Starting phenix.real_space_refine
on Sat May  2 15:30:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9w0p_65511/05_2026/9w0p_65511.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9w0p_65511/05_2026/9w0p_65511.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9w0p_65511/05_2026/9w0p_65511.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9w0p_65511/05_2026/9w0p_65511.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9w0p_65511/05_2026/9w0p_65511.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9w0p_65511/05_2026/9w0p_65511.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.003 sd=   0.085
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     Cl      2      4.86       5
     C    4305      2.51       5
     N    1156      2.21       5
     O    1212      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6721
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1665
          Classifications: {'peptide': 215}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 2, 'TRANS': 212}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 74
          Unresolved non-hydrogen angles: 88
          Unresolved non-hydrogen dihedrals: 63
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 42
    Chain: "B"
      Number of atoms: 2501
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2501
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 83
          Unresolved non-hydrogen angles: 100
          Unresolved non-hydrogen dihedrals: 66
          Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 3, 'ARG:plan': 4, 'GLU:plan': 5, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 67
    Chain: "C"
      Number of atoms: 381
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 381
          Classifications: {'peptide': 54}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 42
          Unresolved non-hydrogen dihedrals: 32
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "R"
      Number of atoms: 2140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2140
          Classifications: {'peptide': 282}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PTRANS': 3, 'TRANS': 278}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 134
          Unresolved non-hydrogen angles: 173
          Unresolved non-hydrogen dihedrals: 115
          Unresolved non-hydrogen chiralities: 17
          Planarities with less than four sites: {'PHE:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1, 'TRP:plan': 2, 'ARG:plan': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 59
    Chain: "R"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 34
          Unusual residues: {'XC9': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.93, per 1000 atoms: 0.29
  Number of scatterers: 6721
  At special positions: 0
  Unit cell: (72.828, 101.745, 127.449, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      2     17.00
     S      46     16.00
     O    1212      8.00
     N    1156      7.00
     C    4305      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.61
  Conformation dependent library (CDL) restraints added in 396.2 milliseconds
  

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1678

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 8 sheets defined
      48.1% alpha, 17.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 33
      removed outlier: 3.881A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   GLU A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.204A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.705A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.927A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.896A  pdb=" N   GLU A 275 " --> pdb=" O   LYS A 271 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.972A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 311
      removed outlier: 3.967A  pdb=" N   ASN A 311 " --> pdb=" O   PHE A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 352
    Processing helix  chain 'B' and resid 6 through 26
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.847A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 10 through 24
    Processing helix  chain 'C' and resid 29 through 46
      removed outlier: 3.527A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
      removed outlier: 4.638A  pdb=" N   LYS C  46 " --> pdb=" O   GLU C  42 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 4 through 36
      removed outlier: 3.536A  pdb=" N   ILE R  27 " --> pdb=" O   GLY R  23 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   VAL R  30 " --> pdb=" O   PHE R  26 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   ASN R  31 " --> pdb=" O   ILE R  27 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 42 through 72
    Processing helix  chain 'R' and resid 78 through 111
      removed outlier: 3.750A  pdb=" N   PHE R  95 " --> pdb=" O   VAL R  91 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 118 through 124
    Processing helix  chain 'R' and resid 125 through 158
      removed outlier: 3.739A  pdb=" N   LEU R 131 " --> pdb=" O   LYS R 127 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ASN R 153 " --> pdb=" O   ASN R 149 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 174 through 214
      removed outlier: 3.633A  pdb=" N   LEU R 178 " --> pdb=" O   ARG R 174 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   LEU R 181 " --> pdb=" O   SER R 177 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   THR R 182 " --> pdb=" O   LEU R 178 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   VAL R 185 " --> pdb=" O   LEU R 181 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   ILE R 189 " --> pdb=" O   VAL R 185 " (cutoff:3.500A)
      Proline residue:  R 190  - end of helix
      removed outlier: 3.789A  pdb=" N   LEU R 200 " --> pdb=" O   ALA R 196 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   MET R 212 " --> pdb=" O   HIS R 208 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   HIS R 214 " --> pdb=" O   LYS R 210 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 224 through 257
      removed outlier: 3.521A  pdb=" N   ARG R 228 " --> pdb=" O   THR R 224 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   PHE R 247 " --> pdb=" O   PHE R 243 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   TRP R 252 " --> pdb=" O   PHE R 248 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   THR R 253 " --> pdb=" O   ILE R 249 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   SER R 254 " --> pdb=" O   SER R 250 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 261 through 282
      removed outlier: 3.861A  pdb=" N   SER R 265 " --> pdb=" O   LEU R 261 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   TYR R 272 " --> pdb=" O   MET R 268 " (cutoff:3.500A)
      Proline residue:  R 273  - end of helix
    Processing helix  chain 'R' and resid 285 through 298
      removed outlier: 4.355A  pdb=" N   GLN R 289 " --> pdb=" O   LYS R 285 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 3.598A  pdb=" N   VAL A 185 " --> pdb=" O   ASP A 200 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   PHE A 189 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL A  34 " --> pdb=" O   HIS A 195 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.436A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 5.825A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.383A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52
      removed outlier: 6.063A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.112A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62
      removed outlier: 4.329A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ALA B  73 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.633A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 5.850A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ASN B 125 " --> pdb=" O   ARG B 134 " (cutoff:3.500A)
      removed outlier: 4.535A  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: 6.972A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.074A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.375A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.682A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.507A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 5.280A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.146A  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: 4.789A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.490A  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: 3.518A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.677A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)

