Starting phenix.real_space_refine
on Fri Jun 13 23:47:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x7a_38096/06_2025/8x7a_38096_neut_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x7a_38096/06_2025/8x7a_38096.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8x7a_38096/06_2025/8x7a_38096.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x7a_38096/06_2025/8x7a_38096.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x7a_38096/06_2025/8x7a_38096_neut_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x7a_38096/06_2025/8x7a_38096_neut_trim.cif"
  }
  resolution = 2.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.029
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      56      5.16       5
     C    5028      2.51       5
     N    1399      2.21       5
     O    1466      1.98       5
     H    7679      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 15628
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 3761
          Classifications: {'peptide': 235}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 228}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 74
          Unresolved non-hydrogen dihedrals: 49
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 36
    Chain: "B"
      Number of atoms: 4782
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 4782
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 120
          Unresolved non-hydrogen angles: 149
          Unresolved non-hydrogen dihedrals: 101
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 2, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 87
    Chain: "G"
      Number of atoms: 851
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 851
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "N"
      Number of atoms: 1849
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 1849
          Classifications: {'peptide': 128}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "R"
      Number of atoms: 4357
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 4357
          Classifications: {'peptide': 287}
          Link IDs: {'PTRANS': 14, 'TRANS': 272}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "R"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'Y9J': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.76, per 1000 atoms: 0.50
  Number of scatterers: 15628
  At special positions: 0
  Unit cell: (81.03, 106.58, 128.48, 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      56     16.00
     O    1466      8.00
     N    1399      7.00
     C    5028      6.00
     H    7679      1.00
    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: 3.85
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1950

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 11 sheets defined
      42.0% alpha, 19.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 39
    Processing helix  chain 'A' and resid 52 through 61
    Processing helix  chain 'A' and resid 62 through 64
      No H-bonds generated for 'chain 'A' and resid 62 through 64'
    Processing helix  chain 'A' and resid 233 through 239
    Processing helix  chain 'A' and resid 255 through 268
    Processing helix  chain 'A' and resid 269 through 273
      removed outlier: 3.678A  pdb=" N   ARG A 273 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 294
    Processing helix  chain 'A' and resid 297 through 302
      removed outlier: 4.256A  pdb=" N   TYR A 301 " --> pdb=" O   LYS A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 307
    Processing helix  chain 'A' and resid 321 through 341
      removed outlier: 3.804A  pdb=" N   ILE A 338 " --> pdb=" O   GLU A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 381
      removed outlier: 3.890A  pdb=" N   TYR A 381 " --> pdb=" O   HIS A 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 7 through 24
      removed outlier: 3.502A  pdb=" N   LYS G  20 " --> pdb=" O   VAL G  16 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.704A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 19 through 41
      removed outlier: 3.608A  pdb=" N   GLY R  27 " --> pdb=" O   MET R  23 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 47 through 66
      removed outlier: 3.605A  pdb=" N   THR R  64 " --> pdb=" O   ASP R  60 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   PHE R  66 " --> pdb=" O   LEU R  62 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 67 through 78
      removed outlier: 3.659A  pdb=" N   VAL R  71 " --> pdb=" O   LEU R  67 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 88 through 123
      removed outlier: 4.768A  pdb=" N   CYS R  92 " --> pdb=" O   GLY R  88 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   ALA R  94 " --> pdb=" O   ALA R  90 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 123 through 129
    Processing helix  chain 'R' and resid 131 through 151
      Proline residue:  R 141  - end of helix
    Processing helix  chain 'R' and resid 152 through 157
    Processing helix  chain 'R' and resid 183 through 221
    Processing helix  chain 'R' and resid 233 through 264
      Proline residue:  R 254  - end of helix
    Processing helix  chain 'R' and resid 271 through 283
    Processing helix  chain 'R' and resid 283 through 292
      Proline residue:  R 289  - end of helix
    Processing helix  chain 'R' and resid 296 through 307
    Processing helix  chain 'R' and resid 307 through 313
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 3.562A  pdb=" N   PHE A 208 " --> pdb=" O   ASP A 223 " (cutoff:3.500A)
      removed outlier: 10.216A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.382A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.338A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.590A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.426A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   PHE A 280 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 280 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   ASN A 282 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 5.984A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 282 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.426A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.764A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.524A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.713A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.511A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 5.717A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.679A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.666A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   THR B 159 " --> pdb=" O   ALA B 167 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ALA B 167 " --> pdb=" O   THR B 159 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.722A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.838A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   GLY B 202 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.701A  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: 6.599A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.116A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.270A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.767A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.317A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 6 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 3.627A  pdb=" N   THR N 125 " --> pdb=" O   GLY N  10 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL N  12 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 5.144A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 161 through 163

    411 hydrogen bonds defined for protein.
