Starting phenix.real_space_refine
on Thu Mar 13 15:28:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j6j_36006/03_2025/8j6j_36006.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j6j_36006/03_2025/8j6j_36006.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j6j_36006/03_2025/8j6j_36006.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j6j_36006/03_2025/8j6j_36006.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j6j_36006/03_2025/8j6j_36006.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j6j_36006/03_2025/8j6j_36006.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      68      5.16       5
     Cl      1      4.86       5
     C    5747      2.51       5
     N    1537      2.21       5
     O    1626      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8979
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1731
          Classifications: {'peptide': 215}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 212}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 2560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2560
          Classifications: {'peptide': 339}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 41
    Chain: "G"
      Number of atoms: 404
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 404
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 23
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "H"
      Number of atoms: 1736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1736
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 60
          Unresolved non-hydrogen dihedrals: 42
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 32
    Chain: "R"
      Number of atoms: 2531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2531
          Classifications: {'peptide': 308}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 296}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "R"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'OKL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.73, per 1000 atoms: 0.64
  Number of scatterers: 8979
  At special positions: 0
  Unit cell: (93.936, 112.064, 139.256, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      68     16.00
     O    1626      8.00
     N    1537      7.00
     C    5747      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.45
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2158

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 13 sheets defined
      37.7% alpha, 21.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 33
      removed outlier: 3.748A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 52
      removed outlier: 3.859A  pdb=" N   LYS A  46 " --> pdb=" O   GLY A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 205
      removed outlier: 3.578A  pdb=" N   ARG A 205 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 202 through 205'
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.809A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.626A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.556A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.621A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   CYS A 286 " --> pdb=" O   LEU A 283 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 282 through 286'
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 352
    Processing helix  chain 'B' and resid 3 through 25
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.674A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 9 through 24
      removed outlier: 3.573A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 36
    Processing helix  chain 'H' and resid 62 through 65
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'H' and resid 220 through 224
    Processing helix  chain 'R' and resid 5 through 10
    Processing helix  chain 'R' and resid 25 through 53
      removed outlier: 3.599A  pdb=" N   VAL R  29 " --> pdb=" O   PHE R  25 " (cutoff:3.500A)
      Proline residue:  R  31  - end of helix
      removed outlier: 3.529A  pdb=" N   CYS R  53 " --> pdb=" O   LEU R  49 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 60 through 89
      Proline residue:  R  81  - end of helix
    Processing helix  chain 'R' and resid 96 through 131
    Processing helix  chain 'R' and resid 131 through 136
      removed outlier: 3.898A  pdb=" N   LEU R 136 " --> pdb=" O   PRO R 132 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 139
      No H-bonds generated for 'chain 'R' and resid 137 through 139'
    Processing helix  chain 'R' and resid 140 through 160
    Processing helix  chain 'R' and resid 161 through 163
      No H-bonds generated for 'chain 'R' and resid 161 through 163'
    Processing helix  chain 'R' and resid 187 through 219
      removed outlier: 3.558A  pdb=" N   ALA R 191 " --> pdb=" O   GLN R 187 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   PHE R 197 " --> pdb=" O   PHE R 193 " (cutoff:3.500A)
      Proline residue:  R 200  - end of helix
      removed outlier: 3.694A  pdb=" N   ARG R 218 " --> pdb=" O   SER R 214 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 223 through 257
      removed outlier: 4.007A  pdb=" N   LYS R 227 " --> pdb=" O   HIS R 223 " (cutoff:3.500A)
      Proline residue:  R 246  - end of helix
    Processing helix  chain 'R' and resid 269 through 295
      removed outlier: 3.849A  pdb=" N   ASP R 273 " --> pdb=" O   TYR R 269 " (cutoff:3.500A)
      Proline residue:  R 291  - end of helix
    Processing helix  chain 'R' and resid 296 through 298
      No H-bonds generated for 'chain 'R' and resid 296 through 298'
    Processing helix  chain 'R' and resid 299 through 308
      removed outlier: 3.937A  pdb=" N   ASN R 303 " --> pdb=" O   PRO R 299 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.824A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.901A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.466A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.513A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.352A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.892A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.669A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE B  80 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.502A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 5.778A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.676A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.427A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.705A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.791A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.699A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.302A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.447A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 4.012A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278
      removed outlier: 3.539A  pdb=" N   ASN B 295 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.028A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 140 through 142
      removed outlier: 3.958A  pdb=" N   VAL H 155 " --> pdb=" O   ILE H 216 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ILE H 216 " --> pdb=" O   VAL H 155 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   PHE H 212 " --> pdb=" O   CYS H 159 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 148
      removed outlier: 3.682A  pdb=" N   GLU H 246 " --> pdb=" O   VAL H 147 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   GLY H 225 " --> pdb=" O   LEU H 245 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   ILE H 189 " --> pdb=" O   TRP H 176 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   LEU H 178 " --> pdb=" O   LEU H 187 " (cutoff:3.500A)
      removed outlier: 5.692A  pdb=" N   LEU H 187 " --> pdb=" O   LEU H 178 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'R' and resid 170 through 171

    427 hydrogen bonds defined for protein.
    1194 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.66