    383 hydrogen bonds defined for protein.
    1113 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: 1.20

  Time building geometry restraints manager: 0.83 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: 2104
        1.34 -     1.45: 945
        1.45 -     1.57: 3734
        1.57 -     1.69: 1
        1.69 -     1.81: 68
  Bond restraints: 6852
  Sorted by residual:
  bond pdb=" C13 XC9 R 401 "
       pdb=" N7  XC9 R 401 "
    ideal  model  delta    sigma   weight residual
    1.282  1.460 -0.178 2.00e-02 2.50e+03 7.89e+01
  bond pdb=" C4  XC9 R 401 "
       pdb=" N4  XC9 R 401 "
    ideal  model  delta    sigma   weight residual
    1.283  1.461 -0.178 2.00e-02 2.50e+03 7.89e+01
  bond pdb=" C5  XC9 R 401 "
       pdb=" N5  XC9 R 401 "
    ideal  model  delta    sigma   weight residual
    1.275  1.451 -0.176 2.00e-02 2.50e+03 7.75e+01
  bond pdb=" C14 XC9 R 401 "
       pdb=" N9  XC9 R 401 "
    ideal  model  delta    sigma   weight residual
    1.278  1.441 -0.163 2.00e-02 2.50e+03 6.61e+01
  bond pdb=" C14 XC9 R 401 "
       pdb=" N8  XC9 R 401 "
    ideal  model  delta    sigma   weight residual
    1.396  1.273  0.123 2.00e-02 2.50e+03 3.78e+01
  ... (remaining 6847 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.93: 9265
        3.93 -     7.85: 27
        7.85 -    11.78: 5
       11.78 -    15.70: 1
       15.70 -    19.63: 1
  Bond angle restraints: 9299
  Sorted by residual:
  angle pdb=" N2  XC9 R 401 "
        pdb=" C5  XC9 R 401 "
        pdb=" N3  XC9 R 401 "
      ideal   model   delta    sigma   weight residual
     110.98  130.61  -19.63 3.00e+00 1.11e-01 4.28e+01
  angle pdb=" CA  PHE R  76 "
        pdb=" C   PHE R  76 "
        pdb=" O   PHE R  76 "
      ideal   model   delta    sigma   weight residual
     122.64  116.22    6.42 1.25e+00 6.40e-01 2.64e+01
  angle pdb=" N3  XC9 R 401 "
        pdb=" C5  XC9 R 401 "
        pdb=" N5  XC9 R 401 "
      ideal   model   delta    sigma   weight residual
     127.15  114.67   12.48 3.00e+00 1.11e-01 1.73e+01
  angle pdb=" CA  PHE R  76 "
        pdb=" C   PHE R  76 "
        pdb=" N   ALA R  77 "
      ideal   model   delta    sigma   weight residual
     114.76  118.82   -4.06 1.14e+00 7.69e-01 1.27e+01
  angle pdb=" N6  XC9 R 401 "
        pdb=" C13 XC9 R 401 "
        pdb=" N8  XC9 R 401 "
      ideal   model   delta    sigma   weight residual
     112.58  122.90  -10.32 3.00e+00 1.11e-01 1.18e+01
  ... (remaining 9294 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.20: 3588
       17.20 -    34.40: 349
       34.40 -    51.60: 61
       51.60 -    68.80: 5
       68.80 -    86.00: 5
  Dihedral angle restraints: 4008
    sinusoidal: 1432
      harmonic: 2576
  Sorted by residual:
  dihedral pdb=" CA  ASP A 229 "
           pdb=" CB  ASP A 229 "
           pdb=" CG  ASP A 229 "
           pdb=" OD1 ASP A 229 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.55   59.55     1      2.00e+01 2.50e-03 1.18e+01
  dihedral pdb=" N   PHE R  76 "
           pdb=" CA  PHE R  76 "
           pdb=" CB  PHE R  76 "
           pdb=" CG  PHE R  76 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -115.47   55.47     3      1.50e+01 4.44e-03 9.35e+00
  dihedral pdb=" CB  LYS R 217 "
           pdb=" CG  LYS R 217 "
           pdb=" CD  LYS R 217 "
           pdb=" CE  LYS R 217 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -128.88  -51.12     3      1.50e+01 4.44e-03 8.98e+00
  ... (remaining 4005 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 793
       0.034 -    0.069: 213
       0.069 -    0.103: 63
       0.103 -    0.138: 26
       0.138 -    0.172: 3
  Chirality restraints: 1098
  Sorted by residual:
  chirality pdb=" CA  GLN A 304 "
            pdb=" N   GLN A 304 "
            pdb=" C   GLN A 304 "
            pdb=" CB  GLN A 304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.39e-01
  chirality pdb=" CB  ILE R 111 "
            pdb=" CA  ILE R 111 "
            pdb=" CG1 ILE R 111 "
            pdb=" CG2 ILE R 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.80   -0.16 2.00e-01 2.50e+01 6.29e-01
  chirality pdb=" CB  THR R  78 "
            pdb=" CA  THR R  78 "
            pdb=" OG1 THR R  78 "
            pdb=" CG2 THR R  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.69   -0.14 2.00e-01 2.50e+01 5.03e-01
  ... (remaining 1095 not shown)

