle     :  0.509  10.574   8856  Z= 0.277
  Chirality :  0.039   0.158   1072
  Planarity :  0.003   0.044   1121
  Dihedral  : 12.959  86.708   1980
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  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:  1.42 (0.28), residues: 886
  helix:  2.52 (0.27), residues: 381
  sheet: -0.14 (0.38), residues: 175
  loop : -0.29 (0.32), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 234 
 HIS   0.004   0.001   HIS R  93 
 PHE   0.011   0.001   PHE A 222 
 TYR   0.016   0.001   TYR B  59 
 ARG   0.006   0.000   ARG R 239 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.717 
Fit side-chains
REVERT: B  249 THR cc_start: 0.9229 (p) cc_final: 0.8761 (p)
REVERT: B  297 TRP cc_start: 0.8742 (m100) cc_final: 0.8335 (m100)
REVERT: R  203 SER cc_start: 0.9392 (t) cc_final: 0.9164 (t)
REVERT: R  227 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8402 (mtpt)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1628
  time to fit residues: 26.0644
Evaluate side-chains
  94 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    0.0670
   chunk 67 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 23 optimal weight:   20.0000
   chunk 45 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 80 optimal weight:    0.6980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
B 225 HIS
B 259 GLN
B 340 ASN
R  93 HIS
R 312 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.110873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.096469 restraints weight = 12802.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.099403 restraints weight = 6011.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.101398 restraints weight = 3650.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.1003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6458  Z= 0.161
  Angle     :  0.474   6.456   8856  Z= 0.256
  Chirality :  0.040   0.144   1072
  Planarity :  0.003   0.042   1121
  Dihedral  :  3.907  16.205    969
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  :  9.86 %
    Favored  : 88.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.50 (0.28), residues: 886
  helix:  2.53 (0.27), residues: 391
  sheet: -0.04 (0.38), residues: 164
  loop : -0.30 (0.32), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.011   0.001   PHE A 222 
 TYR   0.011   0.001   TYR R 199 
 ARG   0.004   0.000   ARG R 239 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.679 
Fit side-chains
   revert: symmetry clash
REVERT: B   57 LYS cc_start: 0.8980 (pttp) cc_final: 0.8699 (pttp)
REVERT: R  122 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8498 (mm-30)
REVERT: R  227 LYS cc_start: 0.8643 (mtpp) cc_final: 0.8399 (mtpt)
  outliers start: 10
  outliers final: 4
  residues processed: 106
  average time/residue: 0.1426
  time to fit residues: 21.5520
Evaluate side-chains
  91 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 87
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue  312 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 72 optimal weight:    0.5980
   chunk 44 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 54 optimal weight:    0.8980
   chunk 69 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 HIS
B 259 GLN
B 340 ASN
R 178 HIS
R 312 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.110839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.096239 restraints weight = 13061.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.099127 restraints weight = 6180.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.101137 restraints weight = 3768.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.1256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6458  Z= 0.166
  Angle     :  0.458   6.328   8856  Z= 0.247
  Chirality :  0.039   0.143   1072
  Planarity :  0.003   0.041   1121
  Dihedral  :  3.816  16.533    969
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 14.89 %
    Favored  : 83.37 %
  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:  1.54 (0.28), residues: 886
  helix:  2.54 (0.27), residues: 392
  sheet:  0.01 (0.37), residues: 176
  loop : -0.28 (0.33), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.008   0.001   PHE A 212 
 TYR   0.011   0.001   TYR R 199 
 ARG   0.003   0.000   ARG R 239 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.750 
Fit side-chains
REVERT: B   57 LYS cc_start: 0.9037 (pttp) cc_final: 0.8765 (pttp)
REVERT: R  227 LYS cc_start: 0.8662 (mtpp) cc_final: 0.8435 (mtpt)
  outliers start: 9
  outliers final: 6
  residues processed: 105
  average time/residue: 0.1508
  time to fit residues: 22.4135
Evaluate side-chains
  94 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   38 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9980
   chunk 53 optimal weight:    8.9990
   chunk 50 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0970
   chunk 67 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 59 optimal weight:    0.7980
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 HIS
B 259 GLN
B 340 ASN
R  93 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.110496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.095950 restraints weight = 13158.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.098863 restraints weight = 6227.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.100814 restraints weight = 3788.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.1440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6458  Z= 0.167
  Angle     :  0.461   7.434   8856  Z= 0.245
  Chirality :  0.039   0.144   1072
  Planarity :  0.003   0.041   1121
  Dihedral  :  3.772  16.726    969
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 16.83 %
    Favored  : 80.85 %
  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:  1.56 (0.29), residues: 886
  helix:  2.57 (0.27), residues: 392
  sheet:  0.03 (0.39), residues: 168
  loop : -0.30 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R  93 
 PHE   0.009   0.001   PHE A 212 
 TYR   0.011   0.001   TYR R 199 
 ARG   0.003   0.000   ARG R 239 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.755 
Fit side-chains
REVERT: B   57 LYS cc_start: 0.9095 (pttp) cc_final: 0.8833 (pttp)
REVERT: R  122 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8515 (mm-30)
REVERT: R  227 LYS cc_start: 0.8671 (mtpp) cc_final: 0.8447 (mtpt)
  outliers start: 12
  outliers final: 8
  residues processed: 104
  average time/residue: 0.1470
  time to fit residues: 21.9192
Evaluate side-chains
  98 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue  303 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 14 optimal weight:    6.9990
   chunk 44 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9990
   chunk 54 optimal weight:    0.5980
   chunk 52 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 72 optimal weight:    0.8980
   chunk 23 optimal weight:   20.0000
   chunk 75 optimal weight:    0.0060
   chunk 66 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
B 225 HIS
B 340 ASN
R 178 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.110786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.096272 restraints weight = 12975.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.099165 restraints weight = 6158.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.101138 restraints weight = 3755.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.1526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6458  Z= 0.159
  Angle     :  0.445   5.970   8856  Z= 0.240
  Chirality :  0.039   0.148   1072
  Planarity :  0.003   0.041   1121
  Dihedral  :  3.746  16.839    969
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 19.34 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.63 (0.29), residues: 886
  helix:  2.62 (0.27), residues: 392
  sheet:  0.07 (0.38), residues: 176
  loop : -0.24 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.011   0.001   HIS B 225 
 PHE   0.016   0.001   PHE R 104 
 TYR   0.011   0.001   TYR R 199 
 ARG   0.003   0.000   ARG R 239 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.665 
Fit side-chains
REVERT: B   57 LYS cc_start: 0.9124 (pttp) cc_final: 0.8866 (pttp)
REVERT: R  227 LYS cc_start: 0.8678 (mtpp) cc_final: 0.8463 (mtpt)
  outliers start: 11
  outliers final: 9
  residues processed: 107
  average time/residue: 0.1434
  time to fit residues: 21.8683
Evaluate side-chains
  104 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue  303 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 87 optimal weight:    0.3980
   chunk 7 optimal weight:    0.0020
   chunk 16 optimal weight:    0.0870
   chunk 88 optimal weight:    0.8980
   chunk 57 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 53 optimal weight:    6.9990
   chunk 50 optimal weight:    0.6980
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.4166