  Time building geometry restraints manager: 2.86 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1429
        1.31 -     1.44: 2591
        1.44 -     1.56: 5062
        1.56 -     1.69: 0
        1.69 -     1.81: 100
  Bond restraints: 9182
  Sorted by residual:
  bond pdb=" C13 OKL R 501 "
       pdb=" N06 OKL R 501 "
    ideal  model  delta    sigma   weight residual
    1.366  1.503 -0.137 2.00e-02 2.50e+03 4.72e+01
  bond pdb=" C10 OKL R 501 "
       pdb=" C12 OKL R 501 "
    ideal  model  delta    sigma   weight residual
    1.426  1.547 -0.121 2.00e-02 2.50e+03 3.64e+01
  bond pdb=" C15 OKL R 501 "
       pdb="CL17 OKL R 501 "
    ideal  model  delta    sigma   weight residual
    1.692  1.782 -0.090 2.00e-02 2.50e+03 2.03e+01
  bond pdb=" C07 OKL R 501 "
       pdb=" N06 OKL R 501 "
    ideal  model  delta    sigma   weight residual
    1.374  1.462 -0.088 2.00e-02 2.50e+03 1.93e+01
  bond pdb=" C07 OKL R 501 "
       pdb=" N09 OKL R 501 "
    ideal  model  delta    sigma   weight residual
    1.384  1.442 -0.058 2.00e-02 2.50e+03 8.31e+00
  ... (remaining 9177 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.24: 12257
        2.24 -     4.49: 163
        4.49 -     6.73: 14
        6.73 -     8.97: 4
        8.97 -    11.22: 3
  Bond angle restraints: 12441
  Sorted by residual:
  angle pdb=" C   HIS R   4 "
        pdb=" CA  HIS R   4 "
        pdb=" CB  HIS R   4 "
      ideal   model   delta    sigma   weight residual
     115.89  110.74    5.15 1.32e+00 5.74e-01 1.52e+01
  angle pdb=" N   ASP R  14 "
        pdb=" CA  ASP R  14 "
        pdb=" C   ASP R  14 "
      ideal   model   delta    sigma   weight residual
     113.18  108.41    4.77 1.33e+00 5.65e-01 1.29e+01
  angle pdb=" C12 OKL R 501 "
        pdb=" C10 OKL R 501 "
        pdb=" N09 OKL R 501 "
      ideal   model   delta    sigma   weight residual
     109.84  119.86  -10.02 3.00e+00 1.11e-01 1.12e+01
  angle pdb=" C07 OKL R 501 "
        pdb=" N09 OKL R 501 "
        pdb=" C10 OKL R 501 "
      ideal   model   delta    sigma   weight residual
     129.77  119.76   10.01 3.00e+00 1.11e-01 1.11e+01
  angle pdb=" CA  LEU R  43 "
        pdb=" CB  LEU R  43 "
        pdb=" CG  LEU R  43 "
      ideal   model   delta    sigma   weight residual
     116.30  127.52  -11.22 3.50e+00 8.16e-02 1.03e+01
  ... (remaining 12436 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.35: 4788
       17.35 -    34.71: 459
       34.71 -    52.06: 134
       52.06 -    69.42: 10
       69.42 -    86.77: 5
  Dihedral angle restraints: 5396
    sinusoidal: 2060
      harmonic: 3336
  Sorted by residual:
  dihedral pdb=" CA  MET R 167 "
           pdb=" C   MET R 167 "
           pdb=" N   PRO R 168 "
           pdb=" CA  PRO R 168 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.27  -17.73     0      5.00e+00 4.00e-02 1.26e+01
  dihedral pdb=" CA  ASP B 154 "
           pdb=" CB  ASP B 154 "
           pdb=" CG  ASP B 154 "
           pdb=" OD1 ASP B 154 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.24   58.24     1      2.00e+01 2.50e-03 1.14e+01
  dihedral pdb=" CG  ARG A 205 "
           pdb=" CD  ARG A 205 "
           pdb=" NE  ARG A 205 "
           pdb=" CZ  ARG A 205 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -135.07  -44.93     2      1.50e+01 4.44e-03 1.06e+01
  ... (remaining 5393 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 976
       0.032 -    0.064: 278
       0.064 -    0.096: 97
       0.096 -    0.128: 51
       0.128 -    0.160: 3
  Chirality restraints: 1405
  Sorted by residual:
  chirality pdb=" CA  ILE B  93 "
            pdb=" N   ILE B  93 "
            pdb=" C   ILE B  93 "
            pdb=" CB  ILE B  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.42e-01
  chirality pdb=" CG  LEU A 232 "
            pdb=" CB  LEU A 232 "
            pdb=" CD1 LEU A 232 "
            pdb=" CD2 LEU A 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 4.95e-01
  chirality pdb=" CA  ILE G  28 "
            pdb=" N   ILE G  28 "
            pdb=" C   ILE G  28 "
            pdb=" CB  ILE G  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.15e-01
  ... (remaining 1402 not shown)

  Planarity restraints: 1567
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP R 290 "   -0.046 5.00e-02 4.00e+02   6.91e-02 7.64e+00
        pdb=" N   PRO R 291 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO R 291 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO R 291 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  38 "   -0.041 5.00e-02 4.00e+02   6.17e-02 6.09e+00
        pdb=" N   PRO B  39 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO B  39 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B  39 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R  80 "    0.026 5.00e-02 4.00e+02   3.93e-02 2.47e+00
        pdb=" N   PRO R  81 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO R  81 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO R  81 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1564 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 151
        2.66 -     3.22: 8663
        3.22 -     3.78: 13703
        3.78 -     4.34: 18802
        4.34 -     4.90: 31338
  Nonbonded interactions: 72657
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.098 3.040
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   MET B 188 "
     model   vdw
     2.163 3.040
  nonbonded pdb=" O   PHE R 276 "
            pdb=" OG1 THR R 279 "
     model   vdw
     2.165 3.040
  nonbonded pdb=" OD1 ASP A 251 "
            pdb=" ND2 ASN A 255 "
     model   vdw
     2.177 3.120
  nonbonded pdb=" O   THR H  63 "
            pdb=" NH2 ARG H  67 "
     model   vdw
     2.178 3.120
  ... (remaining 72652 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.500
  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:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.390
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:15.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6077
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      :  0.004   0.137   9182  Z= 0.243
  Angle     :  0.617  11.216  12441  Z= 0.317
  Chirality :  0.039   0.160   1405
  Planarity :  0.004   0.069   1567
  Dihedral  : 14.729  86.772   3238
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  : 26.17 %
    Favored  : 73.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.26), residues: 1135
  helix:  2.43 (0.28), residues: 378
  sheet:  1.18 (0.32), residues: 268
  loop :  0.09 (0.30), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R  59 
 HIS   0.004   0.000   HIS B 266 
 PHE   0.007   0.001   PHE H 239 
 TYR   0.017   0.001   TYR H 190 
 ARG   0.007   0.000   ARG A 208 