  Planarity restraints: 1162
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 300 "   -0.010 2.00e-02 2.50e+03   1.94e-02 3.76e+00
        pdb=" C   ALA A 300 "    0.034 2.00e-02 2.50e+03
        pdb=" O   ALA A 300 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ALA A 301 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R 189 "    0.027 5.00e-02 4.00e+02   4.07e-02 2.66e+00
        pdb=" N   PRO R 190 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO R 190 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO R 190 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.022 5.00e-02 4.00e+02   3.31e-02 1.75e+00
        pdb=" N   PRO B 236 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.019 5.00e-02 4.00e+02
  ... (remaining 1159 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 278
        2.72 -     3.27: 6798
        3.27 -     3.81: 11179
        3.81 -     4.36: 12690
        4.36 -     4.90: 22216
  Nonbonded interactions: 53161
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 320 "
            pdb=" OD2 ASP A 341 "
     model   vdw
     2.179 3.040
  nonbonded pdb=" OG1 THR B  29 "
            pdb=" OE1 GLN B  32 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" NE  ARG R  55 "
            pdb=" OG  SER R  96 "
     model   vdw
     2.235 3.120
  nonbonded pdb=" O   ARG R 174 "
            pdb=" OG  SER R 177 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" O   ASN R 149 "
            pdb=" ND2 ASN R 153 "
     model   vdw
     2.270 3.120
  ... (remaining 53156 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:             1.690
  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:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.910
  Find NCS groups from input model:        0.030
  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:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6805
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      :  0.006   0.178   6852  Z= 0.300
  Angle     :  0.634  19.627   9299  Z= 0.330
  Chirality :  0.038   0.172   1098
  Planarity :  0.003   0.041   1162
  Dihedral  : 13.751  85.997   2330
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.29 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.67 (0.29), residues: 873
  helix:  2.32 (0.27), residues: 380
  sheet:  1.45 (0.42), residues: 174
  loop : -0.63 (0.34), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  21 
 TYR   0.012   0.001   TYR A 302 
 PHE   0.015   0.001   PHE R 198 
 TRP   0.006   0.001   TRP R  35 
 HIS   0.006   0.001   HIS R  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00603 ( 6852)
  covalent geometry    : angle       0.63364 ( 9299)
  hydrogen bonds       : bond        0.19986 (  383)
  hydrogen bonds       : angle       6.83993 ( 1113)

