Starting phenix.real_space_refine
on Tue Feb  3 22:50:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m57_63638/02_2026/9m57_63638_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m57_63638/02_2026/9m57_63638.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9m57_63638/02_2026/9m57_63638_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m57_63638/02_2026/9m57_63638_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9m57_63638/02_2026/9m57_63638.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m57_63638/02_2026/9m57_63638.map"
  }
  resolution = 3.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      49      5.16       5
     C    4834      2.51       5
     N    1290      2.21       5
     O    1384      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7557
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 177, 1304
          Classifications: {'peptide': 177}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 50}
          Link IDs: {'PTRANS': 1, 'TRANS': 175}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 195
          Unresolved non-hydrogen angles: 237
          Unresolved non-hydrogen dihedrals: 160
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'ASN:plan1': 5, 'GLN:plan1': 2, 'ASP:plan': 5, 'ARG:plan': 9, 'GLU:plan': 3, 'TYR:plan': 1, 'PHE:plan': 2}
          Unresolved non-hydrogen planarities: 114
    Chain: "B"
      Number of atoms: 2390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2390
          Classifications: {'peptide': 329}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PTRANS': 5, 'TRANS': 323}
          Unresolved non-hydrogen bonds: 137
          Unresolved non-hydrogen angles: 170
          Unresolved non-hydrogen dihedrals: 108
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 5, 'ASN:plan1': 5, 'ARG:plan': 5, 'ASP:plan': 6, 'HIS:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 105
    Chain: "G"
      Number of atoms: 302
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 302
          Classifications: {'peptide': 49}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 4, 'TRANS': 44}
          Unresolved non-hydrogen bonds: 78
          Unresolved non-hydrogen angles: 94
          Unresolved non-hydrogen dihedrals: 62
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 38
    Chain: "R"
      Number of atoms: 1944
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 1944
          Classifications: {'peptide': 271}
          Incomplete info: {'truncation_to_alanine': 80}
          Link IDs: {'PTRANS': 8, 'TRANS': 262}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 250
          Unresolved non-hydrogen angles: 318
          Unresolved non-hydrogen dihedrals: 192
          Unresolved non-hydrogen chiralities: 41
          Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 4, 'HIS:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 5}
          Unresolved non-hydrogen planarities: 94
    Chain: "S"
      Number of atoms: 1606
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1606
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 56}
          Link IDs: {'PTRANS': 10, 'TRANS': 219}
          Chain breaks: 1
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 167
          Unresolved non-hydrogen angles: 207
          Unresolved non-hydrogen dihedrals: 129
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 7, 'ASP:plan': 4, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 80
    Chain: "R"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 11
          Unusual residues: {'OTR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.30, per 1000 atoms: 0.17
  Number of scatterers: 7557
  At special positions: 0
  Unit cell: (89.478, 115.161, 118.475, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      49     16.00
     O    1384      8.00
     N    1290      7.00
     C    4834      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 103 " - pdb=" SG  CYS R 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.73
  Conformation dependent library (CDL) restraints added in 230.3 milliseconds
  

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1988

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 12 sheets defined
      37.6% alpha, 17.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 38
    Processing helix  chain 'A' and resid 53 through 59
    Processing helix  chain 'A' and resid 232 through 236
      removed outlier: 4.090A  pdb=" N   ILE A 235 " --> pdb=" O   ARG A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 279
    Processing helix  chain 'A' and resid 293 through 301
    Processing helix  chain 'A' and resid 334 through 350
    Processing helix  chain 'A' and resid 371 through 391
    Processing helix  chain 'B' and resid 13 through 25
    Processing helix  chain 'B' and resid 30 through 35
    Processing helix  chain 'G' and resid 16 through 24
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 4.008A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 29 through 59
      removed outlier: 3.580A  pdb=" N   HIS R  59 " --> pdb=" O   VAL R  55 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 65 through 94
      removed outlier: 4.499A  pdb=" N   ILE R  69 " --> pdb=" O   THR R  65 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   MET R  84 " --> pdb=" O   ALA R  80 " (cutoff:3.500A)
      removed outlier: 4.792A  pdb=" N   THR R  85 " --> pdb=" O   LEU R  81 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   PHE R  86 " --> pdb=" O   PHE R  82 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 99 through 133
    Processing helix  chain 'R' and resid 137 through 141
    Processing helix  chain 'R' and resid 143 through 169
      removed outlier: 4.143A  pdb=" N   ILE R 164 " --> pdb=" O   LEU R 160 " (cutoff:3.500A)
      Proline residue:  R 165  - end of helix
    Processing helix  chain 'R' and resid 173 through 183
      removed outlier: 3.752A  pdb=" N   HIS R 183 " --> pdb=" O   TYR R 179 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 192 through 204
    Processing helix  chain 'R' and resid 204 through 230
      removed outlier: 4.097A  pdb=" N   TRP R 216 " --> pdb=" O   LEU R 212 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   CYS R 230 " --> pdb=" O   GLU R 226 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 285 through 310
      removed outlier: 3.906A  pdb=" N   PHE R 296 " --> pdb=" O   ILE R 292 " (cutoff:3.500A)
      Proline residue:  R 302  - end of helix
    Processing helix  chain 'R' and resid 323 through 345
      Proline residue:  R 339  - end of helix
      removed outlier: 4.136A  pdb=" N   ALA R 343 " --> pdb=" O   PRO R 339 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   PHE R 345 " --> pdb=" O   ILE R 341 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 346 through 360
    Processing helix  chain 'S' and resid 28 through 32
      removed outlier: 3.714A  pdb=" N   SER S  31 " --> pdb=" O   ALA S  28 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 220 through 224
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214
      removed outlier: 7.465A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.518A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.564A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   THR A 248 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51
      removed outlier: 3.535A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   VAL B 327 " --> pdb=" O   TRP B 339 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.256A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.054A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.490A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105
      removed outlier: 3.823A  pdb=" N   ALA B 113 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 148
      removed outlier: 6.789A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.773A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.562A  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: 7.227A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277
      removed outlier: 6.847A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.998A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU B 285 " --> pdb=" O   TRP B 297 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'S' and resid 58 through 60
      removed outlier: 3.566A  pdb=" N   TYR S  59 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   TYR S  50 " --> pdb=" O   TYR S  59 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 155 through 160
    Processing sheet with id=AB3, first strand: chain 'S' and resid 189 through 190
      removed outlier: 3.903A  pdb=" N   ILE S 189 " --> pdb=" O   TRP S 176 " (cutoff:3.500A)

    400 hydrogen bonds defined for protein.
