Starting phenix.real_space_refine
on Sat May 10 14:58:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8geg_29969/05_2025/8geg_29969.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8geg_29969/05_2025/8geg_29969.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8geg_29969/05_2025/8geg_29969.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8geg_29969/05_2025/8geg_29969.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8geg_29969/05_2025/8geg_29969.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8geg_29969/05_2025/8geg_29969.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      33      5.16       5
     C    4150      2.51       5
     N    1141      2.21       5
     O    1157      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6481
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 1925
          Classifications: {'peptide': 307}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 174}
          Link IDs: {'PTRANS': 6, 'TRANS': 300}
          Chain breaks: 7
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 645
          Unresolved non-hydrogen angles: 802
          Unresolved non-hydrogen dihedrals: 519
          Unresolved non-hydrogen chiralities: 43
          Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 18, 'PHE:plan': 4, 'GLU:plan': 24, 'ARG:plan': 20}
          Unresolved non-hydrogen planarities: 398
    Chain: "B"
      Number of atoms: 2286
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2286
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 82}
          Link IDs: {'PTRANS': 5, 'TRANS': 328}
          Unresolved non-hydrogen bonds: 281
          Unresolved non-hydrogen angles: 348
          Unresolved non-hydrogen dihedrals: 214
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 7, 'ARG:plan': 13, 'ASN:plan1': 8, 'ASP:plan': 21}
          Unresolved non-hydrogen planarities: 200
    Chain: "G"
      Number of atoms: 318
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 318
          Classifications: {'peptide': 50}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 4, 'TRANS': 45}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 74
          Unresolved non-hydrogen angles: 87
          Unresolved non-hydrogen dihedrals: 62
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 39
    Chain: "R"
      Number of atoms: 1937
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 1937
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 104}
          Link IDs: {'PTRANS': 7, 'TRANS': 273}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 329
          Unresolved non-hydrogen angles: 418
          Unresolved non-hydrogen dihedrals: 256
          Unresolved non-hydrogen chiralities: 52
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 119
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.10, per 1000 atoms: 0.79
  Number of scatterers: 6481
  At special positions: 0
  Unit cell: (71.02, 96.46, 129.32, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      33     16.00
     O    1157      8.00
     N    1141      7.00
     C    4150      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.72
  Conformation dependent library (CDL) restraints added in 903.4 milliseconds
  

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1848

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 8 sheets defined
      52.3% alpha, 15.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 40
      removed outlier: 3.651A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
      removed outlier: 3.530A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 113
    Processing helix  chain 'A' and resid 125 through 135
    Processing helix  chain 'A' and resid 146 through 153
    Processing helix  chain 'A' and resid 156 through 165
    Processing helix  chain 'A' and resid 172 through 181
      removed outlier: 3.577A  pdb=" N   PHE A 178 " --> pdb=" O   CYS A 174 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LYS A 181 " --> pdb=" O   TYR A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 238
    Processing helix  chain 'A' and resid 251 through 255
      removed outlier: 3.913A  pdb=" N   ASN A 254 " --> pdb=" O   SER A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.635A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
      removed outlier: 4.343A  pdb=" N   ARG A 317 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 4.517A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   GLY A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 390
    Processing helix  chain 'A' and resid 391 through 393
      No H-bonds generated for 'chain 'A' and resid 391 through 393'
    Processing helix  chain 'B' and resid 8 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'B' and resid 128 through 132
      removed outlier: 3.916A  pdb=" N   ASN B 132 " --> pdb=" O   ARG B 129 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 14 through 24
      removed outlier: 4.093A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'R' and resid 32 through 61
      removed outlier: 3.756A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 97
      removed outlier: 4.268A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
      removed outlier: 3.608A  pdb=" N   SER R 137 " --> pdb=" O   PHE R 133 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 145
      removed outlier: 4.122A  pdb=" N   GLN R 142 " --> pdb=" O   PRO R 138 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   SER R 143 " --> pdb=" O   PHE R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 4.388A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
    Processing helix  chain 'R' and resid 181 through 187
    Processing helix  chain 'R' and resid 196 through 208
      removed outlier: 3.509A  pdb=" N   ILE R 201 " --> pdb=" O   GLN R 197 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ALA R 202 " --> pdb=" O   ALA R 198 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 208 through 238
    Processing helix  chain 'R' and resid 270 through 299
      removed outlier: 4.273A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 4.187A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ILE R 298 " --> pdb=" O   ILE R 294 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 327
      removed outlier: 4.010A  pdb=" N   ASN R 318 " --> pdb=" O   ILE R 314 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   SER R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   GLY R 320 " --> pdb=" O   TYR R 316 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 340
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 5.921A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.439A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.334A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.723A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.095A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.416A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.498A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 6.341A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.281A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.573A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.718A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.416A  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: 6.552A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.938A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278
      removed outlier: 3.749A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    422 hydrogen bonds defined for protein.