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
A 294 GLN
B 225 HIS
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  93 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.110745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.096289 restraints weight = 12686.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.099244 restraints weight = 5922.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.101213 restraints weight = 3573.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.1682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6458  Z= 0.137
  Angle     :  0.435   7.677   8856  Z= 0.234
  Chirality :  0.039   0.149   1072
  Planarity :  0.003   0.040   1121
  Dihedral  :  3.672  16.474    969
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 19.54 %
    Favored  : 77.76 %
  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:  1.65 (0.29), residues: 886
  helix:  2.62 (0.26), residues: 394
  sheet:  0.08 (0.38), residues: 176
  loop : -0.23 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.007   0.001   HIS B 225 
 PHE   0.008   0.001   PHE A 212 
 TYR   0.010   0.001   TYR A 253 
 ARG   0.004   0.000   ARG R 239 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.749 
Fit side-chains
REVERT: B   57 LYS cc_start: 0.9119 (pttp) cc_final: 0.8878 (pttp)
REVERT: R  227 LYS cc_start: 0.8646 (mtpp) cc_final: 0.8430 (mtpt)
  outliers start: 14
  outliers final: 10
  residues processed: 112
  average time/residue: 0.1526
  time to fit residues: 24.5259
Evaluate side-chains
  108 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain R residue  303 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 9 optimal weight:    0.0020
   chunk 58 optimal weight:    0.3980
   chunk 85 optimal weight:    0.0870
   chunk 39 optimal weight:    0.6980
   chunk 29 optimal weight:    5.9990
   chunk 19 optimal weight:    0.0970
   chunk 87 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 54 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 45 optimal weight:    0.4980
   overall best weight:    0.2164

