Starting phenix.real_space_refine
on Tue Mar 11 22:08:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8unt_42416/03_2025/8unt_42416.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8unt_42416/03_2025/8unt_42416.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8unt_42416/03_2025/8unt_42416.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8unt_42416/03_2025/8unt_42416.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8unt_42416/03_2025/8unt_42416.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8unt_42416/03_2025/8unt_42416.cif"
  }
  resolution = 3.4
  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=   0.023
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
     P       3      5.49       5
     S      42      5.16       5
     C    4306      2.51       5
     N    1165      2.21       5
     O    1196      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6712
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1787
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 236, 1775
          Classifications: {'peptide': 236}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 51}
          Link IDs: {'PTRANS': 6, 'TRANS': 229}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 188
          Unresolved non-hydrogen angles: 229
          Unresolved non-hydrogen dihedrals: 148
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 11, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 8}
          Unresolved non-hydrogen planarities: 118
      Conformer: "B"
        Number of residues, atoms: 236, 1775
          Classifications: {'peptide': 236}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 51}
          Link IDs: {'PTRANS': 6, 'TRANS': 229}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 188
          Unresolved non-hydrogen angles: 229
          Unresolved non-hydrogen dihedrals: 148
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 11, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 8}
          Unresolved non-hydrogen planarities: 118
          bond proxies already assigned to first conformer: 1797
    Chain: "B"
      Number of atoms: 2413
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2413
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 44}
          Link IDs: {'PTRANS': 5, 'TRANS': 328}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 156
          Unresolved non-hydrogen angles: 192
          Unresolved non-hydrogen dihedrals: 120
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 13}
          Unresolved non-hydrogen planarities: 124
    Chain: "G"
      Number of atoms: 345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 345
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 90
          Unresolved non-hydrogen angles: 107
          Unresolved non-hydrogen dihedrals: 75
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 47
    Chain: "R"
      Number of atoms: 2119
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2119
          Classifications: {'peptide': 287}
          Incomplete info: {'truncation_to_alanine': 52}
          Link IDs: {'PTRANS': 7, 'TRANS': 279}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 197
          Unresolved non-hydrogen angles: 245
          Unresolved non-hydrogen dihedrals: 160
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 119
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 16
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR A 360 " occ=0.51
      ... (22 atoms not shown)
      pdb=" OH BTYR A 360 " occ=0.49
  Time building chain proxies: 6.71, per 1000 atoms: 1.00
  Number of scatterers: 6712
  At special positions: 0
  Unit cell: (82.4315, 135.361, 98.9178, 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)
     S      42     16.00
     P       3     15.00
     O    1196      8.00
     N    1165      7.00
     C    4306      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 184 " - pdb=" SG  CYS R 190 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.83
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1732

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 8 sheets defined
      48.1% alpha, 16.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 40
      removed outlier: 3.727A  pdb=" N   LYS A  17 " --> pdb=" O   ARG A  13 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   THR A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 63
      removed outlier: 3.564A  pdb=" N   LYS A  58 " --> pdb=" O   SER A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 302
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.113A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.653A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.635A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 9 through 24
      removed outlier: 4.144A  pdb=" N   ARG G  13 " --> pdb=" O   ILE G   9 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   LYS G  14 " --> pdb=" O   ALA G  10 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.590A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 47