    1131 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: 1.16

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.11 -     1.25: 1118
        1.25 -     1.39: 2060
        1.39 -     1.53: 3905
        1.53 -     1.67: 572
        1.67 -     1.81: 68
  Bond restraints: 7723
  Sorted by residual:
  bond pdb=" C7  OTR R 401 "
       pdb=" O7  OTR R 401 "
    ideal  model  delta    sigma   weight residual
    1.407  1.186  0.221 2.00e-02 2.50e+03 1.22e+02
  bond pdb=" C   THR S 238 "
       pdb=" O   THR S 238 "
    ideal  model  delta    sigma   weight residual
    1.234  1.107  0.128 1.21e-02 6.83e+03 1.11e+02
  bond pdb=" N   GLY S 242 "
       pdb=" CA  GLY S 242 "
    ideal  model  delta    sigma   weight residual
    1.449  1.511 -0.062 1.00e-02 1.00e+04 3.86e+01
  bond pdb=" C   PHE S 239 "
       pdb=" O   PHE S 239 "
    ideal  model  delta    sigma   weight residual
    1.234  1.156  0.078 1.26e-02 6.30e+03 3.80e+01
  bond pdb=" C   GLY S 240 "
       pdb=" O   GLY S 240 "
    ideal  model  delta    sigma   weight residual
    1.232  1.154  0.077 1.45e-02 4.76e+03 2.86e+01
  ... (remaining 7718 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.68: 10529
        6.68 -    13.35: 20
       13.35 -    20.03: 1
       20.03 -    26.70: 0
       26.70 -    33.38: 1
  Bond angle restraints: 10551
  Sorted by residual:
  angle pdb=" C   PHE S 239 "
        pdb=" CA  PHE S 239 "
        pdb=" CB  PHE S 239 "
      ideal   model   delta    sigma   weight residual
     109.38   76.00   33.38 2.09e+00 2.29e-01 2.55e+02
  angle pdb=" N   ALA S 241 "
        pdb=" CA  ALA S 241 "
        pdb=" C   ALA S 241 "
      ideal   model   delta    sigma   weight residual
     111.28  126.30  -15.02 1.09e+00 8.42e-01 1.90e+02
  angle pdb=" CA  PHE S 239 "
        pdb=" CB  PHE S 239 "
        pdb=" CG  PHE S 239 "
      ideal   model   delta    sigma   weight residual
     113.80  126.79  -12.99 1.00e+00 1.00e+00 1.69e+02
  angle pdb=" CA  ALA S 241 "
        pdb=" C   ALA S 241 "
        pdb=" N   GLY S 242 "
      ideal   model   delta    sigma   weight residual
     117.30  129.54  -12.24 1.16e+00 7.43e-01 1.11e+02
  angle pdb=" N   GLY S 242 "
        pdb=" CA  GLY S 242 "
        pdb=" C   GLY S 242 "
      ideal   model   delta    sigma   weight residual
     111.85  122.83  -10.98 1.06e+00 8.90e-01 1.07e+02
  ... (remaining 10546 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.45: 3852
       17.45 -    34.89: 456
       34.89 -    52.34: 119
       52.34 -    69.79: 12
       69.79 -    87.24: 4
  Dihedral angle restraints: 4443
    sinusoidal: 1374
      harmonic: 3069
  Sorted by residual:
  dihedral pdb=" C   PHE S 239 "
           pdb=" N   PHE S 239 "
           pdb=" CA  PHE S 239 "
           pdb=" CB  PHE S 239 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60  -82.04  -40.56     0      2.50e+00 1.60e-01 2.63e+02
  dihedral pdb=" C   TYR S 235 "
           pdb=" N   TYR S 235 "
           pdb=" CA  TYR S 235 "
           pdb=" CB  TYR S 235 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -141.40   18.80     0      2.50e+00 1.60e-01 5.66e+01
  dihedral pdb=" CB  CYS S  22 "
           pdb=" SG  CYS S  22 "
           pdb=" SG  CYS S  96 "
           pdb=" CB  CYS S  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -134.91   48.91     1      1.00e+01 1.00e-02 3.29e+01
  ... (remaining 4440 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.125: 1214
       0.125 -    0.250: 17
       0.250 -    0.374: 2
       0.374 -    0.499: 0
       0.499 -    0.624: 2
  Chirality restraints: 1235
  Sorted by residual:
  chirality pdb=" CA  TYR S 235 "
            pdb=" N   TYR S 235 "
            pdb=" C   TYR S 235 "
            pdb=" CB  TYR S 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.89    0.62 2.00e-01 2.50e+01 9.73e+00
  chirality pdb=" CA  ALA S 241 "
            pdb=" N   ALA S 241 "
            pdb=" C   ALA S 241 "
            pdb=" CB  ALA S 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.96    0.52 2.00e-01 2.50e+01 6.76e+00
  chirality pdb=" C7  OTR R 401 "
            pdb=" C1  OTR R 401 "
            pdb=" C8  OTR R 401 "
            pdb=" O7  OTR R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    2.05    0.37 2.00e-01 2.50e+01 3.45e+00
  ... (remaining 1232 not shown)

  Planarity restraints: 1338
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO S 236 "   -0.028 2.00e-02 2.50e+03   5.64e-02 3.18e+01
        pdb=" C   PRO S 236 "    0.098 2.00e-02 2.50e+03
        pdb=" O   PRO S 236 "   -0.036 2.00e-02 2.50e+03
        pdb=" N   LEU S 237 "   -0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY S 240 "    0.025 2.00e-02 2.50e+03   5.18e-02 2.68e+01
        pdb=" C   GLY S 240 "   -0.089 2.00e-02 2.50e+03
        pdb=" O   GLY S 240 "    0.034 2.00e-02 2.50e+03
        pdb=" N   ALA S 241 "    0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS S 232 "   -0.026 2.00e-02 2.50e+03   5.11e-02 2.61e+01
        pdb=" C   HIS S 232 "    0.088 2.00e-02 2.50e+03
        pdb=" O   HIS S 232 "   -0.033 2.00e-02 2.50e+03
        pdb=" N   LEU S 233 "   -0.030 2.00e-02 2.50e+03
  ... (remaining 1335 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 851
        2.75 -     3.29: 7406
        3.29 -     3.82: 12389
        3.82 -     4.36: 13477
        4.36 -     4.90: 24437
  Nonbonded interactions: 58560
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP R  76 "
            pdb=" OG  SER R 335 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OD1 ASP B 205 "
            pdb=" OG  SER B 207 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" OG  SER R 125 "
            pdb=" OG1 THR R 214 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OE2 GLU A  15 "
            pdb=" OH  TYR S 175 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   SER R 158 "
            pdb=" OG  SER R 162 "
     model   vdw
     2.274 3.040
  ... (remaining 58555 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:             0.930
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.810
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.221   7726  Z= 0.304
  Angle     :  0.835  33.381  10557  Z= 0.522
  Chirality :  0.051   0.624   1235
  Planarity :  0.006   0.083   1338
  Dihedral  : 16.251  87.235   2446
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  : 37.59 %
    Favored  : 62.26 %
  Cbeta Deviations :  0.20 %
  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: -0.47 (0.26), residues: 1026
  helix:  1.53 (0.27), residues: 366