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
B 225 HIS
B 230 ASN
B 340 ASN
R 178 HIS
R 312 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.112694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.098298 restraints weight = 12784.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.101271 restraints weight = 6015.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.103234 restraints weight = 3629.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6458  Z= 0.126
  Angle     :  0.434   7.449   8856  Z= 0.233
  Chirality :  0.039   0.150   1072
  Planarity :  0.003   0.042   1121
  Dihedral  :  3.601  16.109    969
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 20.12 %
    Favored  : 77.56 %
  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:  1.71 (0.29), residues: 886
  helix:  2.70 (0.26), residues: 393
  sheet:  0.07 (0.38), residues: 176
  loop : -0.22 (0.34), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.009   0.001   HIS B 225 
 PHE   0.008   0.001   PHE B 199 
 TYR   0.012   0.001   TYR A 253 
 ARG   0.004   0.000   ARG R 239 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.711 
Fit side-chains
REVERT: R  122 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8474 (mm-30)
REVERT: R  227 LYS cc_start: 0.8575 (mtpp) cc_final: 0.8362 (mtpt)
  outliers start: 12
  outliers final: 8
  residues processed: 112
  average time/residue: 0.1321
  time to fit residues: 21.3465
Evaluate side-chains
  106 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain R residue  303 ILE
Chi-restraints excluded: chain R residue  312 ASN
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 20 optimal weight:    8.9990
   chunk 40 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 61 optimal weight:    8.9990
   chunk 6 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
A 362 HIS
B 225 HIS
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  93 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.107285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.093008 restraints weight = 13049.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.095787 restraints weight = 6194.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.097725 restraints weight = 3790.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.1816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   6458  Z= 0.327
  Angle     :  0.526   6.588   8856  Z= 0.283
  Chirality :  0.042   0.147   1072
  Planarity :  0.003   0.043   1121
  Dihedral  :  3.961  17.543    969
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 20.89 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.44 (0.29), residues: 886
  helix:  2.56 (0.27), residues: 385
  sheet: -0.13 (0.37), residues: 181
  loop : -0.34 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 339 
 HIS   0.017   0.002   HIS B 225 
 PHE   0.011   0.001   PHE A 212 
 TYR   0.014   0.002   TYR B  59 
 ARG   0.004   0.000   ARG R 239 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.769 
Fit side-chains
REVERT: R  122 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8538 (mm-30)
  outliers start: 14
  outliers final: 10
  residues processed: 103
  average time/residue: 0.1506
  time to fit residues: 22.3744
Evaluate side-chains
  96 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain R residue  303 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 79 optimal weight:    0.0570
   chunk 56 optimal weight:    0.8980
   chunk 15 optimal weight:    0.4980
   chunk 80 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 75 optimal weight:    0.0570
   chunk 22 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.4016

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
B 225 HIS
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 312 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.110832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.096471 restraints weight = 13009.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.099375 restraints weight = 6140.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.101342 restraints weight = 3718.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.1823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6458  Z= 0.146
  Angle     :  0.465   7.646   8856  Z= 0.248
  Chirality :  0.039   0.151   1072
  Planarity :  0.003   0.041   1121
  Dihedral  :  3.783  17.495    969
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 21.47 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.53 (0.29), residues: 886
  helix:  2.56 (0.27), residues: 392
  sheet: -0.10 (0.38), residues: 178
  loop : -0.26 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.010   0.001   HIS B 225 
 PHE   0.009   0.001   PHE A 212 
 TYR   0.021   0.001   TYR R 185 
 ARG   0.004   0.000   ARG R 239 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.717 
Fit side-chains
REVERT: R  122 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8393 (mm-30)
REVERT: R  227 LYS cc_start: 0.8694 (mtpp) cc_final: 0.8440 (mtpt)
  outliers start: 11
  outliers final: 9
  residues processed: 98
  average time/residue: 0.1497
  time to fit residues: 21.1436
Evaluate side-chains
  96 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain R residue  312 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 76 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0070
   chunk 35 optimal weight:    0.0010
   chunk 46 optimal weight:    2.9990
   chunk 85 optimal weight:    0.7980
   chunk 26 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9980
   overall best weight:    0.5404

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  93 HIS
R 312 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.111073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.096611 restraints weight = 13033.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.099536 restraints weight = 6145.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.101506 restraints weight = 3705.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6458  Z= 0.161
  Angle     :  0.470   7.793   8856  Z= 0.250
  Chirality :  0.039   0.147   1072
  Planarity :  0.003   0.041   1121
  Dihedral  :  3.752  17.180    969
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 21.86 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.56 (0.29), residues: 886
  helix:  2.60 (0.27), residues: 393
  sheet: -0.09 (0.38), residues: 178
  loop : -0.27 (0.34), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.010   0.001   PHE R 289 
 TYR   0.019   0.001   TYR R 185 
 ARG   0.004   0.000   ARG R 239 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.749 
Fit side-chains
REVERT: R  173 TRP cc_start: 0.8838 (m-10) cc_final: 0.8539 (m-10)
REVERT: R  227 LYS cc_start: 0.8686 (mtpp) cc_final: 0.8435 (mtpt)
  outliers start: 12
  outliers final: 9
  residues processed: 104
  average time/residue: 0.1445
  time to fit residues: 21.6307
Evaluate side-chains
  102 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain R residue  312 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 26 optimal weight:    0.0270
   chunk 83 optimal weight:    1.9990
   chunk 34 optimal weight:    0.4980
   chunk 33 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 20 optimal weight:   10.0000
   chunk 21 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.6238

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 312 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.111297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.096741 restraints weight = 13240.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.099671 restraints weight = 6261.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.101652 restraints weight = 3792.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6458  Z= 0.166
  Angle     :  0.475   9.393   8856  Z= 0.251
  Chirality :  0.040   0.147   1072
  Planarity :  0.003   0.041   1121
  Dihedral  :  3.703  17.054    969
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 22.05 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.58 (0.29), residues: 886
  helix:  2.59 (0.27), residues: 393
  sheet: -0.08 (0.38), residues: 178
  loop : -0.23 (0.34), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 339 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.010   0.001   PHE R 289 
 TYR   0.013   0.001   TYR R 185 
 ARG   0.004   0.000   ARG R 239 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2154.34 seconds
wall clock time: 38 minutes 0.01 seconds (2280.01 seconds total)