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 160
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 ARG cc_start: 0.6122 (ttm110) cc_final: 0.5877 (mpt90)
REVERT: A  198 MET cc_start: 0.8225 (ttp) cc_final: 0.7958 (ttp)
REVERT: A  247 MET cc_start: 0.7309 (mtp) cc_final: 0.7087 (mtp)
REVERT: A  248 LYS cc_start: 0.7329 (ttmm) cc_final: 0.7058 (pttp)
REVERT: A  275 GLU cc_start: 0.7257 (mm-30) cc_final: 0.7035 (mt-10)
REVERT: A  276 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6793 (mp0)
REVERT: A  305 CYS cc_start: 0.6879 (m) cc_final: 0.6678 (p)
REVERT: A  346 ASN cc_start: 0.6160 (m-40) cc_final: 0.5893 (m-40)
REVERT: B   45 MET cc_start: 0.8288 (mtt) cc_final: 0.7999 (mmm)
REVERT: B   46 ARG cc_start: 0.7048 (mmm-85) cc_final: 0.6577 (mmp80)
REVERT: B   96 ARG cc_start: 0.6151 (tpt170) cc_final: 0.5544 (tpp80)
REVERT: B  146 LEU cc_start: 0.7343 (tp) cc_final: 0.6995 (mm)
REVERT: B  195 ASP cc_start: 0.7199 (p0) cc_final: 0.6951 (p0)
REVERT: B  325 MET cc_start: 0.7883 (tpt) cc_final: 0.7673 (tpp)
REVERT: G   21 MET cc_start: 0.1974 (mtp) cc_final: 0.1563 (pmm)
REVERT: G   38 MET cc_start: 0.1958 (mpm) cc_final: 0.0488 (mpm)
REVERT: H   55 SER cc_start: 0.6386 (m) cc_final: 0.6118 (m)
REVERT: H  234 GLU cc_start: 0.5905 (mt-10) cc_final: 0.5049 (mm-30)
REVERT: R   43 LEU cc_start: 0.5118 (pp) cc_final: 0.4691 (tt)
REVERT: R   50 TRP cc_start: 0.3153 (m-10) cc_final: 0.2559 (m-10)
REVERT: R  234 MET cc_start: 0.6108 (mmt) cc_final: 0.5452 (ptp)
REVERT: R  253 ARG cc_start: 0.4945 (ttt180) cc_final: 0.4740 (tpt-90)
  outliers start: 2
  outliers final: 0
  residues processed: 162
  average time/residue: 1.0988
  time to fit residues: 191.3042
Evaluate side-chains
  116 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 47 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 87 optimal weight:    6.9990
   chunk 33 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 101 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 ASN
B 142 HIS
B 266 HIS
H 171 ASN
R 112 GLN
R 161 HIS
R 219 GLN
R 286 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4572 r_free = 0.4572 target = 0.231681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.173871 restraints weight = 9320.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3994 rms_B_bonded: 1.70
r_work: 0.3824 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3694 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.2207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9182  Z= 0.206
  Angle     :  0.626   8.446  12441  Z= 0.324
  Chirality :  0.044   0.144   1405
  Planarity :  0.005   0.066   1567
  Dihedral  :  4.294  17.622   1241
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 21.06 %
    Favored  : 73.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.26), residues: 1135
  helix:  2.05 (0.27), residues: 391
  sheet:  0.99 (0.30), residues: 283
  loop : -0.30 (0.30), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP R  59 
 HIS   0.009   0.002   HIS R 161 
 PHE   0.017   0.002   PHE R 232 
 TYR   0.023   0.002   TYR B  85 
 ARG   0.005   0.001   ARG B  49 

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 125
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 VAL cc_start: 0.7976 (OUTLIER) cc_final: 0.7485 (t)
REVERT: A  247 MET cc_start: 0.8107 (mtp) cc_final: 0.7816 (mtp)
REVERT: A  305 CYS cc_start: 0.7516 (m) cc_final: 0.7266 (t)
REVERT: A  309 ASP cc_start: 0.7454 (m-30) cc_final: 0.7156 (t70)
REVERT: B   96 ARG cc_start: 0.7447 (tpt170) cc_final: 0.7097 (mtt180)
REVERT: B  217 MET cc_start: 0.8076 (pmt) cc_final: 0.7681 (pmm)
REVERT: B  220 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7458 (mt0)
REVERT: G   21 MET cc_start: 0.1939 (mtp) cc_final: 0.1443 (pmm)
REVERT: G   38 MET cc_start: 0.2524 (mpm) cc_final: 0.0136 (mpm)
REVERT: G   50 LEU cc_start: 0.2736 (OUTLIER) cc_final: 0.1626 (tt)
REVERT: H   30 SER cc_start: 0.6907 (p) cc_final: 0.6639 (p)
REVERT: H   55 SER cc_start: 0.6487 (m) cc_final: 0.6164 (m)
REVERT: H   71 SER cc_start: 0.5564 (p) cc_final: 0.5211 (t)
REVERT: H   82 GLN cc_start: 0.6440 (tt0) cc_final: 0.6162 (mm-40)
REVERT: H   93 MET cc_start: 0.7071 (ttm) cc_final: 0.6861 (ttt)
REVERT: H  234 GLU cc_start: 0.6235 (mt-10) cc_final: 0.5428 (mm-30)
REVERT: R   50 TRP cc_start: 0.3085 (m-10) cc_final: 0.2552 (m-10)
REVERT: R  164 LYS cc_start: 0.5521 (mptp) cc_final: 0.4862 (mppt)
REVERT: R  183 CYS cc_start: 0.8122 (t) cc_final: 0.7850 (m)
REVERT: R  234 MET cc_start: 0.6289 (mmt) cc_final: 0.5696 (mtp)
REVERT: R  253 ARG cc_start: 0.4894 (ttt180) cc_final: 0.4679 (tpt-90)
REVERT: R  288 MET cc_start: 0.5726 (OUTLIER) cc_final: 0.5105 (tmm)
  outliers start: 51
  outliers final: 11
  residues processed: 162
  average time/residue: 0.9196
  time to fit residues: 162.0712
Evaluate side-chains
  116 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue  184 SER
Chi-restraints excluded: chain R residue   78 ILE
Chi-restraints excluded: chain R residue  236 VAL
Chi-restraints excluded: chain R residue  238 ILE
Chi-restraints excluded: chain R residue  283 THR
Chi-restraints excluded: chain R residue  288 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9980
   chunk 80 optimal weight:   10.0000
   chunk 37 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 107 optimal weight:    6.9990
   chunk 86 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 21 optimal weight:    7.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
B  88 ASN
B 259 GLN
B 268 ASN
R 112 GLN
R 161 HIS
** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4510 r_free = 0.4510 target = 0.224636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 118)---------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.165948 restraints weight = 9417.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3903 rms_B_bonded: 1.74
r_work: 0.3687 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3554 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.3255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9182  Z= 0.229
  Angle     :  0.608   7.170  12441  Z= 0.317
  Chirality :  0.043   0.147   1405
  Planarity :  0.004   0.051   1567
  Dihedral  :  4.524  22.423   1241
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 20.33 %
    Favored  : 74.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.26), residues: 1135
  helix:  1.76 (0.26), residues: 397
  sheet:  0.87 (0.31), residues: 287
  loop : -0.47 (0.30), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  99 
 HIS   0.009   0.002   HIS R 161 
 PHE   0.020   0.002   PHE R  21 
 TYR   0.021   0.002   TYR B 105 
 ARG   0.004   0.001   ARG B  49 