    1164 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: 5.46

  Time building geometry restraints manager: 4.65 seconds

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

  Histogram of bond lengths:
        0.82 -     1.25: 8967
        1.25 -     1.68: 6741
        1.68 -     2.11: 78
        2.11 -     2.54: 0
        2.54 -     2.97: 1
  Bond restraints: 15787
  Sorted by residual:
  bond pdb=" C   ALA B 203 "
       pdb=" N   ASP B 205 "
    ideal  model  delta    sigma   weight residual
    1.332  2.972 -1.639 1.40e-02 5.10e+03 1.37e+04
  bond pdb=" C15 Y9J R 401 "
       pdb=" C21 Y9J R 401 "
    ideal  model  delta    sigma   weight residual
    1.393  1.670 -0.277 2.00e-02 2.50e+03 1.92e+02
  bond pdb=" C19 Y9J R 401 "
       pdb=" C20 Y9J R 401 "
    ideal  model  delta    sigma   weight residual
    1.389  1.209  0.180 2.00e-02 2.50e+03 8.10e+01
  bond pdb=" C18 Y9J R 401 "
       pdb=" C19 Y9J R 401 "
    ideal  model  delta    sigma   weight residual
    1.394  1.215  0.179 2.00e-02 2.50e+03 8.05e+01
  bond pdb=" CA  MET R 244 "
       pdb=" C   MET R 244 "
    ideal  model  delta    sigma   weight residual
    1.524  1.422  0.102 1.26e-02 6.30e+03 6.50e+01
  ... (remaining 15782 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    12.53: 28349
       12.53 -    25.06: 6
       25.06 -    37.60: 1
       37.60 -    50.13: 0
       50.13 -    62.66: 2
  Bond angle restraints: 28358
  Sorted by residual:
  angle pdb=" O   ALA B 203 "
        pdb=" C   ALA B 203 "
        pdb=" N   ASP B 205 "
      ideal   model   delta    sigma   weight residual
     122.27   59.61   62.66 1.16e+00 7.43e-01 2.92e+03
  angle pdb=" CA  ALA B 203 "
        pdb=" C   ALA B 203 "
        pdb=" N   ASP B 205 "
      ideal   model   delta    sigma   weight residual
     118.79  150.01  -31.22 1.22e+00 6.72e-01 6.55e+02
  angle pdb=" C   ALA B 203 "
        pdb=" N   ASP B 205 "
        pdb=" H   ASP B 205 "
      ideal   model   delta    sigma   weight residual
     124.38   66.43   57.95 3.00e+00 1.11e-01 3.73e+02
  angle pdb=" C14 Y9J R 401 "
        pdb=" C15 Y9J R 401 "
        pdb=" C21 Y9J R 401 "
      ideal   model   delta    sigma   weight residual
     121.72  143.69  -21.97 3.00e+00 1.11e-01 5.36e+01
  angle pdb=" C   ALA B 203 "
        pdb=" N   ASP B 205 "
        pdb=" CA  ASP B 205 "
      ideal   model   delta    sigma   weight residual
     121.54  135.26  -13.72 1.91e+00 2.74e-01 5.16e+01
  ... (remaining 28353 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.03: 7234
       21.03 -    42.07: 193
       42.07 -    63.10: 73
       63.10 -    84.14: 10
       84.14 -   105.17: 1
  Dihedral angle restraints: 7511
    sinusoidal: 3974
      harmonic: 3537
  Sorted by residual:
  dihedral pdb=" CA  ALA B 203 "
           pdb=" C   ALA B 203 "
           pdb=" N   ASP B 205 "
           pdb=" CA  ASP B 205 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -74.83 -105.17     0      5.00e+00 4.00e-02 4.42e+02
  dihedral pdb=" C   MET R 244 "
           pdb=" N   MET R 244 "
           pdb=" CA  MET R 244 "
           pdb=" CB  MET R 244 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -110.06  -12.54     0      2.50e+00 1.60e-01 2.51e+01
  dihedral pdb=" C   ALA R 265 "
           pdb=" N   ALA R 265 "
           pdb=" CA  ALA R 265 "
           pdb=" CB  ALA R 265 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.35   11.75     0      2.50e+00 1.60e-01 2.21e+01
  ... (remaining 7508 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 1158
       0.074 -    0.149: 86
       0.149 -    0.223: 5
       0.223 -    0.298: 1
       0.298 -    0.372: 1
  Chirality restraints: 1251
  Sorted by residual:
  chirality pdb=" CA  ALA R 265 "
            pdb=" N   ALA R 265 "
            pdb=" C   ALA R 265 "
            pdb=" CB  ALA R 265 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.11    0.37 2.00e-01 2.50e+01 3.46e+00
  chirality pdb=" CA  VAL R  25 "
            pdb=" N   VAL R  25 "
            pdb=" C   VAL R  25 "
            pdb=" CB  VAL R  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.67   -0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" C13 Y9J R 401 "
            pdb=" C12 Y9J R 401 "
            pdb=" C14 Y9J R 401 "
            pdb=" C9  Y9J R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.85   -0.20 2.00e-01 2.50e+01 1.05e+00
  ... (remaining 1248 not shown)

  Planarity restraints: 2422
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 203 "    0.036 2.00e-02 2.50e+03   2.16e-01 4.66e+02
        pdb=" N   ASP B 205 "   -0.362 2.00e-02 2.50e+03
        pdb=" CA  ASP B 205 "    0.141 2.00e-02 2.50e+03
        pdb=" H   ASP B 205 "    0.185 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 203 "    0.182 2.00e-02 2.50e+03   1.90e-01 3.60e+02
        pdb=" C   ALA B 203 "   -0.318 2.00e-02 2.50e+03
        pdb=" O   ALA B 203 "    0.062 2.00e-02 2.50e+03
        pdb=" N   ASP B 205 "    0.075 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R  84 "    0.020 2.00e-02 2.50e+03   4.07e-02 1.66e+01
        pdb=" C   LEU R  84 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   LEU R  84 "    0.027 2.00e-02 2.50e+03
        pdb=" N   ALA R  85 "    0.024 2.00e-02 2.50e+03
  ... (remaining 2419 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 846
        2.21 -     2.80: 32540
        2.80 -     3.40: 42878
        3.40 -     4.00: 55049
        4.00 -     4.60: 86034
  Nonbonded interactions: 217347
  Sorted by model distance:
  nonbonded pdb=" O   SER B 189 "
            pdb=" HG  SER B 201 "
     model   vdw
     1.607 2.450
  nonbonded pdb=" H   THR B 221 "
            pdb=" OE2 GLU G  22 "
     model   vdw
     1.609 2.450
  nonbonded pdb=" O   ASP B 170 "
            pdb=" H   GLY B 174 "
     model   vdw
     1.625 2.450
  nonbonded pdb="HD21 ASN R 203 "
            pdb=" OG1 THR R 245 "
     model   vdw
     1.633 2.450
  nonbonded pdb=" O   LYS N  33 "
            pdb=" H   CYS N  99 "
     model   vdw
     1.645 2.450
  ... (remaining 217342 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:                  0.010
  Normalize map: mean=0, sd=1:             3.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.260
  Extract box with map and model:          0.630
  Check model and map are aligned:         0.110
  Set scattering table:                    0.130
  Process input model:                     34.410
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  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:12.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   52.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7021
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      :  0.019   1.639   8108  Z= 1.342