      No H-bonds generated for 'chain 'G' and resid 45 through 47'
    Processing helix  chain 'R' and resid 30 through 61
      removed outlier: 3.817A  pdb=" N   MET R  36 " --> pdb=" O   TRP R  32 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   GLY R  37 " --> pdb=" O   VAL R  33 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   ILE R  38 " --> pdb=" O   VAL R  34 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ASN R  51 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 62 through 66
      removed outlier: 5.465A  pdb=" N   THR R  66 " --> pdb=" O   ARG R  63 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 67 through 97
      removed outlier: 4.255A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
      removed outlier: 4.047A  pdb=" N   ILE R 121 " --> pdb=" O   VAL R 117 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   GLU R 122 " --> pdb=" O   THR R 118 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   THR R 123 " --> pdb=" O   ALA R 119 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   LEU R 124 " --> pdb=" O   SER R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 3.677A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
      removed outlier: 3.727A  pdb=" N   MET R 171 " --> pdb=" O   LEU R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
      removed outlier: 3.745A  pdb=" N   SER R 204 " --> pdb=" O   ALA R 200 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 209 through 238
      removed outlier: 3.786A  pdb=" N   VAL R 213 " --> pdb=" O   TYR R 209 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ILE R 214 " --> pdb=" O   VAL R 210 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   MET R 215 " --> pdb=" O   PRO R 211 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 287
      removed outlier: 4.329A  pdb=" N   THR R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 288 through 299
      removed outlier: 4.527A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
      removed outlier: 3.531A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 318 through 320
      No H-bonds generated for 'chain 'R' and resid 318 through 320'
    Processing helix  chain 'R' and resid 321 through 327
    Processing helix  chain 'R' and resid 329 through 339
      removed outlier: 3.565A  pdb=" N   LEU R 339 " --> pdb=" O   ALA R 335 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.210A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.766A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.854A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.468A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 7.192A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.287A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.159A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 9.259A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.339A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.683A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.020A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.539A  pdb=" N   THR B 102 " --> pdb=" O   GLY B 115 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ASN B 125 " --> pdb=" O   ARG B 134 " (cutoff:3.500A)
      removed outlier: 4.150A  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: 3.846A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.913A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.702A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.952A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)

    359 hydrogen bonds defined for protein.
    1050 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: 2.04

  Time building geometry restraints manager: 2.19 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1551
        1.33 -     1.45: 1573
        1.45 -     1.58: 3672
        1.58 -     1.70: 5
        1.70 -     1.82: 57
  Bond restraints: 6858
  Sorted by residual:
  bond pdb=" CA  ALA R 271 "
       pdb=" C   ALA R 271 "
    ideal  model  delta    sigma   weight residual
    1.523  1.470  0.054 1.30e-02 5.92e+03 1.71e+01
  bond pdb=" N   LYS R 273 "
       pdb=" CA  LYS R 273 "
    ideal  model  delta    sigma   weight residual
    1.459  1.419  0.040 1.19e-02 7.06e+03 1.13e+01
  bond pdb=" N   GLU A 330 "
       pdb=" CA  GLU A 330 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.036 1.23e-02 6.61e+03 8.75e+00
  bond pdb=" N   VAL A 367 "
       pdb=" CA  VAL A 367 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.19e-02 7.06e+03 8.68e+00
  bond pdb=" CA  ILE R 277 "
       pdb=" C   ILE R 277 "
    ideal  model  delta    sigma   weight residual
    1.523  1.486  0.037 1.27e-02 6.20e+03 8.35e+00
  ... (remaining 6853 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.77: 9207
        2.77 -     5.55: 154
        5.55 -     8.32: 9
        8.32 -    11.09: 6
       11.09 -    13.86: 2
  Bond angle restraints: 9378
  Sorted by residual:
  angle pdb=" N   TYR A 253 "
        pdb=" CA  TYR A 253 "
        pdb=" C   TYR A 253 "
      ideal   model   delta    sigma   weight residual
     113.97  105.77    8.20 1.28e+00 6.10e-01 4.10e+01