  sheet: -0.72 (0.32), residues: 261
  loop : -1.78 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG S  72 
 TYR   0.034   0.001   TYR S 235 
 PHE   0.023   0.001   PHE S  29 
 TRP   0.023   0.002   TRP B  82 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 ( 7723)
  covalent geometry    : angle       0.83409 (10551)
  SS BOND              : bond        0.00218 (    3)
  SS BOND              : angle       1.52429 (    6)
  hydrogen bonds       : bond        0.09672 (  400)
  hydrogen bonds       : angle       6.11345 ( 1131)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 234
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
REVERT: A  238 PHE cc_start: 0.8346 (m-10) cc_final: 0.8118 (m-10)
REVERT: A  269 SER cc_start: 0.8738 (m) cc_final: 0.8361 (p)
REVERT: A  360 TYR cc_start: 0.8738 (m-80) cc_final: 0.8521 (m-80)
REVERT: A  362 HIS cc_start: 0.7384 (m-70) cc_final: 0.6031 (m90)
REVERT: A  373 ARG cc_start: 0.8551 (mmt180) cc_final: 0.8227 (mmm160)
REVERT: B  179 THR cc_start: 0.8190 (p) cc_final: 0.7984 (t)
REVERT: B  280 LYS cc_start: 0.9065 (ttmm) cc_final: 0.8540 (ttpt)
REVERT: B  283 ARG cc_start: 0.7943 (ttt90) cc_final: 0.7667 (tmt170)
REVERT: B  303 ASP cc_start: 0.8416 (t70) cc_final: 0.8011 (m-30)
REVERT: R  217 ARG cc_start: 0.7659 (mtp85) cc_final: 0.7360 (mtp85)
REVERT: S  219 LEU cc_start: 0.6167 (pt) cc_final: 0.5860 (tt)
REVERT: S  231 GLN cc_start: 0.8703 (pp30) cc_final: 0.8206 (pp30)
  outliers start: 1
  outliers final: 0
  residues processed: 235
  average time/residue: 0.0746
  time to fit residues: 23.9338
Evaluate side-chains
  206 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:   20.0000
   chunk 38 optimal weight:    0.4980
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  87 ASN
R 120 HIS
R 338 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.182005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.148275 restraints weight = 10414.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.146594 restraints weight = 8809.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.147915 restraints weight = 9596.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.149029 restraints weight = 6758.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.150262 restraints weight = 5977.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.1180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   7726  Z= 0.132
  Angle     :  0.575  10.808  10557  Z= 0.298
  Chirality :  0.043   0.166   1235
  Planarity :  0.004   0.060   1338
  Dihedral  :  4.404  22.627   1125
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 33.14 %
    Favored  : 60.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.26), residues: 1026
  helix:  1.97 (0.26), residues: 369
  sheet: -0.65 (0.32), residues: 266
  loop : -1.84 (0.28), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG S 160 
 TYR   0.023   0.001   TYR S 235 
 PHE   0.026   0.001   PHE A 222 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 7723)
  covalent geometry    : angle       0.57406 (10551)
  SS BOND              : bond        0.00326 (    3)
  SS BOND              : angle       1.39990 (    6)
  hydrogen bonds       : bond        0.03774 (  400)
  hydrogen bonds       : angle       5.31578 ( 1131)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 208
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A  269 SER cc_start: 0.8262 (m) cc_final: 0.7838 (p)
REVERT: A  362 HIS cc_start: 0.7441 (m-70) cc_final: 0.6356 (m90)
REVERT: A  373 ARG cc_start: 0.8297 (mmt180) cc_final: 0.7949 (mmm160)
REVERT: B  217 MET cc_start: 0.7128 (ppp) cc_final: 0.6890 (pmm)
REVERT: R  137 GLU cc_start: 0.7959 (pt0) cc_final: 0.7741 (pt0)
REVERT: R  211 MET cc_start: 0.7572 (mmt) cc_final: 0.7317 (mmt)
REVERT: S  231 GLN cc_start: 0.8513 (pp30) cc_final: 0.8292 (pp30)
  outliers start: 40
  outliers final: 25
  residues processed: 233
  average time/residue: 0.0702
  time to fit residues: 22.4791
Evaluate side-chains
  220 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 195
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LYS
Chi-restraints excluded: chain A residue  273 PHE
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain G residue   61 PHE
Chi-restraints excluded: chain R residue  130 TYR
Chi-restraints excluded: chain R residue  163 PHE
Chi-restraints excluded: chain R residue  190 VAL
Chi-restraints excluded: chain R residue  289 LEU
Chi-restraints excluded: chain S residue   25 SER
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue   99 SER
Chi-restraints excluded: chain S residue  193 SER
Chi-restraints excluded: chain S residue  204 SER
Chi-restraints excluded: chain S residue  235 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 13 optimal weight:   10.0000
   chunk 10 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 53 optimal weight:   10.0000
   chunk 68 optimal weight:   50.0000
   chunk 39 optimal weight:    7.9990
   chunk 83 optimal weight:    0.7980
   chunk 27 optimal weight:    0.4980
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 155 ASN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 120 HIS
R 338 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.177349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.143179 restraints weight = 10313.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.142418 restraints weight = 9054.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.143905 restraints weight = 9601.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.145122 restraints weight = 5986.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.146047 restraints weight = 5275.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072   7726  Z= 0.199
  Angle     :  0.609   9.823  10557  Z= 0.319
  Chirality :  0.044   0.205   1235
  Planarity :  0.004   0.050   1338
  Dihedral  :  4.484  22.124   1125
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  9.06 %
    Allowed  : 29.72 %
    Favored  : 61.22 %
  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: -0.13 (0.26), residues: 1026
  helix:  1.95 (0.26), residues: 378
  sheet: -0.65 (0.33), residues: 265
  loop : -1.76 (0.29), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 283 
 TYR   0.019   0.002   TYR S 235 
 PHE   0.031   0.002   PHE A 222 
 TRP   0.010   0.001   TRP R 329 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 7723)
  covalent geometry    : angle       0.60829 (10551)
  SS BOND              : bond        0.00482 (    3)
  SS BOND              : angle       1.50715 (    6)