  Angle     :  0.993  62.660  11001  Z= 0.688
  Chirality :  0.040   0.372   1251
  Planarity :  0.006   0.190   1419
  Dihedral  :  8.424 105.175   2894
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.22 %
    Favored  : 96.66 %
  Cbeta Deviations :  0.21 %
  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: -0.63 (0.25), residues: 1028
  helix:  0.95 (0.25), residues: 394
  sheet: -0.65 (0.32), residues: 210
  loop : -1.59 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 271 
 HIS   0.002   0.000   HIS B 142 
 PHE   0.005   0.001   PHE R  24 
 TYR   0.023   0.001   TYR R  75 
 ARG   0.002   0.000   ARG R  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18165 (  411)
  hydrogen bonds       : angle       6.80820 ( 1164)
  covalent geometry    : bond        0.01910 ( 8108)
  covalent geometry    : angle       0.99318 (11001)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   53 is missing expected H atoms. Skipping.
Residue LYS  216 is missing expected H atoms. Skipping.
Residue VAL  224 is missing expected H atoms. Skipping.
Residue VAL  248 is missing expected H atoms. Skipping.
Residue LEU  256 is missing expected H atoms. Skipping.
Residue LEU  260 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue TYR  105 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  320 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   25 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue THR  122 is missing expected H atoms. Skipping.
Residue SER   65 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Evaluate side-chains
  314 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 313
  time to evaluate  : 1.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 313
  average time/residue: 2.4255
  time to fit residues: 807.0859
Evaluate side-chains
  181 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 1.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 26 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 79 optimal weight:    9.9990
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
G  18 GLN
N   5 GLN
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.122966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.093111 restraints weight = 47719.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 3.49
r_work: 0.3351 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.4577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   8108  Z= 0.205
  Angle     :  0.615   6.404  11001  Z= 0.324
  Chirality :  0.040   0.146   1251
  Planarity :  0.005   0.063   1419
  Dihedral  :  5.243  74.090   1171
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.52 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 20.17 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.50 (0.26), residues: 1030
  helix:  2.03 (0.26), residues: 399
  sheet: -0.66 (0.30), residues: 248
  loop : -0.75 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.007   0.001   HIS A  41 
 PHE   0.011   0.001   PHE N  68 
 TYR   0.023   0.002   TYR A  37 
 ARG   0.008   0.001   ARG A 273 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03806 (  411)
  hydrogen bonds       : angle       4.77104 ( 1164)
  covalent geometry    : bond        0.00451 ( 8108)
  covalent geometry    : angle       0.61501 (11001)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   53 is missing expected H atoms. Skipping.
Residue LYS  216 is missing expected H atoms. Skipping.
Residue VAL  224 is missing expected H atoms. Skipping.
Residue VAL  248 is missing expected H atoms. Skipping.
Residue LEU  256 is missing expected H atoms. Skipping.
Residue LEU  260 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue TYR  105 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  320 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   25 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue THR  122 is missing expected H atoms. Skipping.
Residue SER   65 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Evaluate side-chains
  197 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 172
  time to evaluate  : 1.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  368 ASP cc_start: 0.8604 (m-30) cc_final: 0.8390 (m-30)
REVERT: B  226 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7394 (tt0)
REVERT: G   38 MET cc_start: 0.7733 (mtp) cc_final: 0.7275 (mtp)
REVERT: G   42 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8515 (mm-30)
REVERT: N   46 GLU cc_start: 0.7387 (pt0) cc_final: 0.6925 (mm-30)
REVERT: R   41 ARG cc_start: 0.8087 (ptm-80) cc_final: 0.7802 (mpt180)
REVERT: R  107 MET cc_start: 0.8411 (tpp) cc_final: 0.8011 (tpt)
REVERT: R  138 LEU cc_start: 0.8573 (mm) cc_final: 0.8096 (tt)
  outliers start: 25
  outliers final: 12
  residues processed: 190
  average time/residue: 1.9623
  time to fit residues: 401.5378
Evaluate side-chains
  161 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 147
  time to evaluate  : 1.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 GLN
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue  148 VAL
Chi-restraints excluded: chain R residue  207 THR
Chi-restraints excluded: chain R residue  247 VAL
Chi-restraints excluded: chain R residue  252 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9980
   chunk 96 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 77 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
B  88 ASN
N  39 GLN
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 220 HIS
R 284 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.120670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.090600 restraints weight = 47605.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 3.53
r_work: 0.3323 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.5247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8108  Z= 0.147
  Angle     :  0.545   6.580  11001  Z= 0.281
  Chirality :  0.038   0.138   1251
  Planarity :  0.004   0.056   1419
  Dihedral  :  5.091  74.653   1171
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 21.78 %
    Favored  : 75.00 %
  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:  0.81 (0.26), residues: 1030
  helix:  2.30 (0.26), residues: 403
  sheet: -0.50 (0.31), residues: 247
  loop : -0.61 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.006   0.001   HIS R 220 
 PHE   0.016   0.001   PHE R 102 
 TYR   0.016   0.001   TYR A  37 
 ARG   0.010   0.000   ARG R  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03569 (  411)
  hydrogen bonds       : angle       4.39386 ( 1164)
  covalent geometry    : bond        0.00333 ( 8108)
  covalent geometry    : angle       0.54452 (11001)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   53 is missing expected H atoms. Skipping.