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 116
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.7052 (mmtt) cc_final: 0.6785 (mttt)
REVERT: A   51 LYS cc_start: 0.7351 (mmtm) cc_final: 0.7135 (mmtm)
REVERT: A  281 SER cc_start: 0.6914 (m) cc_final: 0.6557 (t)
REVERT: A  309 ASP cc_start: 0.7653 (m-30) cc_final: 0.7339 (t70)
REVERT: A  331 ASN cc_start: 0.7721 (t0) cc_final: 0.6921 (m-40)
REVERT: B   96 ARG cc_start: 0.7636 (tpt170) cc_final: 0.7322 (mtt180)
REVERT: B  219 ARG cc_start: 0.7662 (mmm160) cc_final: 0.7255 (ttm-80)
REVERT: B  294 CYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7223 (m)
REVERT: B  325 MET cc_start: 0.8556 (tpp) cc_final: 0.8355 (mmm)
REVERT: G   21 MET cc_start: 0.1854 (mtp) cc_final: 0.1284 (pmm)
REVERT: G   38 MET cc_start: 0.2777 (mpm) cc_final: 0.0526 (mpm)
REVERT: G   50 LEU cc_start: 0.3009 (OUTLIER) cc_final: 0.2702 (tt)
REVERT: H   30 SER cc_start: 0.7261 (p) cc_final: 0.7000 (p)
REVERT: H   55 SER cc_start: 0.6514 (m) cc_final: 0.6216 (m)
REVERT: H   71 SER cc_start: 0.6141 (p) cc_final: 0.5706 (t)
REVERT: H   82 GLN cc_start: 0.6484 (tt0) cc_final: 0.6143 (mm-40)
REVERT: H   96 CYS cc_start: 0.7480 (OUTLIER) cc_final: 0.6964 (p)
REVERT: H  179 GLN cc_start: 0.6494 (OUTLIER) cc_final: 0.6191 (tt0)
REVERT: H  230 MET cc_start: 0.6801 (tmm) cc_final: 0.6157 (ttp)
REVERT: H  234 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6455 (mt-10)
REVERT: R   47 LEU cc_start: 0.2704 (pp) cc_final: 0.2266 (tp)
REVERT: R  164 LYS cc_start: 0.5461 (mptp) cc_final: 0.4911 (mppt)
REVERT: R  234 MET cc_start: 0.6408 (mmt) cc_final: 0.5888 (mtp)
REVERT: R  253 ARG cc_start: 0.4947 (ttt180) cc_final: 0.4710 (tpt-90)
REVERT: R  288 MET cc_start: 0.5599 (OUTLIER) cc_final: 0.5180 (tmm)
  outliers start: 48
  outliers final: 15
  residues processed: 153
  average time/residue: 1.3194
  time to fit residues: 217.9914
Evaluate side-chains
  124 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  279 SER
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue  144 THR
Chi-restraints excluded: chain H residue  179 GLN
Chi-restraints excluded: chain H residue  184 SER
Chi-restraints excluded: chain R residue   78 ILE
Chi-restraints excluded: chain R residue  236 VAL
Chi-restraints excluded: chain R residue  288 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0060
   chunk 88 optimal weight:    0.0970
   chunk 49 optimal weight:    0.6980
   chunk 68 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   chunk 11 optimal weight:    0.1980
   chunk 37 optimal weight:    0.2980
   chunk 63 optimal weight:    7.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    0.2594

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
A 306 GLN
B  75 GLN
H 142 GLN
R 112 GLN
R 161 HIS
R 170 GLN
R 223 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.228065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.180555 restraints weight = 9359.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.4085 rms_B_bonded: 1.40
r_work: 0.3822 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3701 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.3391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9182  Z= 0.145
  Angle     :  0.539   8.690  12441  Z= 0.278
  Chirality :  0.041   0.137   1405
  Planarity :  0.004   0.049   1567
  Dihedral  :  4.140  20.348   1241
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 22.94 %
    Favored  : 74.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.26), residues: 1135
  helix:  2.29 (0.27), residues: 384
  sheet:  0.81 (0.32), residues: 279
  loop : -0.54 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R  59 
 HIS   0.009   0.001   HIS R 161 
 PHE   0.014   0.001   PHE R 232 
 TYR   0.012   0.001   TYR R 269 
 ARG   0.003   0.000   ARG B  49 

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 109
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
REVERT: A  281 SER cc_start: 0.6561 (m) cc_final: 0.6300 (t)
REVERT: A  309 ASP cc_start: 0.7660 (m-30) cc_final: 0.7378 (t70)
REVERT: A  331 ASN cc_start: 0.7591 (t0) cc_final: 0.6981 (m-40)
REVERT: B   45 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8053 (mtm)
REVERT: B   96 ARG cc_start: 0.7471 (tpt170) cc_final: 0.7237 (mtt180)
REVERT: B  219 ARG cc_start: 0.7429 (mmm160) cc_final: 0.7176 (ttm-80)
REVERT: B  234 PHE cc_start: 0.9112 (OUTLIER) cc_final: 0.7877 (t80)
REVERT: G   21 MET cc_start: 0.2044 (mtp) cc_final: 0.1413 (pmm)
REVERT: G   38 MET cc_start: 0.2557 (mpm) cc_final: 0.0326 (mpm)
REVERT: H   30 SER cc_start: 0.7229 (p) cc_final: 0.6978 (p)
REVERT: H   55 SER cc_start: 0.6526 (m) cc_final: 0.6252 (m)
REVERT: H   71 SER cc_start: 0.6248 (p) cc_final: 0.5765 (t)
REVERT: H   82 GLN cc_start: 0.6413 (tt0) cc_final: 0.6109 (mm-40)
REVERT: H   96 CYS cc_start: 0.7476 (OUTLIER) cc_final: 0.7028 (p)
REVERT: H  179 GLN cc_start: 0.6534 (OUTLIER) cc_final: 0.6251 (tt0)
REVERT: H  230 MET cc_start: 0.6704 (tmm) cc_final: 0.6090 (ttp)
REVERT: H  234 GLU cc_start: 0.6436 (mt-10) cc_final: 0.6222 (mt-10)
REVERT: R    1 MET cc_start: 0.2266 (mtm) cc_final: 0.1489 (tpt)
REVERT: R   47 LEU cc_start: 0.2703 (pp) cc_final: 0.2177 (tp)
REVERT: R  164 LYS cc_start: 0.5596 (mptp) cc_final: 0.5052 (mppt)
REVERT: R  234 MET cc_start: 0.6263 (mmt) cc_final: 0.5830 (mtp)
  outliers start: 25
  outliers final: 12
  residues processed: 127
  average time/residue: 1.1637
  time to fit residues: 159.4391
Evaluate side-chains
  114 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue  142 GLN
Chi-restraints excluded: chain H residue  179 GLN
Chi-restraints excluded: chain R residue   11 LEU
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue   78 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 52 optimal weight:    6.9990
   chunk 29 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 41 optimal weight:    7.9990
   chunk 61 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 24 optimal weight:    8.9990
   chunk 14 optimal weight:    0.0040
   overall best weight:    1.3598