  hydrogen bonds       : bond        0.04058 (  400)
  hydrogen bonds       : angle       5.31518 ( 1131)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 205
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
REVERT: A  373 ARG cc_start: 0.8408 (mmt180) cc_final: 0.8037 (mmm160)
REVERT: B  204 CYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7350 (m)
REVERT: B  308 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6781 (mp)
REVERT: R  192 ASN cc_start: 0.6568 (OUTLIER) cc_final: 0.5205 (p0)
REVERT: S   18 ARG cc_start: 0.7582 (tpp80) cc_final: 0.6828 (tpt-90)
REVERT: S  109 ASP cc_start: 0.7484 (t70) cc_final: 0.7176 (t70)
REVERT: S  231 GLN cc_start: 0.8540 (pp30) cc_final: 0.8246 (pp30)
  outliers start: 61
  outliers final: 43
  residues processed: 242
  average time/residue: 0.0683
  time to fit residues: 22.9873
Evaluate side-chains
  242 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 196
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LYS
Chi-restraints excluded: chain A residue   30 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  132 ASN
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain G residue   61 PHE
Chi-restraints excluded: chain R residue   56 ILE
Chi-restraints excluded: chain R residue  119 MET
Chi-restraints excluded: chain R residue  133 ILE
Chi-restraints excluded: chain R residue  190 VAL
Chi-restraints excluded: chain R residue  192 ASN
Chi-restraints excluded: chain R residue  218 ILE
Chi-restraints excluded: chain R residue  288 THR
Chi-restraints excluded: chain R residue  289 LEU
Chi-restraints excluded: chain S residue   20 LEU
Chi-restraints excluded: chain S residue   25 SER
Chi-restraints excluded: chain S residue   51 ILE
Chi-restraints excluded: chain S residue   58 ILE
Chi-restraints excluded: chain S residue   79 LEU
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue   99 SER
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  157 ILE
Chi-restraints excluded: chain S residue  193 SER
Chi-restraints excluded: chain S residue  204 SER
Chi-restraints excluded: chain S residue  235 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 85 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 83 optimal weight:    0.6980
   chunk 58 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0980
   chunk 32 optimal weight:    5.9990
   chunk 101 optimal weight:    3.9990
   chunk 99 optimal weight:   10.0000
   chunk 100 optimal weight:    9.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
B 155 ASN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.179233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.143977 restraints weight = 10494.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.142708 restraints weight = 8673.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.144023 restraints weight = 8940.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.146942 restraints weight = 6267.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.147323 restraints weight = 4957.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   7726  Z= 0.137
  Angle     :  0.587  12.558  10557  Z= 0.300
  Chirality :  0.043   0.166   1235
  Planarity :  0.004   0.049   1338
  Dihedral  :  4.311  22.341   1125
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  7.58 %
    Allowed  : 31.65 %
    Favored  : 60.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.27), residues: 1026
  helix:  2.16 (0.27), residues: 370
  sheet: -0.63 (0.32), residues: 265
  loop : -1.76 (0.29), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG S 160 
 TYR   0.017   0.001   TYR S 235 
 PHE   0.022   0.001   PHE A 363 
 TRP   0.015   0.001   TRP B  99 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 7723)
  covalent geometry    : angle       0.58627 (10551)
  SS BOND              : bond        0.00389 (    3)
  SS BOND              : angle       1.19574 (    6)
  hydrogen bonds       : bond        0.03743 (  400)
  hydrogen bonds       : angle       5.18484 ( 1131)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 209
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
REVERT: A  362 HIS cc_start: 0.7502 (m-70) cc_final: 0.6625 (m90)
REVERT: A  373 ARG cc_start: 0.8381 (mmt180) cc_final: 0.7995 (mmm160)
REVERT: B   86 THR cc_start: 0.8896 (p) cc_final: 0.8666 (p)
REVERT: B  205 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8330 (p0)
REVERT: B  217 MET cc_start: 0.7571 (pmm) cc_final: 0.7262 (ptp)
REVERT: R  192 ASN cc_start: 0.6592 (OUTLIER) cc_final: 0.5275 (p0)
  outliers start: 51
  outliers final: 39
  residues processed: 238
  average time/residue: 0.0618
  time to fit residues: 20.4730
Evaluate side-chains
  239 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 198
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LYS
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  132 ASN
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain G residue   61 PHE
Chi-restraints excluded: chain R residue   56 ILE
Chi-restraints excluded: chain R residue  119 MET
Chi-restraints excluded: chain R residue  163 PHE
Chi-restraints excluded: chain R residue  190 VAL
Chi-restraints excluded: chain R residue  192 ASN
Chi-restraints excluded: chain R residue  199 SER
Chi-restraints excluded: chain R residue  288 THR
Chi-restraints excluded: chain R residue  289 LEU
Chi-restraints excluded: chain R residue  298 LEU
Chi-restraints excluded: chain S residue    7 SER
Chi-restraints excluded: chain S residue   20 LEU
Chi-restraints excluded: chain S residue   25 SER
Chi-restraints excluded: chain S residue   51 ILE
Chi-restraints excluded: chain S residue   58 ILE
Chi-restraints excluded: chain S residue   79 LEU
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue   99 SER
Chi-restraints excluded: chain S residue  157 ILE
Chi-restraints excluded: chain S residue  193 SER
Chi-restraints excluded: chain S residue  204 SER
Chi-restraints excluded: chain S residue  235 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 87 optimal weight:    0.6980
   chunk 66 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9990
   chunk 77 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9980
   chunk 93 optimal weight:    0.0170
   chunk 102 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   chunk 98 optimal weight:    3.9990
   chunk 70 optimal weight:    0.2980
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
B  75 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 120 HIS