Residue LYS  216 is missing expected H atoms. Skipping.
Residue VAL  224 is missing expected H atoms. Skipping.
Residue VAL  248 is missing expected H atoms. Skipping.
Residue LEU  256 is missing expected H atoms. Skipping.
Residue LEU  260 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue TYR  105 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  320 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   25 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue THR  122 is missing expected H atoms. Skipping.
Residue SER   65 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Evaluate side-chains
  182 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 156
  time to evaluate  : 1.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  368 ASP cc_start: 0.8607 (m-30) cc_final: 0.8382 (m-30)
REVERT: B  239 ASN cc_start: 0.8794 (m110) cc_final: 0.8349 (m110)
REVERT: G   32 LYS cc_start: 0.8673 (tppp) cc_final: 0.8081 (tmmt)
REVERT: N   46 GLU cc_start: 0.7461 (pt0) cc_final: 0.7020 (mm-30)
REVERT: N  120 GLN cc_start: 0.8910 (tp40) cc_final: 0.8659 (mm-40)
REVERT: R   86 ARG cc_start: 0.5663 (OUTLIER) cc_final: 0.3828 (mtm180)
REVERT: R  107 MET cc_start: 0.8411 (tpp) cc_final: 0.8022 (tpt)
REVERT: R  138 LEU cc_start: 0.8585 (mm) cc_final: 0.8113 (tt)
REVERT: R  301 GLN cc_start: 0.9508 (mt0) cc_final: 0.9261 (mt0)
  outliers start: 26
  outliers final: 13
  residues processed: 172
  average time/residue: 1.9369
  time to fit residues: 359.4431
Evaluate side-chains
  158 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 144
  time to evaluate  : 1.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   86 ARG
Chi-restraints excluded: chain R residue  106 SER
Chi-restraints excluded: chain R residue  148 VAL
Chi-restraints excluded: chain R residue  234 GLU
Chi-restraints excluded: chain R residue  247 VAL
Chi-restraints excluded: chain R residue  252 SER
Chi-restraints excluded: chain R residue  286 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 89 optimal weight:    9.9990
   chunk 99 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 78 optimal weight:    8.9990
   chunk 10 optimal weight:    5.9990
   chunk 24 optimal weight:   10.0000
   chunk 79 optimal weight:   10.0000
   chunk 98 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 178 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.117138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.086558 restraints weight = 48063.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 3.54
r_work: 0.3248 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.5904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8108  Z= 0.217
  Angle     :  0.581   6.801  11001  Z= 0.303
  Chirality :  0.039   0.144   1251
  Planarity :  0.004   0.046   1419
  Dihedral  :  5.361  74.554   1171
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 20.67 %
    Favored  : 75.00 %
  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:  0.94 (0.26), residues: 1030
  helix:  2.54 (0.26), residues: 397
  sheet: -0.61 (0.31), residues: 249
  loop : -0.52 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.005   0.001   HIS A  41 
 PHE   0.015   0.001   PHE R 102 
 TYR   0.016   0.002   TYR R 188 
 ARG   0.006   0.001   ARG R 302 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03671 (  411)
  hydrogen bonds       : angle       4.40365 ( 1164)
  covalent geometry    : bond        0.00485 ( 8108)
  covalent geometry    : angle       0.58119 (11001)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   53 is missing expected H atoms. Skipping.
Residue LYS  216 is missing expected H atoms. Skipping.
Residue VAL  224 is missing expected H atoms. Skipping.
Residue VAL  248 is missing expected H atoms. Skipping.
Residue LEU  256 is missing expected H atoms. Skipping.
Residue LEU  260 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue TYR  105 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  320 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   25 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue THR  122 is missing expected H atoms. Skipping.