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 ASN
A 306 GLN
H 142 GLN
R 161 HIS
R 170 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.221896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 122)---------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.159670 restraints weight = 9221.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.3806 rms_B_bonded: 2.04
r_work: 0.3644 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3512 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.3931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9182  Z= 0.234
  Angle     :  0.598   8.316  12441  Z= 0.311
  Chirality :  0.043   0.156   1405
  Planarity :  0.004   0.049   1567
  Dihedral  :  4.620  22.561   1241
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 21.17 %
    Favored  : 74.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.25), residues: 1135
  helix:  2.00 (0.26), residues: 387
  sheet:  0.76 (0.31), residues: 277
  loop : -0.56 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  99 
 HIS   0.006   0.001   HIS R 161 
 PHE   0.021   0.002   PHE R  21 
 TYR   0.017   0.002   TYR B 105 
 ARG   0.007   0.000   ARG B 137 

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 109
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
REVERT: A  281 SER cc_start: 0.6823 (m) cc_final: 0.6522 (t)
REVERT: A  309 ASP cc_start: 0.7634 (m-30) cc_final: 0.7312 (t70)
REVERT: A  331 ASN cc_start: 0.7721 (t0) cc_final: 0.7241 (m110)
REVERT: B   45 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8340 (mtm)
REVERT: B   96 ARG cc_start: 0.7646 (tpt170) cc_final: 0.7284 (mtt180)
REVERT: B  219 ARG cc_start: 0.7717 (mmm160) cc_final: 0.7342 (ttm-80)
REVERT: G   21 MET cc_start: 0.1828 (mtp) cc_final: 0.1227 (pmm)
REVERT: G   38 MET cc_start: 0.2585 (mpm) cc_final: 0.2303 (mpm)
REVERT: H   30 SER cc_start: 0.7323 (p) cc_final: 0.7039 (p)
REVERT: H   55 SER cc_start: 0.6559 (m) cc_final: 0.6265 (m)
REVERT: H   82 GLN cc_start: 0.6457 (tt0) cc_final: 0.6138 (mm-40)
REVERT: H   93 MET cc_start: 0.7382 (ttt) cc_final: 0.6320 (tpp)
REVERT: H   96 CYS cc_start: 0.7449 (OUTLIER) cc_final: 0.7046 (p)
REVERT: H   98 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7260 (ptt-90)
REVERT: H  179 GLN cc_start: 0.6609 (OUTLIER) cc_final: 0.6247 (tt0)
REVERT: H  230 MET cc_start: 0.7054 (tmm) cc_final: 0.6183 (ttp)
REVERT: H  234 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6692 (mt-10)
REVERT: R    1 MET cc_start: 0.2466 (mtm) cc_final: 0.1620 (tpt)
REVERT: R   47 LEU cc_start: 0.2752 (pp) cc_final: 0.2205 (tp)
REVERT: R   60 LYS cc_start: 0.5651 (OUTLIER) cc_final: 0.5138 (mttp)
REVERT: R   91 TRP cc_start: 0.5438 (OUTLIER) cc_final: 0.3926 (m100)
REVERT: R  164 LYS cc_start: 0.5345 (mptp) cc_final: 0.4768 (mppt)
REVERT: R  234 MET cc_start: 0.6579 (mmt) cc_final: 0.5935 (mtm)
  outliers start: 46
  outliers final: 22
  residues processed: 146
  average time/residue: 1.0193
  time to fit residues: 161.1541
Evaluate side-chains
  134 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 106
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue   98 ARG
Chi-restraints excluded: chain H residue  144 THR
Chi-restraints excluded: chain H residue  179 GLN
Chi-restraints excluded: chain H residue  184 SER
Chi-restraints excluded: chain R residue   11 LEU
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue   60 LYS
Chi-restraints excluded: chain R residue   78 ILE
Chi-restraints excluded: chain R residue   91 TRP
Chi-restraints excluded: chain R residue  107 LEU
Chi-restraints excluded: chain R residue  201 LEU
Chi-restraints excluded: chain R residue  236 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 54 optimal weight:   20.0000
   chunk 75 optimal weight:    0.4980
   chunk 25 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0970
   chunk 13 optimal weight:    0.7980
   chunk 82 optimal weight:    7.9990
   chunk 71 optimal weight:   10.0000
   chunk 47 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 ASN
A 306 GLN
H 142 GLN
R 161 HIS
R 170 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.224204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.173721 restraints weight = 9266.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3999 rms_B_bonded: 1.40
r_work: 0.3753 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3630 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.4043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9182  Z= 0.167
  Angle     :  0.560  11.276  12441  Z= 0.287
  Chirality :  0.041   0.136   1405
  Planarity :  0.004   0.051   1567
  Dihedral  :  4.387  21.743   1241
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 23.36 %
    Favored  : 72.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.26), residues: 1135
  helix:  2.10 (0.26), residues: 387
  sheet:  0.68 (0.31), residues: 277
  loop : -0.60 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  99 
 HIS   0.007   0.001   HIS R 161 
 PHE   0.019   0.001   PHE R 301 
 TYR   0.009   0.001   TYR R 269 
 ARG   0.005   0.000   ARG B 137 