** R 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.181109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.142571 restraints weight = 10437.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.143206 restraints weight = 6709.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.143229 restraints weight = 5847.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.143973 restraints weight = 5677.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.144184 restraints weight = 4892.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.2066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   7726  Z= 0.118
  Angle     :  0.576  12.883  10557  Z= 0.291
  Chirality :  0.042   0.164   1235
  Planarity :  0.003   0.047   1338
  Dihedral  :  4.145  22.278   1125
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  7.43 %
    Allowed  : 32.39 %
    Favored  : 60.18 %
  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:  0.10 (0.27), residues: 1026
  helix:  2.26 (0.27), residues: 370
  sheet: -0.40 (0.33), residues: 256
  loop : -1.78 (0.28), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG S 160 
 TYR   0.016   0.001   TYR S 235 
 PHE   0.015   0.001   PHE A 212 
 TRP   0.013   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 7723)
  covalent geometry    : angle       0.57530 (10551)
  SS BOND              : bond        0.00246 (    3)
  SS BOND              : angle       0.99788 (    6)
  hydrogen bonds       : bond        0.03557 (  400)
  hydrogen bonds       : angle       5.04071 ( 1131)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 204
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
REVERT: A  362 HIS cc_start: 0.7622 (m-70) cc_final: 0.6695 (m90)
REVERT: A  373 ARG cc_start: 0.8378 (mmt180) cc_final: 0.8014 (mmm160)
REVERT: B   86 THR cc_start: 0.8828 (p) cc_final: 0.8592 (p)
REVERT: B  204 CYS cc_start: 0.7368 (OUTLIER) cc_final: 0.7085 (m)
REVERT: B  205 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8258 (p0)
REVERT: R   86 PHE cc_start: 0.8289 (m-80) cc_final: 0.8024 (m-80)
REVERT: R  192 ASN cc_start: 0.6575 (OUTLIER) cc_final: 0.5208 (p0)
REVERT: S   18 ARG cc_start: 0.7626 (tpp80) cc_final: 0.6821 (tpt-90)
  outliers start: 50
  outliers final: 41
  residues processed: 235
  average time/residue: 0.0644
  time to fit residues: 20.9525
Evaluate side-chains
  239 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 195
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  132 ASN
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain G residue   61 PHE
Chi-restraints excluded: chain R residue   56 ILE
Chi-restraints excluded: chain R residue  130 TYR
Chi-restraints excluded: chain R residue  151 LEU
Chi-restraints excluded: chain R residue  163 PHE
Chi-restraints excluded: chain R residue  190 VAL
Chi-restraints excluded: chain R residue  192 ASN
Chi-restraints excluded: chain R residue  199 SER
Chi-restraints excluded: chain R residue  218 ILE
Chi-restraints excluded: chain R residue  289 LEU
Chi-restraints excluded: chain R residue  298 LEU
Chi-restraints excluded: chain S residue    7 SER
Chi-restraints excluded: chain S residue   20 LEU
Chi-restraints excluded: chain S residue   25 SER
Chi-restraints excluded: chain S residue   29 PHE
Chi-restraints excluded: chain S residue   51 ILE
Chi-restraints excluded: chain S residue   58 ILE
Chi-restraints excluded: chain S residue   74 ASP
Chi-restraints excluded: chain S residue   79 LEU
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue   99 SER
Chi-restraints excluded: chain S residue  157 ILE
Chi-restraints excluded: chain S residue  235 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 61 optimal weight:    0.8980
   chunk 27 optimal weight:    0.1980
   chunk 37 optimal weight:    2.9990
   chunk 94 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 59 optimal weight:    7.9990
   chunk 68 optimal weight:    8.9990
   chunk 92 optimal weight:    6.9990
   chunk 98 optimal weight:    5.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
B  75 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 120 HIS
S  77 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.179785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.141181 restraints weight = 10479.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.140583 restraints weight = 7602.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.142043 restraints weight = 6052.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.142562 restraints weight = 5381.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.143376 restraints weight = 4936.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   7726  Z= 0.142
  Angle     :  0.586  12.134  10557  Z= 0.298
  Chirality :  0.042   0.174   1235
  Planarity :  0.004   0.050   1338
  Dihedral  :  4.158  22.263   1125
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  8.17 %
    Allowed  : 32.24 %
    Favored  : 59.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.27), residues: 1026
  helix:  2.29 (0.27), residues: 376
  sheet: -0.43 (0.32), residues: 260
  loop : -1.69 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG S 160 
 TYR   0.019   0.001   TYR S 235 
 PHE   0.023   0.001   PHE A 363 
 TRP   0.015   0.001   TRP B  99 
 HIS   0.005   0.001   HIS R 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 7723)
  covalent geometry    : angle       0.58593 (10551)
  SS BOND              : bond        0.00381 (    3)
  SS BOND              : angle       1.11205 (    6)
  hydrogen bonds       : bond        0.03631 (  400)
  hydrogen bonds       : angle       5.01290 ( 1131)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 202
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
REVERT: A  362 HIS cc_start: 0.7693 (m-70) cc_final: 0.6778 (m90)
REVERT: A  373 ARG cc_start: 0.8362 (mmt180) cc_final: 0.7995 (mmm160)
REVERT: B   86 THR cc_start: 0.8894 (p) cc_final: 0.8672 (p)
REVERT: B  204 CYS cc_start: 0.7370 (OUTLIER) cc_final: 0.7165 (m)
REVERT: B  205 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8269 (p0)
REVERT: B  280 LYS cc_start: 0.9191 (ttpt) cc_final: 0.8933 (ttmm)
REVERT: R   86 PHE cc_start: 0.8222 (m-80) cc_final: 0.7997 (m-80)
REVERT: R  192 ASN cc_start: 0.6469 (OUTLIER) cc_final: 0.5180 (p0)
REVERT: R  211 MET cc_start: 0.7369 (mmt) cc_final: 0.7119 (mmp)
  outliers start: 55
  outliers final: 46
  residues processed: 236
  average time/residue: 0.0604
  time to fit residues: 19.9064
Evaluate side-chains
  246 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 197