Residue SER   65 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Evaluate side-chains
  178 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 143
  time to evaluate  : 1.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.8762 (mt0) cc_final: 0.8303 (tp40)
REVERT: A  368 ASP cc_start: 0.8789 (m-30) cc_final: 0.8377 (m-30)
REVERT: B  279 SER cc_start: 0.9264 (m) cc_final: 0.8951 (t)
REVERT: G   47 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8104 (mp0)
REVERT: N   46 GLU cc_start: 0.7608 (pt0) cc_final: 0.7205 (mm-30)
REVERT: N   81 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7183 (tm)
REVERT: R   86 ARG cc_start: 0.5768 (OUTLIER) cc_final: 0.3940 (mtm180)
REVERT: R  107 MET cc_start: 0.8477 (tpp) cc_final: 0.8110 (tpt)
REVERT: R  138 LEU cc_start: 0.8620 (mm) cc_final: 0.8137 (tt)
REVERT: R  301 GLN cc_start: 0.9470 (mt0) cc_final: 0.9245 (mt0)
  outliers start: 35
  outliers final: 11
  residues processed: 163
  average time/residue: 2.1888
  time to fit residues: 384.3317
Evaluate side-chains
  138 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 125
  time to evaluate  : 1.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   86 ARG
Chi-restraints excluded: chain R residue  148 VAL
Chi-restraints excluded: chain R residue  247 VAL
Chi-restraints excluded: chain R residue  252 SER
Chi-restraints excluded: chain R residue  287 LEU
Chi-restraints excluded: chain R residue  302 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 88 optimal weight:    8.9990
   chunk 60 optimal weight:    0.8980
   chunk 94 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 77 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
G  18 GLN
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 163 GLN
** R 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.117527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.087155 restraints weight = 47986.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 3.52
r_work: 0.3276 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.6201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8108  Z= 0.129
  Angle     :  0.544   7.062  11001  Z= 0.279
  Chirality :  0.038   0.146   1251
  Planarity :  0.004   0.045   1419
  Dihedral  :  5.079  74.616   1171
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 22.15 %
    Favored  : 74.38 %
  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:  1.13 (0.27), residues: 1030
  helix:  2.75 (0.26), residues: 397
  sheet: -0.64 (0.31), residues: 249
  loop : -0.37 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 169 
 HIS   0.005   0.001   HIS R 237 
 PHE   0.015   0.001   PHE R 102 
 TYR   0.013   0.001   TYR A  37 
 ARG   0.004   0.000   ARG A 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03367 (  411)
  hydrogen bonds       : angle       4.21167 ( 1164)
  covalent geometry    : bond        0.00293 ( 8108)
  covalent geometry    : angle       0.54354 (11001)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   53 is missing expected H atoms. Skipping.
Residue LYS  216 is missing expected H atoms. Skipping.
Residue VAL  224 is missing expected H atoms. Skipping.
Residue VAL  248 is missing expected H atoms. Skipping.
Residue LEU  256 is missing expected H atoms. Skipping.
Residue LEU  260 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue TYR  105 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  320 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   25 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue THR  122 is missing expected H atoms. Skipping.
Residue SER   65 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Evaluate side-chains
  171 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 143
  time to evaluate  : 1.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.8708 (mt0) cc_final: 0.8258 (tp40)
REVERT: A  368 ASP cc_start: 0.8708 (m-30) cc_final: 0.8428 (m-30)
REVERT: B  264 TYR cc_start: 0.6682 (m-80) cc_final: 0.6159 (m-80)
REVERT: B  279 SER cc_start: 0.9273 (m) cc_final: 0.8948 (t)
REVERT: N   46 GLU cc_start: 0.7490 (pt0) cc_final: 0.7171 (mm-30)
REVERT: R   86 ARG cc_start: 0.5663 (OUTLIER) cc_final: 0.3882 (mtm180)
REVERT: R   93 ASP cc_start: 0.8505 (m-30) cc_final: 0.8283 (m-30)
REVERT: R  107 MET cc_start: 0.8429 (tpp) cc_final: 0.8060 (tpt)
REVERT: R  138 LEU cc_start: 0.8630 (mm) cc_final: 0.8166 (tt)
REVERT: R  301 GLN cc_start: 0.9482 (mt0) cc_final: 0.9249 (mt0)
  outliers start: 28
  outliers final: 12
  residues processed: 164
  average time/residue: 1.9772
  time to fit residues: 348.9155
Evaluate side-chains
  146 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 133
  time to evaluate  : 1.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   86 ARG
Chi-restraints excluded: chain R residue  148 VAL
Chi-restraints excluded: chain R residue  220 HIS
Chi-restraints excluded: chain R residue  247 VAL
Chi-restraints excluded: chain R residue  252 SER
Chi-restraints excluded: chain R residue  286 ILE
Chi-restraints excluded: chain R residue  287 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 100 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 24 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9980
   chunk 56 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9980
   chunk 89 optimal weight:   10.0000
   chunk 37 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
G  18 GLN
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.117466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.087109 restraints weight = 48124.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 3.54
r_work: 0.3279 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.6405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8108  Z= 0.120
  Angle     :  0.540   7.479  11001  Z= 0.275
  Chirality :  0.038   0.138   1251
  Planarity :  0.004   0.044   1419
  Dihedral  :  4.876  73.104   1171
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 23.89 %
    Favored  : 73.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.27), residues: 1030
  helix:  2.87 (0.26), residues: 398
  sheet: -0.62 (0.31), residues: 251
  loop : -0.19 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 169 
 HIS   0.005   0.001   HIS R 237 
 PHE   0.015   0.001   PHE R 102 
 TYR   0.012   0.001   TYR A  37 
 ARG   0.008   0.000   ARG G  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03231 (  411)
  hydrogen bonds       : angle       4.10239 ( 1164)
  covalent geometry    : bond        0.00277 ( 8108)
  covalent geometry    : angle       0.54021 (11001)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   53 is missing expected H atoms. Skipping.
Residue LYS  216 is missing expected H atoms. Skipping.