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 119
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A  251 ASP cc_start: 0.8204 (t0) cc_final: 0.7998 (t0)
REVERT: R   29 LEU cc_start: 0.6454 (pt) cc_final: 0.6045 (mp)
REVERT: R  217 LYS cc_start: 0.3371 (tttt) cc_final: 0.3137 (pttp)
REVERT: R  270 MET cc_start: 0.4613 (tmm) cc_final: 0.3995 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 120
  average time/residue: 0.0812
  time to fit residues: 13.3564
Evaluate side-chains
  97 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0870
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    1.6166

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

Flipped N/Q/H residues before XYZ refinement:
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 322 HIS
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 113 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.189573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.151969 restraints weight = 7640.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.149329 restraints weight = 9108.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.152050 restraints weight = 8594.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.151762 restraints weight = 5599.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.152267 restraints weight = 6178.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   6852  Z= 0.240
  Angle     :  0.668  12.996   9299  Z= 0.348
  Chirality :  0.045   0.158   1098
  Planarity :  0.004   0.039   1162
  Dihedral  :  5.164  59.237    941
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 12.26 %
    Favored  : 85.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.29), residues: 873
  helix:  2.09 (0.26), residues: 393
  sheet:  0.66 (0.39), residues: 179
  loop : -0.82 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 208 
 TYR   0.019   0.002   TYR A 320 
 PHE   0.022   0.003   PHE R 106 
 TRP   0.016   0.002   TRP B 169 
 HIS   0.012   0.002   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00561 ( 6852)
  covalent geometry    : angle       0.66755 ( 9299)
  hydrogen bonds       : bond        0.04411 (  383)
  hydrogen bonds       : angle       4.76386 ( 1113)

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.233 
Fit side-chains
REVERT: B  234 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.7184 (m-10)
  outliers start: 13
  outliers final: 6
  residues processed: 110
  average time/residue: 0.0791
  time to fit residues: 12.0205
Evaluate side-chains
  90 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  236 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 39 optimal weight:    0.4980
   chunk 83 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 48 optimal weight:    0.8980
   chunk 14 optimal weight:    5.9990
   chunk 78 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 255 ASN
R 113 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.193207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.155658 restraints weight = 7597.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.154009 restraints weight = 7784.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.156628 restraints weight = 7709.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.156301 restraints weight = 5456.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.157253 restraints weight = 5078.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.3887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7104
moved from start:          0.2566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6852  Z= 0.135
  Angle     :  0.561  13.122   9299  Z= 0.284
  Chirality :  0.041   0.155   1098
  Planarity :  0.003   0.033   1162
  Dihedral  :  4.888  54.861    941
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 15.91 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.29), residues: 873
  helix:  2.44 (0.26), residues: 387
  sheet:  0.35 (0.39), residues: 177
  loop : -0.78 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  68 
 TYR   0.016   0.001   TYR A 302 
 PHE   0.017   0.002   PHE R 106 
 TRP   0.011   0.001   TRP B 211 
 HIS   0.002   0.001   HIS R  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 6852)
  covalent geometry    : angle       0.56141 ( 9299)
  hydrogen bonds       : bond        0.03832 (  383)
  hydrogen bonds       : angle       4.36062 ( 1113)