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LYS
Chi-restraints excluded: chain A residue   30 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  132 ASN
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain G residue   61 PHE
Chi-restraints excluded: chain R residue   56 ILE
Chi-restraints excluded: chain R residue  130 TYR
Chi-restraints excluded: chain R residue  163 PHE
Chi-restraints excluded: chain R residue  190 VAL
Chi-restraints excluded: chain R residue  192 ASN
Chi-restraints excluded: chain R residue  199 SER
Chi-restraints excluded: chain R residue  218 ILE
Chi-restraints excluded: chain R residue  288 THR
Chi-restraints excluded: chain R residue  289 LEU
Chi-restraints excluded: chain R residue  298 LEU
Chi-restraints excluded: chain S residue    7 SER
Chi-restraints excluded: chain S residue   20 LEU
Chi-restraints excluded: chain S residue   25 SER
Chi-restraints excluded: chain S residue   29 PHE
Chi-restraints excluded: chain S residue   51 ILE
Chi-restraints excluded: chain S residue   58 ILE
Chi-restraints excluded: chain S residue   74 ASP
Chi-restraints excluded: chain S residue   79 LEU
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue   99 SER
Chi-restraints excluded: chain S residue  157 ILE
Chi-restraints excluded: chain S residue  193 SER
Chi-restraints excluded: chain S residue  204 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 84 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 57 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 81 optimal weight:    9.9990
   chunk 89 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9980
   chunk 88 optimal weight:    5.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 120 HIS
** R 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.180611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.145169 restraints weight = 10447.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.146339 restraints weight = 7976.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.147969 restraints weight = 6829.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.148613 restraints weight = 5172.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.149411 restraints weight = 4910.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7726  Z= 0.130
  Angle     :  0.590  14.647  10557  Z= 0.297
  Chirality :  0.043   0.161   1235
  Planarity :  0.004   0.047   1338
  Dihedral  :  4.119  22.224   1125
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  8.17 %
    Allowed  : 31.50 %
    Favored  : 60.33 %
  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:  0.24 (0.27), residues: 1026
  helix:  2.25 (0.26), residues: 378
  sheet: -0.37 (0.33), residues: 257
  loop : -1.60 (0.29), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG S 160 
 TYR   0.020   0.001   TYR S 235 
 PHE   0.017   0.001   PHE A 238 
 TRP   0.010   0.001   TRP B  82 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7723)
  covalent geometry    : angle       0.58982 (10551)
  SS BOND              : bond        0.00328 (    3)
  SS BOND              : angle       1.01476 (    6)
  hydrogen bonds       : bond        0.03596 (  400)
  hydrogen bonds       : angle       4.97431 ( 1131)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 201
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: A  362 HIS cc_start: 0.7658 (m-70) cc_final: 0.6743 (m90)
REVERT: A  373 ARG cc_start: 0.8289 (mmt180) cc_final: 0.7924 (mmm160)
REVERT: B   86 THR cc_start: 0.8904 (p) cc_final: 0.8653 (p)
REVERT: B  204 CYS cc_start: 0.7415 (OUTLIER) cc_final: 0.7174 (m)
REVERT: B  205 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8213 (p0)
REVERT: B  280 LYS cc_start: 0.9185 (ttpt) cc_final: 0.8917 (ttmm)
REVERT: R   67 TYR cc_start: 0.7309 (OUTLIER) cc_final: 0.6933 (m-10)
REVERT: R  137 GLU cc_start: 0.7863 (pt0) cc_final: 0.7085 (pt0)
REVERT: R  141 LYS cc_start: 0.8369 (mttm) cc_final: 0.8119 (mttp)
REVERT: S   18 ARG cc_start: 0.7592 (tpp80) cc_final: 0.6824 (tpt-90)
  outliers start: 55
  outliers final: 51
  residues processed: 232
  average time/residue: 0.0661
  time to fit residues: 21.4196
Evaluate side-chains
  253 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 199
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LYS
Chi-restraints excluded: chain A residue   30 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  132 ASN
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain G residue   61 PHE
Chi-restraints excluded: chain R residue   56 ILE
Chi-restraints excluded: chain R residue   67 TYR
Chi-restraints excluded: chain R residue  130 TYR
Chi-restraints excluded: chain R residue  163 PHE
Chi-restraints excluded: chain R residue  190 VAL
Chi-restraints excluded: chain R residue  199 SER
Chi-restraints excluded: chain R residue  218 ILE
Chi-restraints excluded: chain R residue  288 THR
Chi-restraints excluded: chain R residue  289 LEU
Chi-restraints excluded: chain R residue  298 LEU
Chi-restraints excluded: chain S residue    7 SER
Chi-restraints excluded: chain S residue   20 LEU
Chi-restraints excluded: chain S residue   25 SER
Chi-restraints excluded: chain S residue   29 PHE
Chi-restraints excluded: chain S residue   51 ILE
Chi-restraints excluded: chain S residue   55 SER
Chi-restraints excluded: chain S residue   58 ILE
Chi-restraints excluded: chain S residue   74 ASP
Chi-restraints excluded: chain S residue   79 LEU
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue   99 SER
Chi-restraints excluded: chain S residue  157 ILE
Chi-restraints excluded: chain S residue  193 SER
Chi-restraints excluded: chain S residue  204 SER
Chi-restraints excluded: chain S residue  235 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 74 optimal weight:    0.7980
   chunk 18 optimal weight:   20.0000
   chunk 26 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 50 optimal weight:   20.0000
   chunk 3 optimal weight:    0.9980
   chunk 48 optimal weight:    0.1980
   chunk 88 optimal weight:   10.0000
   chunk 46 optimal weight:   10.0000
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
B  75 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 311 HIS
R 120 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.177769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.142764 restraints weight = 10540.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.142227 restraints weight = 8778.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.143430 restraints weight = 8984.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.146073 restraints weight = 6271.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.146402 restraints weight = 5091.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.2519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078   7726  Z= 0.173