Residue VAL  224 is missing expected H atoms. Skipping.
Residue VAL  248 is missing expected H atoms. Skipping.
Residue LEU  256 is missing expected H atoms. Skipping.
Residue LEU  260 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue TYR  105 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  320 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   25 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue THR  122 is missing expected H atoms. Skipping.
Residue SER   65 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Evaluate side-chains
  160 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 141
  time to evaluate  : 1.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.8733 (mt0) cc_final: 0.8276 (tp40)
REVERT: A  368 ASP cc_start: 0.8679 (m-30) cc_final: 0.8398 (m-30)
REVERT: B  264 TYR cc_start: 0.6682 (m-80) cc_final: 0.6189 (m-80)
REVERT: N   18 LEU cc_start: 0.7293 (tp) cc_final: 0.6945 (mp)
REVERT: N   46 GLU cc_start: 0.7514 (pt0) cc_final: 0.7130 (mm-30)
REVERT: R   86 ARG cc_start: 0.5679 (OUTLIER) cc_final: 0.3892 (mtm180)
REVERT: R   93 ASP cc_start: 0.8528 (m-30) cc_final: 0.8293 (m-30)
REVERT: R  107 MET cc_start: 0.8426 (tpp) cc_final: 0.8119 (tpt)
REVERT: R  138 LEU cc_start: 0.8593 (mm) cc_final: 0.8141 (tt)
REVERT: R  301 GLN cc_start: 0.9484 (mt0) cc_final: 0.9231 (mt0)
  outliers start: 19
  outliers final: 12
  residues processed: 153
  average time/residue: 2.0450
  time to fit residues: 336.8383
Evaluate side-chains
  147 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 134
  time to evaluate  : 1.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   86 ARG
Chi-restraints excluded: chain R residue  148 VAL
Chi-restraints excluded: chain R residue  220 HIS
Chi-restraints excluded: chain R residue  234 GLU
Chi-restraints excluded: chain R residue  247 VAL
Chi-restraints excluded: chain R residue  252 SER
Chi-restraints excluded: chain R residue  255 LEU
Chi-restraints excluded: chain R residue  286 ILE
Chi-restraints excluded: chain R residue  287 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 71 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.118065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.087643 restraints weight = 48085.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 3.55
r_work: 0.3279 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.6502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8108  Z= 0.113
  Angle     :  0.532   7.336  11001  Z= 0.271
  Chirality :  0.038   0.150   1251
  Planarity :  0.004   0.050   1419
  Dihedral  :  4.731  71.165   1171
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 25.00 %
    Favored  : 73.27 %
  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 (0.27), residues: 1030
  helix:  3.04 (0.26), residues: 398
  sheet: -0.59 (0.31), residues: 251
  loop : -0.10 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 169 
 HIS   0.007   0.001   HIS R 237 
 PHE   0.015   0.001   PHE R 102 
 TYR   0.012   0.001   TYR A  37 
 ARG   0.006   0.000   ARG R 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03103 (  411)
  hydrogen bonds       : angle       3.98130 ( 1164)
  covalent geometry    : bond        0.00260 ( 8108)
  covalent geometry    : angle       0.53152 (11001)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   53 is missing expected H atoms. Skipping.
Residue LYS  216 is missing expected H atoms. Skipping.
Residue VAL  224 is missing expected H atoms. Skipping.
Residue VAL  248 is missing expected H atoms. Skipping.
Residue LEU  256 is missing expected H atoms. Skipping.
Residue LEU  260 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue TYR  105 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  320 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   25 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue THR  122 is missing expected H atoms. Skipping.
Residue SER   65 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Evaluate side-chains
  154 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 140
  time to evaluate  : 1.731 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.8735 (mt0) cc_final: 0.8273 (tp40)
REVERT: A  368 ASP cc_start: 0.8658 (m-30) cc_final: 0.8435 (m-30)
REVERT: B  190 LEU cc_start: 0.8848 (tt) cc_final: 0.8544 (pp)
REVERT: G   13 ARG cc_start: 0.9001 (ttp80) cc_final: 0.8712 (tmm160)
REVERT: N   46 GLU cc_start: 0.7481 (pt0) cc_final: 0.7109 (mm-30)
REVERT: R   86 ARG cc_start: 0.5606 (OUTLIER) cc_final: 0.3824 (mtm180)
REVERT: R  107 MET cc_start: 0.8420 (tpp) cc_final: 0.8111 (tpt)
REVERT: R  138 LEU cc_start: 0.8574 (mm) cc_final: 0.8129 (tt)
REVERT: R  290 TRP cc_start: 0.8083 (m-10) cc_final: 0.7876 (m100)
REVERT: R  301 GLN cc_start: 0.9482 (mt0) cc_final: 0.9225 (mt0)
  outliers start: 14
  outliers final: 9
  residues processed: 150
  average time/residue: 2.5497
  time to fit residues: 418.3034
Evaluate side-chains
  144 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 134
  time to evaluate  : 1.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain R residue   64 THR
Chi-restraints excluded: chain R residue   86 ARG
Chi-restraints excluded: chain R residue  148 VAL
Chi-restraints excluded: chain R residue  247 VAL
Chi-restraints excluded: chain R residue  252 SER
Chi-restraints excluded: chain R residue  255 LEU
Chi-restraints excluded: chain R residue  287 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 80 optimal weight:   10.0000
   chunk 4 optimal weight:    0.7980
   chunk 92 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 84 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 12 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.116031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.085478 restraints weight = 48341.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 3.52
r_work: 0.3240 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.6713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8108  Z= 0.172
  Angle     :  0.551   7.791  11001  Z= 0.284
  Chirality :  0.038   0.144   1251
  Planarity :  0.004   0.043   1419
  Dihedral  :  4.905  71.506   1171
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 24.38 %
    Favored  : 73.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.27), residues: 1030
  helix:  2.98 (0.26), residues: 397
  sheet: -0.60 (0.32), residues: 251
  loop : -0.18 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  99 
 HIS   0.006   0.001   HIS R 237 
 PHE   0.015   0.001   PHE R 102 
 TYR   0.013   0.001   TYR R 188 
 ARG   0.003   0.000   ARG A 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03354 (  411)
  hydrogen bonds       : angle       4.13165 ( 1164)
  covalent geometry    : bond        0.00387 ( 8108)
  covalent geometry    : angle       0.55149 (11001)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   53 is missing expected H atoms. Skipping.