  angle pdb=" C   ILE R 277 "
        pdb=" N   ILE R 278 "
        pdb=" CA  ILE R 278 "
      ideal   model   delta    sigma   weight residual
     122.63  115.03    7.60 1.19e+00 7.06e-01 4.08e+01
  angle pdb=" CA  GLY A  49 "
        pdb=" C   GLY A  49 "
        pdb=" O   GLY A  49 "
      ideal   model   delta    sigma   weight residual
     121.58  116.71    4.87 9.00e-01 1.23e+00 2.93e+01
  angle pdb=" N   ILE A  62 "
        pdb=" CA  ILE A  62 "
        pdb=" C   ILE A  62 "
      ideal   model   delta    sigma   weight residual
     110.62  105.23    5.39 1.02e+00 9.61e-01 2.80e+01
  angle pdb=" N   PHE A 315 "
        pdb=" CA  PHE A 315 "
        pdb=" C   PHE A 315 "
      ideal   model   delta    sigma   weight residual
     111.71  105.79    5.92 1.15e+00 7.56e-01 2.65e+01
  ... (remaining 9373 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.57: 3898
       33.57 -    67.13: 65
       67.13 -   100.70: 3
      100.70 -   134.26: 0
      134.26 -   167.83: 4
  Dihedral angle restraints: 3970
    sinusoidal: 1302
      harmonic: 2668
  Sorted by residual:
  dihedral pdb=" C8  GTP A 401 "
           pdb=" C1' GTP A 401 "
           pdb=" N9  GTP A 401 "
           pdb=" O4' GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -63.24  167.83     1      2.00e+01 2.50e-03 4.75e+01
  dihedral pdb=" C5' GTP A 401 "
           pdb=" O5' GTP A 401 "
           pdb=" PA  GTP A 401 "
           pdb=" O3A GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -129.48 -161.25     1      2.00e+01 2.50e-03 4.67e+01
  dihedral pdb=" O3B GTP A 401 "
           pdb=" O3A GTP A 401 "
           pdb=" PB  GTP A 401 "
           pdb=" PA  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -68.92   84.26 -153.18     1      2.00e+01 2.50e-03 4.54e+01
  ... (remaining 3967 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 824
       0.047 -    0.093: 195
       0.093 -    0.140: 69
       0.140 -    0.187: 20
       0.187 -    0.234: 9
  Chirality restraints: 1117
  Sorted by residual:
  chirality pdb=" CA  ILE A  62 "
            pdb=" N   ILE A  62 "
            pdb=" C   ILE A  62 "
            pdb=" CB  ILE A  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" CA  ASP A 223 "
            pdb=" N   ASP A 223 "
            pdb=" C   ASP A 223 "
            pdb=" CB  ASP A 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CA  VAL A 224 "
            pdb=" N   VAL A 224 "
            pdb=" C   VAL A 224 "
            pdb=" CB  VAL A 224 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.65   -0.21 2.00e-01 2.50e+01 1.13e+00
  ... (remaining 1114 not shown)

  Planarity restraints: 1175
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  44 "    0.015 2.00e-02 2.50e+03   2.94e-02 8.64e+00
        pdb=" C   LEU A  44 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   LEU A  44 "    0.019 2.00e-02 2.50e+03
        pdb=" N   LEU A  45 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R  33 "    0.010 2.00e-02 2.50e+03   2.11e-02 4.46e+00
        pdb=" C   VAL R  33 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   VAL R  33 "    0.014 2.00e-02 2.50e+03
        pdb=" N   VAL R  34 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 315 "    0.010 2.00e-02 2.50e+03   2.09e-02 4.36e+00
        pdb=" C   PHE A 315 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   PHE A 315 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ALA A 316 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1172 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1233
        2.77 -     3.30: 6256
        3.30 -     3.84: 10500
        3.84 -     4.37: 11540
        4.37 -     4.90: 21136
  Nonbonded interactions: 50665
  Sorted by model distance:
  nonbonded pdb=" N   GLU A  50 "
            pdb=" O3G GTP A 401 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" N   SER A  51 "
            pdb=" O3G GTP A 401 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   LEU A  63 "
            pdb=" C   HIS A  64 "
     model   vdw
     2.330 3.270
  nonbonded pdb=" O   ILE B  37 "
            pdb=" NZ  LYS B 301 "
     model   vdw
     2.357 3.120
  ... (remaining 50660 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=0.49 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:             4.410
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     24.650
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   6858  Z= 0.350
  Angle     :  0.808  13.863   9378  Z= 0.520
  Chirality :  0.052   0.234   1117
  Planarity :  0.004   0.064   1175
  Dihedral  : 14.498 167.830   2232
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  0.97 %
    Favored  : 98.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.28), residues: 900
  helix:  2.15 (0.27), residues: 392
  sheet:  1.01 (0.41), residues: 168
  loop : -0.79 (0.31), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 234 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.012   0.001   PHE A 222 
 TYR   0.015   0.001   TYR B  59 
 ARG   0.006   0.000   ARG R 239 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 105