  Angle     :  0.617  13.385  10557  Z= 0.315
  Chirality :  0.043   0.181   1235
  Planarity :  0.004   0.049   1338
  Dihedral  :  4.252  22.074   1125
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  8.17 %
    Allowed  : 32.24 %
    Favored  : 59.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.20 (0.27), residues: 1026
  helix:  2.18 (0.27), residues: 379
  sheet: -0.42 (0.33), residues: 258
  loop : -1.57 (0.29), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG S 160 
 TYR   0.024   0.001   TYR S 235 
 PHE   0.026   0.002   PHE A 363 
 TRP   0.010   0.001   TRP B  99 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 7723)
  covalent geometry    : angle       0.61650 (10551)
  SS BOND              : bond        0.00421 (    3)
  SS BOND              : angle       1.19746 (    6)
  hydrogen bonds       : bond        0.03841 (  400)
  hydrogen bonds       : angle       5.06250 ( 1131)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 202
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: B   86 THR cc_start: 0.9003 (p) cc_final: 0.8763 (p)
REVERT: B  205 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.8279 (p0)
  outliers start: 55
  outliers final: 51
  residues processed: 234
  average time/residue: 0.0548
  time to fit residues: 18.5091
Evaluate side-chains
  249 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 197
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LYS
Chi-restraints excluded: chain A residue   30 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  132 ASN
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain G residue   61 PHE
Chi-restraints excluded: chain R residue   56 ILE
Chi-restraints excluded: chain R residue  163 PHE
Chi-restraints excluded: chain R residue  190 VAL
Chi-restraints excluded: chain R residue  199 SER
Chi-restraints excluded: chain R residue  218 ILE
Chi-restraints excluded: chain R residue  288 THR
Chi-restraints excluded: chain R residue  289 LEU
Chi-restraints excluded: chain R residue  298 LEU
Chi-restraints excluded: chain S residue    7 SER
Chi-restraints excluded: chain S residue   20 LEU
Chi-restraints excluded: chain S residue   25 SER
Chi-restraints excluded: chain S residue   29 PHE
Chi-restraints excluded: chain S residue   51 ILE
Chi-restraints excluded: chain S residue   55 SER
Chi-restraints excluded: chain S residue   58 ILE
Chi-restraints excluded: chain S residue   74 ASP
Chi-restraints excluded: chain S residue   79 LEU
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue   99 SER
Chi-restraints excluded: chain S residue  157 ILE
Chi-restraints excluded: chain S residue  193 SER
Chi-restraints excluded: chain S residue  204 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 53 optimal weight:    8.9990
   chunk 27 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0670
   chunk 96 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 85 optimal weight:    3.9990
   chunk 76 optimal weight:    6.9990
   chunk 83 optimal weight:    0.5980
   chunk 71 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 311 HIS
R 120 HIS
** R 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.181061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.136673 restraints weight = 10456.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.140312 restraints weight = 6934.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.142568 restraints weight = 5380.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.144197 restraints weight = 4607.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.144673 restraints weight = 4160.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.2570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7726  Z= 0.119
  Angle     :  0.590  12.945  10557  Z= 0.299
  Chirality :  0.043   0.157   1235
  Planarity :  0.004   0.047   1338
  Dihedral  :  4.130  22.880   1125
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  7.73 %
    Allowed  : 32.39 %
    Favored  : 59.88 %
  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:  0.23 (0.27), residues: 1026
  helix:  2.29 (0.27), residues: 371
  sheet: -0.33 (0.33), residues: 263
  loop : -1.65 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG S 160 
 TYR   0.018   0.001   TYR S 235 
 PHE   0.015   0.001   PHE A 212 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 7723)
  covalent geometry    : angle       0.58934 (10551)
  SS BOND              : bond        0.00281 (    3)
  SS BOND              : angle       0.92141 (    6)
  hydrogen bonds       : bond        0.03548 (  400)
  hydrogen bonds       : angle       4.94546 ( 1131)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 208
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: A  266 LEU cc_start: 0.8209 (mt) cc_final: 0.7980 (mp)
REVERT: A  362 HIS cc_start: 0.7677 (m-70) cc_final: 0.6997 (m90)
REVERT: B   86 THR cc_start: 0.8840 (p) cc_final: 0.8577 (p)
REVERT: B  205 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8012 (p0)
REVERT: B  283 ARG cc_start: 0.7920 (ttp80) cc_final: 0.7628 (tmt170)
REVERT: R   67 TYR cc_start: 0.7342 (OUTLIER) cc_final: 0.6894 (m-10)
  outliers start: 52
  outliers final: 48
  residues processed: 239
  average time/residue: 0.0571
  time to fit residues: 19.3074
Evaluate side-chains
  250 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 200
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LYS
Chi-restraints excluded: chain A residue   30 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  132 ASN
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain G residue   61 PHE
Chi-restraints excluded: chain R residue   56 ILE
Chi-restraints excluded: chain R residue   67 TYR
Chi-restraints excluded: chain R residue  120 HIS
Chi-restraints excluded: chain R residue  130 TYR
Chi-restraints excluded: chain R residue  163 PHE
Chi-restraints excluded: chain R residue  199 SER
Chi-restraints excluded: chain R residue  218 ILE
Chi-restraints excluded: chain R residue  288 THR
Chi-restraints excluded: chain R residue  289 LEU
Chi-restraints excluded: chain R residue  298 LEU
Chi-restraints excluded: chain S residue    7 SER
Chi-restraints excluded: chain S residue   20 LEU
Chi-restraints excluded: chain S residue   25 SER
Chi-restraints excluded: chain S residue   29 PHE