Residue LYS  216 is missing expected H atoms. Skipping.
Residue VAL  224 is missing expected H atoms. Skipping.
Residue VAL  248 is missing expected H atoms. Skipping.
Residue LEU  256 is missing expected H atoms. Skipping.
Residue LEU  260 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue TYR  105 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  320 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   25 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue THR  122 is missing expected H atoms. Skipping.
Residue SER   65 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Evaluate side-chains
  148 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 133
  time to evaluate  : 1.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.8854 (tpp80) cc_final: 0.8577 (tpp80)
REVERT: A   31 GLN cc_start: 0.8786 (mt0) cc_final: 0.8334 (tp40)
REVERT: A  368 ASP cc_start: 0.8790 (m-30) cc_final: 0.8387 (m-30)
REVERT: G   13 ARG cc_start: 0.9016 (ttp80) cc_final: 0.8788 (tmm160)
REVERT: N   46 GLU cc_start: 0.7498 (pt0) cc_final: 0.7202 (mm-30)
REVERT: R   86 ARG cc_start: 0.5658 (OUTLIER) cc_final: 0.3748 (ttm170)
REVERT: R  107 MET cc_start: 0.8454 (tpp) cc_final: 0.8096 (tpt)
REVERT: R  138 LEU cc_start: 0.8597 (mm) cc_final: 0.8140 (tt)
REVERT: R  301 GLN cc_start: 0.9494 (mt0) cc_final: 0.9233 (mt0)
  outliers start: 15
  outliers final: 9
  residues processed: 143
  average time/residue: 2.2702
  time to fit residues: 350.2459
Evaluate side-chains
  136 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 1.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   86 ARG
Chi-restraints excluded: chain R residue  148 VAL
Chi-restraints excluded: chain R residue  247 VAL
Chi-restraints excluded: chain R residue  252 SER
Chi-restraints excluded: chain R residue  255 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 80 optimal weight:    9.9990
   chunk 72 optimal weight:    1.9990
   chunk 23 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   chunk 82 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 42 optimal weight:    0.1980
   chunk 33 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   chunk 76 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.117281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.087166 restraints weight = 48178.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 3.49
r_work: 0.3271 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.6793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8108  Z= 0.109
  Angle     :  0.538   7.991  11001  Z= 0.272
  Chirality :  0.038   0.145   1251
  Planarity :  0.004   0.044   1419
  Dihedral  :  4.754  70.303   1171
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 25.00 %
    Favored  : 73.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.27), residues: 1030
  helix:  3.15 (0.26), residues: 398
  sheet: -0.56 (0.32), residues: 244
  loop : -0.15 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 169 
 HIS   0.005   0.001   HIS R 237 
 PHE   0.017   0.001   PHE R 102 
 TYR   0.011   0.001   TYR A  37 
 ARG   0.005   0.000   ARG R 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03085 (  411)
  hydrogen bonds       : angle       3.97121 ( 1164)
  covalent geometry    : bond        0.00252 ( 8108)
  covalent geometry    : angle       0.53778 (11001)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   53 is missing expected H atoms. Skipping.
Residue LYS  216 is missing expected H atoms. Skipping.
Residue VAL  224 is missing expected H atoms. Skipping.
Residue VAL  248 is missing expected H atoms. Skipping.
Residue LEU  256 is missing expected H atoms. Skipping.
Residue LEU  260 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue TYR  105 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  320 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   25 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue THR  122 is missing expected H atoms. Skipping.