  time to evaluate  : 0.762 
Fit side-chains
REVERT: A  222 PHE cc_start: 0.8370 (m-80) cc_final: 0.8134 (m-80)
REVERT: A  295 ASP cc_start: 0.8008 (p0) cc_final: 0.7742 (p0)
REVERT: A  314 GLU cc_start: 0.6428 (mm-30) cc_final: 0.6221 (tp30)
  outliers start: 2
  outliers final: 1
  residues processed: 107
  average time/residue: 0.2042
  time to fit residues: 28.7550
Evaluate side-chains
  85 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  269 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 23 optimal weight:   10.0000
   chunk 45 optimal weight:    4.9990
   chunk 36 optimal weight:    0.6980
   chunk 69 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 80 optimal weight:    0.6980
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
R 170 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.132092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.106966 restraints weight = 35247.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 4.60
r_work: 0.3231 rms_B_bonded: 4.81 restraints_weight: 0.5000
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3239
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3239 r_free = 0.3239    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3239 r_free = 0.3239    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3239
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.1335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6858  Z= 0.254
  Angle     :  0.533   6.252   9378  Z= 0.288
  Chirality :  0.042   0.151   1117
  Planarity :  0.003   0.037   1175
  Dihedral  : 10.528 160.709   1006
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  :  7.61 %
    Favored  : 90.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.29), residues: 900
  helix:  2.08 (0.26), residues: 402
  sheet:  0.52 (0.40), residues: 173
  loop : -0.63 (0.33), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 297 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.022   0.001   PHE A 208 
 TYR   0.014   0.001   TYR B  59 
 ARG   0.006   0.000   ARG A 389 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.763 
Fit side-chains
  outliers start: 12
  outliers final: 12
  residues processed: 96
  average time/residue: 0.1981
  time to fit residues: 25.2134
Evaluate side-chains
  92 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain R residue  152 VAL
Chi-restraints excluded: chain R residue  170 GLN
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  237 GLU
Chi-restraints excluded: chain R residue  269 HIS
Chi-restraints excluded: chain R residue  272 LEU
Chi-restraints excluded: chain R residue  294 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 77 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 78 optimal weight:    0.6980
   chunk 51 optimal weight:    5.9990
   chunk 24 optimal weight:    5.9990
   chunk 86 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 79 optimal weight:    0.0170
   overall best weight:    1.0822

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
R 170 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.132126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.106221 restraints weight = 43648.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.3375 rms_B_bonded: 5.18
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3375
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3375 r_free = 0.3375    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3375 r_free = 0.3375    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3375
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.1534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6858  Z= 0.196
  Angle     :  0.490   6.648   9378  Z= 0.264
  Chirality :  0.041   0.151   1117
  Planarity :  0.003   0.040   1175
  Dihedral  : 10.049 154.424   1006
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  :  9.87 %
    Favored  : 88.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.29), residues: 900
  helix:  2.17 (0.26), residues: 404
  sheet:  0.37 (0.40), residues: 179
  loop : -0.43 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 297 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.017   0.001   PHE A 208 
 TYR   0.011   0.001   TYR A 339 
 ARG   0.005   0.000   ARG A 389 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.832 
Fit side-chains
  outliers start: 11
  outliers final: 11
  residues processed: 91
  average time/residue: 0.2019
  time to fit residues: 24.8138
Evaluate side-chains
  94 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  152 VAL
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  237 GLU
Chi-restraints excluded: chain R residue  269 HIS
Chi-restraints excluded: chain R residue  272 LEU
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 71 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 87 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 45 optimal weight:    0.2980
   chunk 54 optimal weight:    4.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A  64 HIS