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A  304 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7295 (mp10)
REVERT: C   21 MET cc_start: 0.6910 (tmm) cc_final: 0.6524 (tmm)
REVERT: R   76 PHE cc_start: 0.3535 (OUTLIER) cc_final: 0.3098 (t80)
REVERT: R  142 PHE cc_start: 0.6469 (OUTLIER) cc_final: 0.6090 (t80)
  outliers start: 20
  outliers final: 10
  residues processed: 107
  average time/residue: 0.0781
  time to fit residues: 11.6646
Evaluate side-chains
  95 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  304 GLN
Chi-restraints excluded: chain B residue   62 HIS
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue   76 PHE
Chi-restraints excluded: chain R residue   91 VAL
Chi-restraints excluded: chain R residue  142 PHE
Chi-restraints excluded: chain R residue  151 HIS
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  236 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 38 optimal weight:    0.0030
   chunk 71 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 29 optimal weight:    0.4980
   chunk 36 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 10 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.6792

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

Flipped N/Q/H residues before XYZ refinement:
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  35 ASN
R 113 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.194121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 89)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.145608 restraints weight = 7788.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.147377 restraints weight = 6723.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.148930 restraints weight = 5567.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.148916 restraints weight = 4811.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.149287 restraints weight = 4794.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7269
moved from start:          0.2897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6852  Z= 0.128
  Angle     :  0.553  13.178   9299  Z= 0.277
  Chirality :  0.040   0.159   1098
  Planarity :  0.003   0.034   1162
  Dihedral  :  4.839  53.428    941
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 18.39 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.31 (0.29), residues: 873
  helix:  2.38 (0.26), residues: 392
  sheet:  0.24 (0.40), residues: 170
  loop : -0.76 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 214 
 TYR   0.015   0.001   TYR A 302 
 PHE   0.015   0.001   PHE B 199 
 TRP   0.009   0.001   TRP B  63 
 HIS   0.003   0.001   HIS R  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6852)
  covalent geometry    : angle       0.55334 ( 9299)
  hydrogen bonds       : bond        0.03500 (  383)
  hydrogen bonds       : angle       4.12745 ( 1113)

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A  304 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7442 (mp10)
REVERT: B   61 MET cc_start: 0.8235 (tmm) cc_final: 0.8009 (tmm)
REVERT: R  142 PHE cc_start: 0.6383 (OUTLIER) cc_final: 0.6020 (t80)
  outliers start: 22
  outliers final: 13
  residues processed: 117
  average time/residue: 0.0926
  time to fit residues: 14.4706
Evaluate side-chains
  107 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  304 GLN
Chi-restraints excluded: chain B residue   62 HIS
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain R residue  142 PHE
Chi-restraints excluded: chain R residue  145 ILE
Chi-restraints excluded: chain R residue  151 HIS
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  195 LEU
Chi-restraints excluded: chain R residue  236 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 57 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   chunk 38 optimal weight:    0.3980
   chunk 63 optimal weight:    0.6980
   chunk 83 optimal weight:   10.0000
   chunk 64 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 113 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.206613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.199318 restraints weight = 7135.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.198524 restraints weight = 13009.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.198197 restraints weight = 11093.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.197200 restraints weight = 11197.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.196696 restraints weight = 9851.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.4064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6835
moved from start:          0.3170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6852  Z= 0.133
  Angle     :  0.557  13.167   9299  Z= 0.278
  Chirality :  0.040   0.158   1098
  Planarity :  0.003   0.033   1162
  Dihedral  :  4.893  53.440    941
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 20.15 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.29), residues: 873
  helix:  2.49 (0.26), residues: 391
  sheet: -0.10 (0.39), residues: 177
  loop : -0.84 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 209 
 TYR   0.014   0.001   TYR A 302 
 PHE   0.014   0.001   PHE R 106 
 TRP   0.010   0.001   TRP B  63 
 HIS   0.003   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 6852)
  covalent geometry    : angle       0.55701 ( 9299)
  hydrogen bonds       : bond        0.03423 (  383)
  hydrogen bonds       : angle       4.05130 ( 1113)