Residue SER   65 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Evaluate side-chains
  145 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 135
  time to evaluate  : 1.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.8852 (tpp80) cc_final: 0.8574 (tpp80)
REVERT: A   31 GLN cc_start: 0.8767 (mt0) cc_final: 0.8313 (tp40)
REVERT: A  368 ASP cc_start: 0.8668 (m-30) cc_final: 0.8386 (m-30)
REVERT: B  190 LEU cc_start: 0.8895 (tt) cc_final: 0.8553 (pp)
REVERT: B  264 TYR cc_start: 0.6392 (m-80) cc_final: 0.5860 (m-80)
REVERT: G   13 ARG cc_start: 0.9022 (ttp80) cc_final: 0.8794 (tmm160)
REVERT: G   21 MET cc_start: 0.9042 (ttp) cc_final: 0.8780 (ttp)
REVERT: N   46 GLU cc_start: 0.7494 (pt0) cc_final: 0.7168 (mm-30)
REVERT: R   86 ARG cc_start: 0.5600 (OUTLIER) cc_final: 0.3629 (ttm170)
REVERT: R  107 MET cc_start: 0.8420 (tpp) cc_final: 0.8062 (tpt)
REVERT: R  138 LEU cc_start: 0.8575 (mm) cc_final: 0.8122 (tt)
REVERT: R  301 GLN cc_start: 0.9516 (mt0) cc_final: 0.9306 (mt0)
  outliers start: 10
  outliers final: 6
  residues processed: 144
  average time/residue: 2.3644
  time to fit residues: 367.1234
Evaluate side-chains
  133 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 126
  time to evaluate  : 1.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain R residue   86 ARG
Chi-restraints excluded: chain R residue  148 VAL
Chi-restraints excluded: chain R residue  252 SER
Chi-restraints excluded: chain R residue  255 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 48 optimal weight:    5.9990
   chunk 4 optimal weight:    0.5980
   chunk 64 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.116630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.086334 restraints weight = 48471.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 3.52
r_work: 0.3263 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.6855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8108  Z= 0.130
  Angle     :  0.565   8.265  11001  Z= 0.288
  Chirality :  0.038   0.137   1251
  Planarity :  0.004   0.042   1419
  Dihedral  :  4.754  69.486   1171
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 25.50 %
    Favored  : 73.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.27), residues: 1030
  helix:  3.12 (0.26), residues: 398
  sheet: -0.55 (0.32), residues: 244
  loop : -0.19 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 290 
 HIS   0.008   0.001   HIS R 237 
 PHE   0.016   0.001   PHE R 102 
 TYR   0.011   0.001   TYR A  37 
 ARG   0.006   0.000   ARG R 302 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03129 (  411)
  hydrogen bonds       : angle       3.97812 ( 1164)
  covalent geometry    : bond        0.00303 ( 8108)
  covalent geometry    : angle       0.56469 (11001)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   53 is missing expected H atoms. Skipping.
Residue LYS  216 is missing expected H atoms. Skipping.
Residue VAL  224 is missing expected H atoms. Skipping.
Residue VAL  248 is missing expected H atoms. Skipping.
Residue LEU  256 is missing expected H atoms. Skipping.
Residue LEU  260 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue TYR  105 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  320 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   25 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue THR  122 is missing expected H atoms. Skipping.
Residue SER   65 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Evaluate side-chains
  139 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 130
  time to evaluate  : 1.867 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.8842 (tpp80) cc_final: 0.8563 (tpp80)
REVERT: A   31 GLN cc_start: 0.8777 (mt0) cc_final: 0.8326 (tp40)
REVERT: A  368 ASP cc_start: 0.8701 (m-30) cc_final: 0.8425 (m-30)
REVERT: B  190 LEU cc_start: 0.8919 (tt) cc_final: 0.8582 (pp)
REVERT: B  264 TYR cc_start: 0.6419 (m-80) cc_final: 0.5862 (m-80)
REVERT: G   13 ARG cc_start: 0.9032 (ttp80) cc_final: 0.8804 (tmm160)
REVERT: G   21 MET cc_start: 0.9012 (ttp) cc_final: 0.8777 (ttp)
REVERT: G   57 SER cc_start: 0.9603 (m) cc_final: 0.9367 (p)
REVERT: N   46 GLU cc_start: 0.7505 (pt0) cc_final: 0.7163 (mm-30)
REVERT: R   86 ARG cc_start: 0.5623 (OUTLIER) cc_final: 0.3639 (ttm170)
REVERT: R  107 MET cc_start: 0.8422 (tpp) cc_final: 0.8065 (tpt)
REVERT: R  138 LEU cc_start: 0.8568 (mm) cc_final: 0.8112 (tt)
REVERT: R  301 GLN cc_start: 0.9504 (mt0) cc_final: 0.9288 (mt0)
  outliers start: 9
  outliers final: 7
  residues processed: 137
  average time/residue: 2.4999
  time to fit residues: 368.4277
Evaluate side-chains
  133 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 125
  time to evaluate  : 1.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain R residue   86 ARG
Chi-restraints excluded: chain R residue  148 VAL
Chi-restraints excluded: chain R residue  252 SER
Chi-restraints excluded: chain R residue  255 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 88 optimal weight:   10.0000
   chunk 32 optimal weight:    0.5980
   chunk 96 optimal weight:    0.8980
   chunk 59 optimal weight:    6.9990
   chunk 57 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.115474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.084978 restraints weight = 48744.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 3.52
r_work: 0.3236 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.7003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8108  Z= 0.167
  Angle     :  0.578   8.282  11001  Z= 0.300
  Chirality :  0.038   0.135   1251
  Planarity :  0.004   0.042   1419
  Dihedral  :  4.919  69.378   1171
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 25.25 %
    Favored  : 73.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.40 (0.27), residues: 1030
  helix:  3.02 (0.26), residues: 397
  sheet: -0.55 (0.32), residues: 244
  loop : -0.25 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 290 
 HIS   0.010   0.001   HIS R 237 
 PHE   0.015   0.001   PHE R 102 
 TYR   0.013   0.001   TYR R 188 
 ARG   0.006   0.000   ARG A 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03331 (  411)
  hydrogen bonds       : angle       4.09573 ( 1164)
  covalent geometry    : bond        0.00380 ( 8108)
  covalent geometry    : angle       0.57845 (11001)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 13244.84 seconds
wall clock time: 231 minutes 8.02 seconds (13868.02 seconds total)