A 218 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.134378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.110473 restraints weight = 26809.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 3.92
r_work: 0.3292 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3298
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3298 r_free = 0.3298    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3298 r_free = 0.3298    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3298
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.1710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6858  Z= 0.160
  Angle     :  0.464   6.772   9378  Z= 0.248
  Chirality :  0.041   0.147   1117
  Planarity :  0.003   0.039   1175
  Dihedral  :  9.458 152.180   1006
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 2.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  :  9.87 %
    Favored  : 87.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.29), residues: 900
  helix:  2.30 (0.26), residues: 405
  sheet:  0.54 (0.40), residues: 177
  loop : -0.48 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 297 
 HIS   0.002   0.001   HIS A 357 
 PHE   0.015   0.001   PHE A 208 
 TYR   0.010   0.001   TYR A 339 
 ARG   0.005   0.000   ARG R 239 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.718 
Fit side-chains
REVERT: A  295 ASP cc_start: 0.8238 (p0) cc_final: 0.8027 (p0)
REVERT: A  314 GLU cc_start: 0.8910 (tp30) cc_final: 0.8221 (mt-10)
REVERT: R  113 ASP cc_start: 0.8293 (t70) cc_final: 0.7949 (t0)
  outliers start: 14
  outliers final: 13
  residues processed: 100
  average time/residue: 0.1847
  time to fit residues: 25.0122
Evaluate side-chains
  100 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  111 SER
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  237 GLU
Chi-restraints excluded: chain R residue  272 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 83 optimal weight:    0.7980
   chunk 70 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   chunk 82 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9980
   chunk 87 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 7 optimal weight:   20.0000
   chunk 28 optimal weight:    5.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.134770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.108328 restraints weight = 46958.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 5.43
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3394
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3394 r_free = 0.3394    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3394 r_free = 0.3394    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3394
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6858  Z= 0.156
  Angle     :  0.462   6.833   9378  Z= 0.245
  Chirality :  0.040   0.149   1117
  Planarity :  0.003   0.039   1175
  Dihedral  :  8.929 152.263   1004
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 11.33 %
    Favored  : 86.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.29), residues: 900
  helix:  2.36 (0.26), residues: 405
  sheet:  0.51 (0.41), residues: 177
  loop : -0.40 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 297 
 HIS   0.003   0.001   HIS A  64 
 PHE   0.013   0.001   PHE A 208 
 TYR   0.009   0.001   TYR A 339 
 ARG   0.006   0.000   ARG A 389 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.765 
Fit side-chains
REVERT: A  314 GLU cc_start: 0.8831 (tp30) cc_final: 0.8131 (mt-10)
REVERT: R  113 ASP cc_start: 0.8151 (t70) cc_final: 0.7912 (t0)
  outliers start: 16
  outliers final: 15
  residues processed: 99
  average time/residue: 0.1837
  time to fit residues: 24.5419
Evaluate side-chains
  99 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  111 SER
Chi-restraints excluded: chain R residue  152 VAL
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  237 GLU
Chi-restraints excluded: chain R residue  272 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 67 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0060
   chunk 43 optimal weight:    2.9990
   chunk 77 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 27 optimal weight:    6.9990
   chunk 40 optimal weight:    0.7980
   overall best weight:    1.1602

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.129928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.105517 restraints weight = 32840.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 4.44
r_work: 0.3206 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3220
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3220
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6858  Z= 0.201
  Angle     :  0.480   6.728   9378  Z= 0.255
  Chirality :  0.041   0.152   1117
  Planarity :  0.003   0.039   1175
  Dihedral  :  8.614 150.190   1004
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 11.65 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.43 (0.29), residues: 900
  helix:  2.29 (0.26), residues: 405
  sheet:  0.32 (0.40), residues: 178
  loop : -0.41 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 297 
 HIS   0.003   0.001   HIS A  64 