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 110
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.7819 (m-40) cc_final: 0.7609 (m-40)
REVERT: A  309 ASP cc_start: 0.7656 (m-30) cc_final: 0.7362 (t70)
REVERT: A  331 ASN cc_start: 0.7601 (t0) cc_final: 0.7245 (m110)
REVERT: B   96 ARG cc_start: 0.7561 (tpt170) cc_final: 0.7335 (mpt-90)
REVERT: B  219 ARG cc_start: 0.7551 (mmm160) cc_final: 0.7346 (ttm-80)
REVERT: G   21 MET cc_start: 0.1954 (mtp) cc_final: 0.1377 (pmm)
REVERT: H   30 SER cc_start: 0.7339 (p) cc_final: 0.7043 (p)
REVERT: H   55 SER cc_start: 0.6635 (m) cc_final: 0.6364 (m)
REVERT: H   82 GLN cc_start: 0.6454 (tt0) cc_final: 0.6175 (mm-40)
REVERT: H   93 MET cc_start: 0.7447 (ttt) cc_final: 0.6414 (tpp)
REVERT: H   96 CYS cc_start: 0.7451 (OUTLIER) cc_final: 0.7155 (p)
REVERT: H   98 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7080 (ptt-90)
REVERT: H  179 GLN cc_start: 0.6683 (OUTLIER) cc_final: 0.6319 (tt0)
REVERT: H  230 MET cc_start: 0.7053 (tmm) cc_final: 0.6292 (ttp)
REVERT: H  234 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6576 (mt-10)
REVERT: R    1 MET cc_start: 0.2472 (mtm) cc_final: 0.1665 (tpt)
REVERT: R   47 LEU cc_start: 0.2709 (pp) cc_final: 0.2237 (tp)
REVERT: R   60 LYS cc_start: 0.5586 (OUTLIER) cc_final: 0.5183 (mttp)
REVERT: R  164 LYS cc_start: 0.5443 (mptp) cc_final: 0.4907 (mppt)
REVERT: R  234 MET cc_start: 0.6391 (mmt) cc_final: 0.5868 (mtm)
  outliers start: 36
  outliers final: 19
  residues processed: 140
  average time/residue: 0.9788
  time to fit residues: 148.5112
Evaluate side-chains
  125 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  279 SER
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue   98 ARG
Chi-restraints excluded: chain H residue  179 GLN
Chi-restraints excluded: chain H residue  184 SER
Chi-restraints excluded: chain R residue   11 LEU
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue   60 LYS
Chi-restraints excluded: chain R residue   78 ILE
Chi-restraints excluded: chain R residue  120 VAL
Chi-restraints excluded: chain R residue  201 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 108 optimal weight:    0.2980
   chunk 82 optimal weight:    4.9990
   chunk 58 optimal weight:    0.3980
   chunk 61 optimal weight:   20.0000
   chunk 75 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 60 optimal weight:    9.9990
   chunk 109 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 ASN
A 306 GLN
H 142 GLN
H 194 ASN
R 161 HIS
R 170 GLN
** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.224181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 123)---------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.170024 restraints weight = 9404.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3952 rms_B_bonded: 1.60
r_work: 0.3765 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3647 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.4162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9182  Z= 0.165
  Angle     :  0.559  10.138  12441  Z= 0.286
  Chirality :  0.041   0.134   1405
  Planarity :  0.004   0.050   1567
  Dihedral  :  4.382  22.506   1241
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 23.57 %
    Favored  : 72.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.26), residues: 1135
  helix:  2.10 (0.26), residues: 386
  sheet:  0.60 (0.31), residues: 284
  loop : -0.55 (0.30), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  99 
 HIS   0.007   0.001   HIS R 161 
 PHE   0.015   0.001   PHE R  21 
 TYR   0.010   0.001   TYR R 269 
 ARG   0.005   0.000   ARG B 137 

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 106
  time to evaluate  : 1.015 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.7776 (m-40) cc_final: 0.7563 (m-40)
REVERT: A  309 ASP cc_start: 0.7638 (m-30) cc_final: 0.7333 (t70)
REVERT: A  331 ASN cc_start: 0.7664 (t0) cc_final: 0.7307 (m110)
REVERT: B  294 CYS cc_start: 0.7425 (OUTLIER) cc_final: 0.7109 (m)
REVERT: G   21 MET cc_start: 0.1888 (mtp) cc_final: 0.1287 (pmm)
REVERT: G   38 MET cc_start: 0.1859 (mpm) cc_final: 0.0459 (mpm)
REVERT: H   30 SER cc_start: 0.7335 (p) cc_final: 0.7035 (p)
REVERT: H   55 SER cc_start: 0.6601 (m) cc_final: 0.6335 (m)
REVERT: H   82 GLN cc_start: 0.6499 (tt0) cc_final: 0.6179 (mm-40)
REVERT: H   93 MET cc_start: 0.7465 (ttt) cc_final: 0.6602 (tpp)
REVERT: H   96 CYS cc_start: 0.7412 (OUTLIER) cc_final: 0.7120 (p)
REVERT: H   98 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.6970 (ptt-90)
REVERT: H  179 GLN cc_start: 0.6670 (OUTLIER) cc_final: 0.6324 (tt0)
REVERT: H  230 MET cc_start: 0.7032 (tmm) cc_final: 0.6201 (ttp)
REVERT: H  234 GLU cc_start: 0.6790 (mt-10) cc_final: 0.6560 (mt-10)
REVERT: R    1 MET cc_start: 0.2513 (mtm) cc_final: 0.1685 (tpt)
REVERT: R   25 PHE cc_start: 0.6302 (t80) cc_final: 0.5857 (t80)
REVERT: R   47 LEU cc_start: 0.2700 (pp) cc_final: 0.2244 (tp)
REVERT: R   60 LYS cc_start: 0.5744 (OUTLIER) cc_final: 0.5261 (mttp)
REVERT: R  100 CYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6660 (t)
REVERT: R  164 LYS cc_start: 0.5436 (mptp) cc_final: 0.4900 (mppt)
REVERT: R  170 GLN cc_start: 0.4466 (OUTLIER) cc_final: 0.4070 (tp-100)
REVERT: R  234 MET cc_start: 0.6477 (mmt) cc_final: 0.5916 (mtm)
  outliers start: 39
  outliers final: 21
  residues processed: 136
  average time/residue: 1.1108
  time to fit residues: 163.3496
Evaluate side-chains
  133 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 105
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  279 SER
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue   98 ARG
Chi-restraints excluded: chain H residue  179 GLN
Chi-restraints excluded: chain H residue  184 SER
Chi-restraints excluded: chain R residue   11 LEU
Chi-restraints excluded: chain R residue   20 VAL
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue   60 LYS
Chi-restraints excluded: chain R residue   78 ILE
Chi-restraints excluded: chain R residue  100 CYS
Chi-restraints excluded: chain R residue  120 VAL
Chi-restraints excluded: chain R residue  170 GLN
Chi-restraints excluded: chain R residue  201 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 17 optimal weight:    8.9990
   chunk 76 optimal weight:    5.9990
   chunk 37 optimal weight:    0.8980
   chunk 89 optimal weight:    7.9990
   chunk 47 optimal weight:    4.9990
   chunk 43 optimal weight:    0.4980
   chunk 106 optimal weight:    2.9990
   chunk 65 optimal weight:    9.9990
   chunk 101 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 ASN
A 306 GLN
H 142 GLN
R 112 GLN
R 161 HIS
R 170 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.219226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.168766 restraints weight = 9387.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3953 rms_B_bonded: 1.36
r_work: 0.3686 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3562 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.4609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9182  Z= 0.270
  Angle     :  0.631  10.413  12441  Z= 0.328
  Chirality :  0.044   0.171   1405
  Planarity :  0.004   0.050   1567
  Dihedral  :  4.845  25.357   1241
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 23.25 %
    Favored  : 72.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.25), residues: 1135
  helix:  1.80 (0.26), residues: 385
  sheet:  0.45 (0.31), residues: 286
  loop : -0.61 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  82 
 HIS   0.010   0.001   HIS R 223 
 PHE   0.024   0.002   PHE R  21 
 TYR   0.013   0.002   TYR A 290 
 ARG   0.005   0.001   ARG B 137 