Chi-restraints excluded: chain S residue   51 ILE
Chi-restraints excluded: chain S residue   55 SER
Chi-restraints excluded: chain S residue   58 ILE
Chi-restraints excluded: chain S residue   74 ASP
Chi-restraints excluded: chain S residue   79 LEU
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue  204 SER
Chi-restraints excluded: chain S residue  235 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 82 optimal weight:    5.9990
   chunk 63 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 55 optimal weight:    0.5980
   chunk 64 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 59 optimal weight:   10.0000
   chunk 16 optimal weight:    0.6980
   chunk 0 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 311 HIS
R 120 HIS
S 142 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.179876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.141228 restraints weight = 10429.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.141666 restraints weight = 6809.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.141847 restraints weight = 5840.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.143297 restraints weight = 5643.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.143183 restraints weight = 4887.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.2673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7726  Z= 0.141
  Angle     :  0.615  15.854  10557  Z= 0.310
  Chirality :  0.044   0.174   1235
  Planarity :  0.004   0.048   1338
  Dihedral  :  4.157  22.381   1125
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  7.43 %
    Allowed  : 32.84 %
    Favored  : 59.73 %
  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:  0.29 (0.27), residues: 1026
  helix:  2.31 (0.26), residues: 376
  sheet: -0.33 (0.33), residues: 263
  loop : -1.61 (0.29), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG S 160 
 TYR   0.020   0.001   TYR S 235 
 PHE   0.026   0.001   PHE A 363 
 TRP   0.012   0.001   TRP B  82 
 HIS   0.008   0.001   HIS R 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 7723)
  covalent geometry    : angle       0.61466 (10551)
  SS BOND              : bond        0.00274 (    3)
  SS BOND              : angle       1.16952 (    6)
  hydrogen bonds       : bond        0.03643 (  400)
  hydrogen bonds       : angle       4.96338 ( 1131)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 201
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
REVERT: A  266 LEU cc_start: 0.8158 (mt) cc_final: 0.7918 (mp)
REVERT: A  362 HIS cc_start: 0.7751 (m-70) cc_final: 0.7080 (m90)
REVERT: B   86 THR cc_start: 0.8932 (p) cc_final: 0.8688 (p)
REVERT: B  205 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7971 (p0)
REVERT: R   67 TYR cc_start: 0.7342 (OUTLIER) cc_final: 0.6902 (m-10)
  outliers start: 50
  outliers final: 48
  residues processed: 232
  average time/residue: 0.0575
  time to fit residues: 18.9379
Evaluate side-chains
  250 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 200
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LYS
Chi-restraints excluded: chain A residue   30 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  132 ASN
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain G residue   61 PHE
Chi-restraints excluded: chain R residue   56 ILE
Chi-restraints excluded: chain R residue   67 TYR
Chi-restraints excluded: chain R residue  120 HIS
Chi-restraints excluded: chain R residue  163 PHE
Chi-restraints excluded: chain R residue  199 SER
Chi-restraints excluded: chain R residue  218 ILE
Chi-restraints excluded: chain R residue  288 THR
Chi-restraints excluded: chain R residue  289 LEU
Chi-restraints excluded: chain R residue  298 LEU
Chi-restraints excluded: chain S residue    7 SER
Chi-restraints excluded: chain S residue   20 LEU
Chi-restraints excluded: chain S residue   25 SER
Chi-restraints excluded: chain S residue   29 PHE
Chi-restraints excluded: chain S residue   51 ILE
Chi-restraints excluded: chain S residue   55 SER
Chi-restraints excluded: chain S residue   58 ILE
Chi-restraints excluded: chain S residue   74 ASP
Chi-restraints excluded: chain S residue   79 LEU
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue  204 SER
Chi-restraints excluded: chain S residue  235 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 101 optimal weight:    0.9980
   chunk 66 optimal weight:    0.0370
   chunk 98 optimal weight:    3.9990
   chunk 92 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 83 optimal weight:    0.5980
   chunk 61 optimal weight:    0.7980
   chunk 81 optimal weight:    7.9990
   chunk 30 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.6858

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
B  75 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 311 HIS
R 120 HIS
** R 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.181212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.141488 restraints weight = 10459.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.141234 restraints weight = 6728.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.141650 restraints weight = 5894.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.142640 restraints weight = 5382.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.143213 restraints weight = 4836.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.2716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7726  Z= 0.125
  Angle     :  0.610  15.689  10557  Z= 0.307
  Chirality :  0.043   0.158   1235
  Planarity :  0.004   0.050   1338
  Dihedral  :  4.116  22.726   1125
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  7.88 %
    Allowed  : 32.39 %
    Favored  : 59.73 %
  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:  0.30 (0.27), residues: 1026
  helix:  2.36 (0.26), residues: 370
  sheet: -0.27 (0.33), residues: 263
  loop : -1.62 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG S 160 
 TYR   0.019   0.001   TYR S 235 
 PHE   0.017   0.001   PHE A 212 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.007   0.001   HIS R 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 7723)
  covalent geometry    : angle       0.60934 (10551)
  SS BOND              : bond        0.00221 (    3)
  SS BOND              : angle       1.04443 (    6)
  hydrogen bonds       : bond        0.03571 (  400)
  hydrogen bonds       : angle       4.93041 ( 1131)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1166.81 seconds
wall clock time: 20 minutes 50.76 seconds (1250.76 seconds total)