 PHE   0.012   0.001   PHE A 208 
 TYR   0.011   0.001   TYR A 339 
 ARG   0.007   0.000   ARG A 389 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.692 
Fit side-chains
REVERT: A  314 GLU cc_start: 0.8954 (tp30) cc_final: 0.8185 (mt-10)
REVERT: B  278 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8195 (m-80)
  outliers start: 22
  outliers final: 18
  residues processed: 97
  average time/residue: 0.2001
  time to fit residues: 25.8994
Evaluate side-chains
  101 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  278 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  111 SER
Chi-restraints excluded: chain R residue  152 VAL
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  237 GLU
Chi-restraints excluded: chain R residue  272 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 39 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 26 optimal weight:    9.9990
   chunk 13 optimal weight:    0.5980
   chunk 73 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0970
   chunk 52 optimal weight:    3.9990
   chunk 85 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.6578

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.132130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.106732 restraints weight = 36293.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 4.80
r_work: 0.3220 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3235
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3235 r_free = 0.3235    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3235 r_free = 0.3235    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3235
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6858  Z= 0.138
  Angle     :  0.457   6.679   9378  Z= 0.240
  Chirality :  0.040   0.143   1117
  Planarity :  0.003   0.040   1175
  Dihedral  :  8.210 149.027   1004
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 13.11 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.29), residues: 900
  helix:  2.38 (0.26), residues: 405
  sheet:  0.38 (0.40), residues: 177
  loop : -0.40 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 297 
 HIS   0.002   0.000   HIS A 220 
 PHE   0.011   0.001   PHE A 208 
 TYR   0.009   0.001   TYR A 339 
 ARG   0.007   0.000   ARG A 389 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.779 
Fit side-chains
REVERT: A  314 GLU cc_start: 0.8911 (tp30) cc_final: 0.8140 (mt-10)
REVERT: R  113 ASP cc_start: 0.8469 (t70) cc_final: 0.8150 (t0)
  outliers start: 17
  outliers final: 13
  residues processed: 100
  average time/residue: 0.1940
  time to fit residues: 25.9842
Evaluate side-chains
  101 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  111 SER
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  237 GLU
Chi-restraints excluded: chain R residue  272 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 85 optimal weight:    0.8980
   chunk 25 optimal weight:    7.9990
   chunk 48 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 49 optimal weight:    0.5980
   chunk 67 optimal weight:    0.0870
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.132641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.107934 restraints weight = 30682.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 4.36
r_work: 0.3239 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3261
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3261 r_free = 0.3261    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3261 r_free = 0.3261    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3261
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.2103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6858  Z= 0.139
  Angle     :  0.453   8.094   9378  Z= 0.238
  Chirality :  0.040   0.145   1117
  Planarity :  0.003   0.039   1175
  Dihedral  :  7.928 149.944   1004
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 2.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 13.27 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.29), residues: 900
  helix:  2.42 (0.26), residues: 405
  sheet:  0.35 (0.40), residues: 178
  loop : -0.36 (0.34), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 297 
 HIS   0.002   0.001   HIS A  64 
 PHE   0.011   0.001   PHE A 208 
 TYR   0.008   0.001   TYR A 339 
 ARG   0.007   0.000   ARG A 389 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.862 
Fit side-chains
REVERT: A  314 GLU cc_start: 0.8916 (tp30) cc_final: 0.8152 (mt-10)
REVERT: R  113 ASP cc_start: 0.8450 (t70) cc_final: 0.8147 (t0)
  outliers start: 15
  outliers final: 14
  residues processed: 100
  average time/residue: 0.1845
  time to fit residues: 25.0026
Evaluate side-chains
  101 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  111 SER
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  272 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 64 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 76 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 73 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.131551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.106556 restraints weight = 27103.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 3.89