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 105
  time to evaluate  : 1.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7306 (ttt90)
REVERT: A  309 ASP cc_start: 0.7730 (m-30) cc_final: 0.7459 (t70)
REVERT: B   45 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8306 (mtm)
REVERT: B  294 CYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7298 (m)
REVERT: G   38 MET cc_start: 0.2075 (mpm) cc_final: 0.0511 (mpm)
REVERT: H   30 SER cc_start: 0.7507 (p) cc_final: 0.7229 (p)
REVERT: H   55 SER cc_start: 0.6721 (m) cc_final: 0.6132 (t)
REVERT: H   82 GLN cc_start: 0.6459 (tt0) cc_final: 0.6164 (mm-40)
REVERT: H   93 MET cc_start: 0.7508 (ttt) cc_final: 0.6777 (tpp)
REVERT: H   96 CYS cc_start: 0.7449 (OUTLIER) cc_final: 0.7154 (p)
REVERT: H   98 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7122 (ptt-90)
REVERT: H  142 GLN cc_start: 0.4422 (OUTLIER) cc_final: 0.3639 (tp40)
REVERT: H  179 GLN cc_start: 0.6745 (OUTLIER) cc_final: 0.6375 (tt0)
REVERT: H  234 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6838 (mt-10)
REVERT: R    1 MET cc_start: 0.2533 (mtm) cc_final: 0.1683 (tpt)
REVERT: R   25 PHE cc_start: 0.6301 (t80) cc_final: 0.5923 (t80)
REVERT: R   47 LEU cc_start: 0.2739 (pp) cc_final: 0.2235 (tp)
REVERT: R   60 LYS cc_start: 0.5962 (OUTLIER) cc_final: 0.5441 (mttp)
REVERT: R  100 CYS cc_start: 0.7320 (OUTLIER) cc_final: 0.6718 (t)
REVERT: R  164 LYS cc_start: 0.5344 (mptp) cc_final: 0.4783 (mppt)
REVERT: R  234 MET cc_start: 0.6579 (mmt) cc_final: 0.6096 (mtm)
REVERT: R  296 PHE cc_start: 0.5714 (m-10) cc_final: 0.4917 (t80)
  outliers start: 44
  outliers final: 28
  residues processed: 140
  average time/residue: 1.0766
  time to fit residues: 163.4690
Evaluate side-chains
  137 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 100
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  279 SER
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue   98 ARG
Chi-restraints excluded: chain H residue  142 GLN
Chi-restraints excluded: chain H residue  174 LEU
Chi-restraints excluded: chain H residue  179 GLN
Chi-restraints excluded: chain H residue  184 SER
Chi-restraints excluded: chain R residue   11 LEU
Chi-restraints excluded: chain R residue   20 VAL
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue   60 LYS
Chi-restraints excluded: chain R residue   78 ILE
Chi-restraints excluded: chain R residue  100 CYS
Chi-restraints excluded: chain R residue  107 LEU
Chi-restraints excluded: chain R residue  120 VAL
Chi-restraints excluded: chain R residue  141 ASN
Chi-restraints excluded: chain R residue  201 LEU
Chi-restraints excluded: chain R residue  236 VAL
Chi-restraints excluded: chain R residue  283 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 51 optimal weight:    6.9990
   chunk 95 optimal weight:    3.9990
   chunk 13 optimal weight:    6.9990
   chunk 18 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 70 optimal weight:    5.9990
   chunk 7 optimal weight:    0.6980
   chunk 104 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 ASN
A 306 GLN
A 346 ASN
H 142 GLN
R 161 HIS
R 170 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.218917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.167378 restraints weight = 9370.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.3938 rms_B_bonded: 1.33
r_work: 0.3698 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3575 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.4808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9182  Z= 0.252
  Angle     :  0.619  10.119  12441  Z= 0.321
  Chirality :  0.043   0.152   1405
  Planarity :  0.004   0.050   1567
  Dihedral  :  4.888  26.124   1241
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 23.15 %
    Favored  : 72.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.25), residues: 1135
  helix:  1.61 (0.26), residues: 393
  sheet:  0.33 (0.31), residues: 292
  loop : -0.67 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  82 
 HIS   0.009   0.001   HIS R 223 
 PHE   0.023   0.002   PHE R 117 
 TYR   0.012   0.002   TYR A 290 
 ARG   0.009   0.001   ARG A 205 

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 99
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7248 (ttt90)
REVERT: A   34 VAL cc_start: 0.7857 (OUTLIER) cc_final: 0.7440 (t)
REVERT: B   45 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8290 (mtm)
REVERT: G   31 SER cc_start: 0.3762 (OUTLIER) cc_final: 0.3520 (t)
REVERT: G   38 MET cc_start: 0.2081 (mpm) cc_final: 0.0434 (mpm)
REVERT: H   30 SER cc_start: 0.7603 (p) cc_final: 0.7317 (p)
REVERT: H   55 SER cc_start: 0.6749 (m) cc_final: 0.6164 (t)
REVERT: H   82 GLN cc_start: 0.6446 (tt0) cc_final: 0.6171 (mm-40)
REVERT: H   93 MET cc_start: 0.7558 (ttt) cc_final: 0.6848 (tpp)
REVERT: H   96 CYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7199 (p)
REVERT: H   98 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7045 (ptt-90)
REVERT: H  179 GLN cc_start: 0.6840 (OUTLIER) cc_final: 0.6522 (tt0)
REVERT: H  234 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6874 (mt-10)
REVERT: R    1 MET cc_start: 0.2369 (mtm) cc_final: 0.1559 (tpt)
REVERT: R   25 PHE cc_start: 0.6306 (t80) cc_final: 0.5922 (t80)
REVERT: R   47 LEU cc_start: 0.2689 (pp) cc_final: 0.2244 (tp)
REVERT: R   60 LYS cc_start: 0.6020 (OUTLIER) cc_final: 0.5510 (mttp)
REVERT: R  100 CYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6598 (t)
REVERT: R  164 LYS cc_start: 0.5304 (mptp) cc_final: 0.4733 (mppt)
REVERT: R  234 MET cc_start: 0.6583 (mmt) cc_final: 0.6107 (mtm)
REVERT: R  296 PHE cc_start: 0.5640 (m-10) cc_final: 0.4793 (t80)
  outliers start: 45
  outliers final: 25
  residues processed: 134
  average time/residue: 0.9703
  time to fit residues: 140.9216
Evaluate side-chains
  128 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 94
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  279 SER
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue   98 ARG
Chi-restraints excluded: chain H residue  179 GLN
Chi-restraints excluded: chain H residue  184 SER
Chi-restraints excluded: chain R residue   11 LEU
Chi-restraints excluded: chain R residue   20 VAL
Chi-restraints excluded: chain R residue   60 LYS
Chi-restraints excluded: chain R residue   78 ILE
Chi-restraints excluded: chain R residue  100 CYS
Chi-restraints excluded: chain R residue  107 LEU
Chi-restraints excluded: chain R residue  120 VAL
Chi-restraints excluded: chain R residue  141 ASN
Chi-restraints excluded: chain R residue  236 VAL
Chi-restraints excluded: chain R residue  283 THR
Chi-restraints excluded: chain R residue  288 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 55 optimal weight:    0.0020
   chunk 54 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 92 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 60 optimal weight:    9.9990
   chunk 69 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.6388