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A  304 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7595 (mp10)
REVERT: B  234 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.7037 (m-10)
REVERT: R  142 PHE cc_start: 0.6455 (OUTLIER) cc_final: 0.6132 (t80)
REVERT: R  212 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7111 (ttm)
  outliers start: 21
  outliers final: 13
  residues processed: 118
  average time/residue: 0.0854
  time to fit residues: 13.3538
Evaluate side-chains
  108 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  304 GLN
Chi-restraints excluded: chain B residue   62 HIS
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain R residue  113 ASN
Chi-restraints excluded: chain R residue  142 PHE
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  195 LEU
Chi-restraints excluded: chain R residue  202 ILE
Chi-restraints excluded: chain R residue  212 MET
Chi-restraints excluded: chain R residue  236 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 79 optimal weight:    8.9990
   chunk 84 optimal weight:    0.9980
   chunk 13 optimal weight:    0.4980
   chunk 18 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0570
   chunk 54 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0980
   chunk 56 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.4498

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
R 113 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.210945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.203814 restraints weight = 7177.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.190734 restraints weight = 13739.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.186611 restraints weight = 12460.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.185573 restraints weight = 11661.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.185471 restraints weight = 9457.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
moved from start:          0.3277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   6852  Z= 0.111
  Angle     :  0.556  13.109   9299  Z= 0.273
  Chirality :  0.040   0.203   1098
  Planarity :  0.003   0.034   1162
  Dihedral  :  4.817  46.817    941
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 20.73 %
    Favored  : 75.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.29), residues: 873
  helix:  2.40 (0.26), residues: 398
  sheet:  0.03 (0.41), residues: 170
  loop : -0.93 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 209 
 TYR   0.013   0.001   TYR A 302 
 PHE   0.012   0.001   PHE R 106 
 TRP   0.009   0.001   TRP B 211 
 HIS   0.003   0.001   HIS R  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 6852)
  covalent geometry    : angle       0.55616 ( 9299)
  hydrogen bonds       : bond        0.03239 (  383)
  hydrogen bonds       : angle       3.97976 ( 1113)

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A  304 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7509 (mp10)
REVERT: B  234 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7247 (m-10)
REVERT: R  133 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6757 (tp)
REVERT: R  142 PHE cc_start: 0.6519 (OUTLIER) cc_final: 0.6226 (t80)
  outliers start: 24
  outliers final: 10
  residues processed: 113
  average time/residue: 0.0802
  time to fit residues: 12.1954
Evaluate side-chains
  101 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  304 GLN
Chi-restraints excluded: chain B residue   62 HIS
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  101 THR
Chi-restraints excluded: chain R residue  133 LEU
Chi-restraints excluded: chain R residue  142 PHE
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  195 LEU
Chi-restraints excluded: chain R residue  202 ILE
Chi-restraints excluded: chain R residue  279 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 82 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 34 optimal weight:    0.3980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 113 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.209661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.201847 restraints weight = 7034.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.200679 restraints weight = 13722.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.200140 restraints weight = 13412.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.199144 restraints weight = 11936.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.199082 restraints weight = 10115.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.4180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6855
moved from start:          0.3409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6852  Z= 0.134
  Angle     :  0.571  12.985   9299  Z= 0.283
  Chirality :  0.041   0.172   1098
  Planarity :  0.003   0.043   1162
  Dihedral  :  4.880  48.665    941
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.78 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 20.44 %
    Favored  : 76.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.14 (0.29), residues: 873
  helix:  2.43 (0.26), residues: 398
  sheet: -0.22 (0.40), residues: 172
  loop : -0.95 (0.35), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 209 
 TYR   0.013   0.001   TYR A 302 
 PHE   0.016   0.001   PHE R 237 
 TRP   0.010   0.001   TRP B  63 
 HIS   0.003   0.001   HIS R  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6852)
  covalent geometry    : angle       0.57051 ( 9299)
  hydrogen bonds       : bond        0.03285 (  383)
  hydrogen bonds       : angle       3.96808 ( 1113)