r_work: 0.3236 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3250
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3250 r_free = 0.3250    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3250 r_free = 0.3250    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3250
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.2137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6858  Z= 0.160
  Angle     :  0.455   6.566   9378  Z= 0.242
  Chirality :  0.040   0.147   1117
  Planarity :  0.003   0.040   1175
  Dihedral  :  7.944 150.244   1004
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 13.59 %
    Favored  : 83.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.29), residues: 900
  helix:  2.39 (0.26), residues: 405
  sheet:  0.31 (0.40), residues: 178
  loop : -0.37 (0.34), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 297 
 HIS   0.002   0.001   HIS A 220 
 PHE   0.011   0.001   PHE A 208 
 TYR   0.009   0.001   TYR A 339 
 ARG   0.007   0.000   ARG A 389 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 1.283 
Fit side-chains
REVERT: A  314 GLU cc_start: 0.8891 (tp30) cc_final: 0.8152 (mt-10)
REVERT: R  333 ARG cc_start: 0.8227 (mmm-85) cc_final: 0.8025 (mmm-85)
  outliers start: 16
  outliers final: 15
  residues processed: 96
  average time/residue: 0.1926
  time to fit residues: 25.4573
Evaluate side-chains
  101 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  111 SER
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  272 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 76 optimal weight:    1.9990
   chunk 56 optimal weight:    5.9990
   chunk 81 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 21 optimal weight:    0.0980
   chunk 29 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0570
   chunk 38 optimal weight:    0.6980
   chunk 54 optimal weight:    0.4980
   overall best weight:    0.4498

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.134219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.108097 restraints weight = 35804.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 4.53
r_work: 0.3248 rms_B_bonded: 4.98 restraints_weight: 0.5000
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3260
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3260
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.2229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6858  Z= 0.117
  Angle     :  0.434   6.713   9378  Z= 0.230
  Chirality :  0.040   0.142   1117
  Planarity :  0.003   0.039   1175
  Dihedral  :  7.814 149.905   1004
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 14.08 %
    Favored  : 83.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.29), residues: 900
  helix:  2.46 (0.26), residues: 405
  sheet:  0.42 (0.41), residues: 177
  loop : -0.35 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 297 
 HIS   0.002   0.000   HIS A 220 
 PHE   0.011   0.001   PHE A 208 
 TYR   0.007   0.001   TYR A 339 
 ARG   0.007   0.000   ARG A 389 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.709 
Fit side-chains
REVERT: A  314 GLU cc_start: 0.8905 (tp30) cc_final: 0.8211 (mt-10)
REVERT: R  113 ASP cc_start: 0.8474 (t70) cc_final: 0.8174 (t0)
REVERT: R  333 ARG cc_start: 0.8131 (mmm-85) cc_final: 0.7919 (mmm-85)
  outliers start: 13
  outliers final: 13
  residues processed: 100
  average time/residue: 0.1699
  time to fit residues: 23.3631
Evaluate side-chains
  102 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  111 SER
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  272 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 32 optimal weight:    0.3980
   chunk 13 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 83 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 56 optimal weight:    9.9990
   chunk 25 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.132601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.107150 restraints weight = 29400.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 4.06
r_work: 0.3245 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3259
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3259
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.2240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6858  Z= 0.156
  Angle     :  0.449   6.673   9378  Z= 0.238
  Chirality :  0.040   0.146   1117
  Planarity :  0.003   0.039   1175
  Dihedral  :  7.845 151.319   1004
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 13.59 %
    Favored  : 83.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.29), residues: 900
  helix:  2.43 (0.26), residues: 405
  sheet:  0.31 (0.40), residues: 179
  loop : -0.36 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 297 
 HIS   0.002   0.001   HIS A 357 
 PHE   0.010   0.001   PHE A 208 
 TYR   0.009   0.001   TYR A 339 
 ARG   0.008   0.000   ARG A 389 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3606.40 seconds
wall clock time: 62 minutes 29.90 seconds (3749.90 seconds total)