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 ASN
A 306 GLN
H 142 GLN
R 161 HIS
R 170 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.222649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 114)---------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.168115 restraints weight = 9366.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3922 rms_B_bonded: 1.64
r_work: 0.3749 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3624 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.4798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9182  Z= 0.168
  Angle     :  0.576  11.695  12441  Z= 0.293
  Chirality :  0.041   0.134   1405
  Planarity :  0.004   0.051   1567
  Dihedral  :  4.509  23.060   1241
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 24.19 %
    Favored  : 72.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.26), residues: 1135
  helix:  1.79 (0.27), residues: 397
  sheet:  0.38 (0.31), residues: 286
  loop : -0.67 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  99 
 HIS   0.008   0.001   HIS R 161 
 PHE   0.027   0.001   PHE R 117 
 TYR   0.008   0.001   TYR B  85 
 ARG   0.008   0.001   ARG A 205 

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 105
  time to evaluate  : 0.917 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 ASP cc_start: 0.7728 (t70) cc_final: 0.7439 (t70)
REVERT: A  346 ASN cc_start: 0.7706 (m-40) cc_final: 0.7466 (m-40)
REVERT: B   45 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8238 (mtm)
REVERT: G   31 SER cc_start: 0.3760 (OUTLIER) cc_final: 0.3520 (t)
REVERT: G   38 MET cc_start: 0.2178 (mpm) cc_final: 0.0438 (mpm)
REVERT: H   30 SER cc_start: 0.7507 (p) cc_final: 0.7213 (p)
REVERT: H   55 SER cc_start: 0.6690 (m) cc_final: 0.6097 (t)
REVERT: H   57 THR cc_start: 0.7012 (p) cc_final: 0.6717 (t)
REVERT: H   78 THR cc_start: 0.5488 (m) cc_final: 0.5102 (t)
REVERT: H   82 GLN cc_start: 0.6439 (tt0) cc_final: 0.6144 (mm-40)
REVERT: H   93 MET cc_start: 0.7519 (ttt) cc_final: 0.6751 (tpp)
REVERT: H   96 CYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7228 (p)
REVERT: H   98 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6864 (ptt-90)
REVERT: H  179 GLN cc_start: 0.6778 (OUTLIER) cc_final: 0.6353 (tt0)
REVERT: H  230 MET cc_start: 0.7567 (ttp) cc_final: 0.6887 (ttp)
REVERT: H  234 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6696 (mt-10)
REVERT: R    1 MET cc_start: 0.2423 (mtm) cc_final: 0.1550 (tpt)
REVERT: R   25 PHE cc_start: 0.6139 (t80) cc_final: 0.5785 (t80)
REVERT: R   43 LEU cc_start: 0.5644 (pt) cc_final: 0.4917 (tt)
REVERT: R   47 LEU cc_start: 0.2624 (pp) cc_final: 0.2201 (tp)
REVERT: R   60 LYS cc_start: 0.5824 (OUTLIER) cc_final: 0.5302 (mttp)
REVERT: R  100 CYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6565 (t)
REVERT: R  164 LYS cc_start: 0.5395 (mptp) cc_final: 0.4800 (mppt)
REVERT: R  170 GLN cc_start: 0.4607 (OUTLIER) cc_final: 0.4406 (tm-30)
REVERT: R  227 LYS cc_start: 0.6460 (mttp) cc_final: 0.5729 (mtmt)
REVERT: R  234 MET cc_start: 0.6484 (mmt) cc_final: 0.5990 (mtm)
REVERT: R  296 PHE cc_start: 0.5500 (m-10) cc_final: 0.4634 (t80)
  outliers start: 36
  outliers final: 22
  residues processed: 134
  average time/residue: 0.9683
  time to fit residues: 141.2249
Evaluate side-chains
  130 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 100
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue   98 ARG
Chi-restraints excluded: chain H residue  142 GLN
Chi-restraints excluded: chain H residue  174 LEU
Chi-restraints excluded: chain H residue  179 GLN
Chi-restraints excluded: chain H residue  184 SER
Chi-restraints excluded: chain R residue   11 LEU
Chi-restraints excluded: chain R residue   60 LYS
Chi-restraints excluded: chain R residue   78 ILE
Chi-restraints excluded: chain R residue  100 CYS
Chi-restraints excluded: chain R residue  120 VAL
Chi-restraints excluded: chain R residue  170 GLN
Chi-restraints excluded: chain R residue  236 VAL
Chi-restraints excluded: chain R residue  288 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 74 optimal weight:   10.0000
   chunk 68 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 71 optimal weight:   10.0000
   chunk 48 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0770
   overall best weight:    0.7744

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 ASN
A 306 GLN
H 142 GLN
R 112 GLN
R 161 HIS
R 170 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.221860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 101)---------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.167487 restraints weight = 9340.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3928 rms_B_bonded: 1.59
r_work: 0.3750 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3629 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.4828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9182  Z= 0.179
  Angle     :  0.581  10.726  12441  Z= 0.297
  Chirality :  0.041   0.133   1405
  Planarity :  0.004   0.051   1567
  Dihedral  :  4.515  23.301   1241
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 24.19 %
    Favored  : 71.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.26), residues: 1135
  helix:  1.82 (0.26), residues: 394
  sheet:  0.40 (0.31), residues: 285
  loop : -0.65 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  99 
 HIS   0.009   0.001   HIS R 161 
 PHE   0.028   0.002   PHE R 117 
 TYR   0.009   0.001   TYR R 269 
 ARG   0.008   0.000   ARG B 137 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8473.03 seconds
wall clock time: 147 minutes 56.33 seconds (8876.33 seconds total)