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 94
  time to evaluate  : 0.310 
Fit side-chains
REVERT: A  243 MET cc_start: 0.8127 (mmm) cc_final: 0.7905 (tpt)
REVERT: A  304 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7605 (mp10)
REVERT: B  234 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7126 (m-10)
REVERT: R  133 LEU cc_start: 0.6584 (OUTLIER) cc_final: 0.6355 (tp)
  outliers start: 23
  outliers final: 16
  residues processed: 115
  average time/residue: 0.0943
  time to fit residues: 14.5295
Evaluate side-chains
  112 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ASN
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  304 GLN
Chi-restraints excluded: chain B residue   62 HIS
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain R residue  101 THR
Chi-restraints excluded: chain R residue  113 ASN
Chi-restraints excluded: chain R residue  133 LEU
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  195 LEU
Chi-restraints excluded: chain R residue  236 PHE
Chi-restraints excluded: chain R residue  279 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 27 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   chunk 52 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 76 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 10 optimal weight:    7.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 113 ASN
R 227 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.208141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.200502 restraints weight = 7061.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.198705 restraints weight = 12260.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.198160 restraints weight = 13258.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.197070 restraints weight = 13749.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.183954 restraints weight = 12961.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7206
moved from start:          0.3547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6852  Z= 0.140
  Angle     :  0.580  12.949   9299  Z= 0.287
  Chirality :  0.041   0.178   1098
  Planarity :  0.003   0.040   1162
  Dihedral  :  4.925  48.263    941
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.01 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 21.02 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.29), residues: 873
  helix:  2.40 (0.26), residues: 398
  sheet: -0.45 (0.39), residues: 177
  loop : -1.01 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 228 
 TYR   0.013   0.001   TYR A 302 
 PHE   0.017   0.001   PHE R 237 
 TRP   0.010   0.001   TRP B  63 
 HIS   0.003   0.001   HIS R 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 6852)
  covalent geometry    : angle       0.58019 ( 9299)
  hydrogen bonds       : bond        0.03301 (  383)
  hydrogen bonds       : angle       3.98526 ( 1113)

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A  243 MET cc_start: 0.8293 (mmm) cc_final: 0.8074 (tpt)
REVERT: A  304 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7561 (mp10)
REVERT: B  234 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7251 (m-10)
REVERT: R  133 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6823 (tp)
  outliers start: 20
  outliers final: 16
  residues processed: 110
  average time/residue: 0.0879
  time to fit residues: 13.0043
Evaluate side-chains
  108 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 89
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  304 GLN
Chi-restraints excluded: chain B residue   62 HIS
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain R residue   91 VAL
Chi-restraints excluded: chain R residue  101 THR
Chi-restraints excluded: chain R residue  113 ASN
Chi-restraints excluded: chain R residue  133 LEU
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  195 LEU
Chi-restraints excluded: chain R residue  236 PHE
Chi-restraints excluded: chain R residue  279 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 32 optimal weight:    0.4980
   chunk 66 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 84 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 4 optimal weight:   10.0000
   chunk 74 optimal weight:    6.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 113 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.207513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.200129 restraints weight = 7126.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.188620 restraints weight = 12319.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.183451 restraints weight = 10638.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.182748 restraints weight = 9711.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.182216 restraints weight = 8951.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.3631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6852  Z= 0.140
  Angle     :  0.580  12.915   9299  Z= 0.288
  Chirality :  0.041   0.187   1098
  Planarity :  0.003   0.040   1162
  Dihedral  :  4.957  47.885    941
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.78 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 20.44 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.30), residues: 873
  helix:  2.40 (0.26), residues: 398
  sheet: -0.55 (0.39), residues: 177
  loop : -1.02 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 228 
 TYR   0.013   0.001   TYR A 302 
 PHE   0.017   0.001   PHE R 237 
 TRP   0.010   0.001   TRP B  63 
 HIS   0.003   0.001   HIS R 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 6852)
  covalent geometry    : angle       0.57979 ( 9299)
  hydrogen bonds       : bond        0.03316 (  383)
  hydrogen bonds       : angle       3.99423 ( 1113)

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 0.253 
Fit side-chains
REVERT: A  243 MET cc_start: 0.8310 (mmm) cc_final: 0.8070 (tpt)
REVERT: A  304 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7585 (mp10)
REVERT: B  234 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.7189 (m-10)
REVERT: R  133 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6823 (tp)
  outliers start: 21
  outliers final: 16
  residues processed: 104
  average time/residue: 0.0884
  time to fit residues: 12.3002
Evaluate side-chains
  104 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  304 GLN
Chi-restraints excluded: chain B residue   62 HIS
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue   29 LEU
Chi-restraints excluded: chain R residue   91 VAL
Chi-restraints excluded: chain R residue  101 THR
Chi-restraints excluded: chain R residue  133 LEU
Chi-restraints excluded: chain R residue  151 HIS
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  195 LEU
Chi-restraints excluded: chain R residue  236 PHE
Chi-restraints excluded: chain R residue  279 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 83 optimal weight:   20.0000
   chunk 38 optimal weight:    2.9990
   chunk 59 optimal weight:    6.9990
   chunk 75 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0970
   chunk 35 optimal weight:    0.0970
   chunk 3 optimal weight:    0.2980
   chunk 69 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9990
   overall best weight:    0.3576

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

Flipped N/Q/H residues before XYZ refinement:
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 113 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.210615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.203210 restraints weight = 7217.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.201714 restraints weight = 13749.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.186671 restraints weight = 14064.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.180788 restraints weight = 15141.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.182597 restraints weight = 13601.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7238
moved from start:          0.3640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6852  Z= 0.106
  Angle     :  0.560  12.815   9299  Z= 0.274
  Chirality :  0.040   0.185   1098
  Planarity :  0.003   0.035   1162
  Dihedral  :  4.821  47.102    941
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.67 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 21.90 %
    Favored  : 76.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.30), residues: 873
  helix:  2.47 (0.26), residues: 399
  sheet: -0.32 (0.40), residues: 176
  loop : -0.90 (0.36), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 228 
 TYR   0.012   0.001   TYR A 302 
 PHE   0.014   0.001   PHE R 237 
 TRP   0.008   0.001   TRP B  63 
 HIS   0.004   0.001   HIS R  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 6852)
  covalent geometry    : angle       0.55965 ( 9299)
  hydrogen bonds       : bond        0.03104 (  383)
  hydrogen bonds       : angle       3.88305 ( 1113)

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A  243 MET cc_start: 0.8235 (mmm) cc_final: 0.8002 (tpt)
REVERT: A  304 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7322 (mp10)
REVERT: B   61 MET cc_start: 0.7986 (tmm) cc_final: 0.7730 (tmm)
REVERT: B  188 MET cc_start: 0.8180 (mmm) cc_final: 0.7248 (mtp)
REVERT: B  197 ARG cc_start: 0.7488 (ttp-170) cc_final: 0.7079 (ttm110)
REVERT: B  234 PHE cc_start: 0.7918 (OUTLIER) cc_final: 0.7373 (m-10)
REVERT: R   29 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.5584 (mp)
  outliers start: 13
  outliers final: 8
  residues processed: 103
  average time/residue: 0.0898
  time to fit residues: 12.3734
Evaluate side-chains
  100 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  304 GLN
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue   29 LEU
Chi-restraints excluded: chain R residue  101 THR
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  195 LEU
Chi-restraints excluded: chain R residue  236 PHE
Chi-restraints excluded: chain R residue  279 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 51 optimal weight:    9.9990
   chunk 46 optimal weight:    4.9990
   overall best weight:    0.9780

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

Flipped N/Q/H residues before XYZ refinement:
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 113 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.204927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.197358 restraints weight = 7047.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.195760 restraints weight = 13311.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.195348 restraints weight = 13805.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.194596 restraints weight = 13679.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.194541 restraints weight = 11839.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.4248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6893
moved from start:          0.3863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6852  Z= 0.159
  Angle     :  0.596  12.861   9299  Z= 0.298
  Chirality :  0.042   0.183   1098
  Planarity :  0.003   0.048   1162
  Dihedral  :  4.988  49.413    941
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.24 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 22.04 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.30), residues: 873
  helix:  2.44 (0.26), residues: 399
  sheet: -0.71 (0.39), residues: 179
  loop : -1.00 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 214 
 TYR   0.014   0.001   TYR A 302 
 PHE   0.016   0.002   PHE R 237 
 TRP   0.011   0.001   TRP B  63 
 HIS   0.005   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 6852)
  covalent geometry    : angle       0.59563 ( 9299)
  hydrogen bonds       : bond        0.03323 (  383)
  hydrogen bonds       : angle       3.98586 ( 1113)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1203.46 seconds
wall clock time: 21 minutes 40.23 seconds (1300.23 seconds total)