    1218 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.99

  Time building geometry restraints manager: 1.93 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1317
        1.33 -     1.45: 1647
        1.45 -     1.57: 3605
        1.57 -     1.69: 1
        1.69 -     1.81: 44
  Bond restraints: 6614
  Sorted by residual:
  bond pdb=" CA  ARG B 137 "
       pdb=" C   ARG B 137 "
    ideal  model  delta    sigma   weight residual
    1.521  1.465  0.056 1.28e-02 6.10e+03 1.88e+01
  bond pdb=" CA  GLU B 138 "
       pdb=" C   GLU B 138 "
    ideal  model  delta    sigma   weight residual
    1.522  1.487  0.036 1.20e-02 6.94e+03 8.80e+00
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.451 -0.054 2.00e-02 2.50e+03 7.37e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.574 -0.051 2.00e-02 2.50e+03 6.60e+00
  bond pdb=" CA  ALA B 140 "
       pdb=" C   ALA B 140 "
    ideal  model  delta    sigma   weight residual
    1.525  1.492  0.033 1.32e-02 5.74e+03 6.25e+00
  ... (remaining 6609 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.96: 8966
        1.96 -     3.91: 98
        3.91 -     5.87: 20
        5.87 -     7.83: 3
        7.83 -     9.78: 2
  Bond angle restraints: 9089
  Sorted by residual:
  angle pdb=" N   HIS B 142 "
        pdb=" CA  HIS B 142 "
        pdb=" C   HIS B 142 "
      ideal   model   delta    sigma   weight residual
     108.52  100.36    8.16 1.63e+00 3.76e-01 2.51e+01
  angle pdb=" N   ARG B 137 "
        pdb=" CA  ARG B 137 "
        pdb=" C   ARG B 137 "
      ideal   model   delta    sigma   weight residual
     108.76  101.07    7.69 1.58e+00 4.01e-01 2.37e+01
  angle pdb=" N   LEU A 132 "
        pdb=" CA  LEU A 132 "
        pdb=" C   LEU A 132 "
      ideal   model   delta    sigma   weight residual
     111.28  106.18    5.10 1.09e+00 8.42e-01 2.19e+01
  angle pdb=" C   THR B 143 "
        pdb=" N   GLY B 144 "
        pdb=" CA  GLY B 144 "
      ideal   model   delta    sigma   weight residual
     122.63  116.60    6.03 1.34e+00 5.57e-01 2.03e+01
  angle pdb=" N   GLY B 141 "
        pdb=" CA  GLY B 141 "
        pdb=" C   GLY B 141 "
      ideal   model   delta    sigma   weight residual
     113.18  122.96   -9.78 2.37e+00 1.78e-01 1.70e+01
  ... (remaining 9084 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.03: 3500
       16.03 -    32.06: 218
       32.06 -    48.08: 39
       48.08 -    64.11: 4
       64.11 -    80.14: 7
  Dihedral angle restraints: 3768
    sinusoidal: 931
      harmonic: 2837
  Sorted by residual:
  dihedral pdb=" CA  TYR B  59 "
           pdb=" C   TYR B  59 "
           pdb=" N   ALA B  60 "
           pdb=" CA  ALA B  60 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.72  -19.28     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" CA  PHE R 208 "
           pdb=" C   PHE R 208 "
           pdb=" N   TYR R 209 "
           pdb=" CA  TYR R 209 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.39  -17.61     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  ALA R  85 "
           pdb=" C   ALA R  85 "
           pdb=" N   VAL R  86 "
           pdb=" CA  VAL R  86 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.24  -16.76     0      5.00e+00 4.00e-02 1.12e+01
  ... (remaining 3765 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 815
       0.042 -    0.083: 217
       0.083 -    0.125: 68
       0.125 -    0.166: 2
       0.166 -    0.208: 3
  Chirality restraints: 1105
  Sorted by residual:
  chirality pdb=" CA  LEU B 139 "
            pdb=" N   LEU B 139 "
            pdb=" C   LEU B 139 "
            pdb=" CB  LEU B 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CB  THR B  47 "
            pdb=" CA  THR B  47 "
            pdb=" OG1 THR B  47 "
            pdb=" CG2 THR B  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.18 2.00e-01 2.50e+01 7.82e-01
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.57   -0.17 2.00e-01 2.50e+01 7.00e-01
  ... (remaining 1102 not shown)

  Planarity restraints: 1169
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 140 "   -0.009 2.00e-02 2.50e+03   1.80e-02 3.26e+00
        pdb=" C   ALA B 140 "    0.031 2.00e-02 2.50e+03
        pdb=" O   ALA B 140 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   GLY B 141 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 322 "    0.027 5.00e-02 4.00e+02   4.02e-02 2.59e+00
        pdb=" N   PRO R 323 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO R 323 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO R 323 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A 357 "    0.012 2.00e-02 2.50e+03   1.23e-02 2.28e+00
        pdb=" CG  HIS A 357 "   -0.027 2.00e-02 2.50e+03
        pdb=" ND1 HIS A 357 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 HIS A 357 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 HIS A 357 "    0.002 2.00e-02 2.50e+03
        pdb=" NE2 HIS A 357 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1166 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1001
        2.76 -     3.29: 6506
        3.29 -     3.83: 11005
        3.83 -     4.36: 11133
        4.36 -     4.90: 20225
  Nonbonded interactions: 49870
  Sorted by model distance:
  nonbonded pdb=" OG1 THR R  66 "
            pdb=" OD1 ASN R  69 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O   GLY B  77 "
            pdb=" N   LEU B  95 "
     model   vdw
     2.302 3.120
  nonbonded pdb=" OH  TYR B 264 "
            pdb=" O   ALA B 299 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" O   GLU A 327 "
            pdb=" N   GLU A 330 "
     model   vdw
     2.377 3.120
  nonbonded pdb=" OE1 GLN A 384 "
            pdb=" NE2 GLN R 229 "
     model   vdw
     2.385 3.120
  ... (remaining 49865 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.090
  Set scattering table:                    0.090
  Process input model:                     21.070
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
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      :  0.003   0.056   6614  Z= 0.185
  Angle     :  0.582   9.782   9089  Z= 0.330
  Chirality :  0.041   0.208   1105
  Planarity :  0.003   0.040   1169
  Dihedral  : 12.032  80.140   1920
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  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:  1.48 (0.28), residues: 948
  helix:  2.68 (0.25), residues: 433
  sheet:  0.03 (0.38), residues: 180
  loop : -0.76 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 281 
 HIS   0.013   0.001   HIS A 357 
 PHE   0.015   0.001   PHE R 289 
 TYR   0.015   0.001   TYR B  59 
 ARG   0.002   0.000   ARG B  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17454 (  422)
  hydrogen bonds       : angle       6.35722 ( 1218)
  covalent geometry    : bond        0.00321 ( 6614)
  covalent geometry    : angle       0.58178 ( 9089)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.687 
Fit side-chains
REVERT: A  281 TRP cc_start: 0.7514 (m100) cc_final: 0.7237 (m100)
REVERT: B  139 LEU cc_start: 0.7897 (mt) cc_final: 0.7693 (mt)
REVERT: B  333 ASP cc_start: 0.8033 (p0) cc_final: 0.7706 (p0)
REVERT: R  279 MET cc_start: 0.8616 (tpp) cc_final: 0.8286 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.1237
  time to fit residues: 18.0750
Evaluate side-chains
  70 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    0.0050
   chunk 72 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 38 optimal weight:    0.1980
   chunk 75 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   chunk 87 optimal weight:    0.7980
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
A 271 ASN
B  75 GLN
B 311 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.115881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.099363 restraints weight = 15509.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.101781 restraints weight = 8911.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.103065 restraints weight = 6078.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.1226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6614  Z= 0.123
  Angle     :  0.506   5.546   9089  Z= 0.279
  Chirality :  0.041   0.143   1105
  Planarity :  0.003   0.036   1169
  Dihedral  :  4.359  27.986   1027
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 10.63 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.77 (0.28), residues: 948
  helix:  2.83 (0.24), residues: 448
  sheet:  0.02 (0.37), residues: 193
  loop : -0.58 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 173 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.018   0.001   PHE B 292 
 TYR   0.021   0.001   TYR B  59 
 ARG   0.003   0.000   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03532 (  422)
  hydrogen bonds       : angle       4.64582 ( 1218)
  covalent geometry    : bond        0.00250 ( 6614)
  covalent geometry    : angle       0.50556 ( 9089)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.757 
Fit side-chains
REVERT: B  333 ASP cc_start: 0.8259 (p0) cc_final: 0.7979 (p0)
REVERT: G   48 ASP cc_start: 0.7611 (t0) cc_final: 0.7072 (t70)
REVERT: R  169 ILE cc_start: 0.9056 (mm) cc_final: 0.8686 (mt)
  outliers start: 14
  outliers final: 12
  residues processed: 84
  average time/residue: 0.1175
  time to fit residues: 15.3156
Evaluate side-chains
  81 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  129 VAL
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  183 ASN
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  311 LEU
Chi-restraints excluded: chain R residue  321 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 82 optimal weight:    0.6980
   chunk 50 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 95 optimal weight:    0.8980
   chunk 26 optimal weight:   10.0000
   chunk 90 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
R 178 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.115210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.098372 restraints weight = 15618.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.100768 restraints weight = 9029.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.102263 restraints weight = 6183.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6614  Z= 0.124
  Angle     :  0.489   5.375   9089  Z= 0.268
  Chirality :  0.040   0.179   1105
  Planarity :  0.003   0.031   1169
  Dihedral  :  4.203  27.727   1027
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 13.88 %
    Favored  : 82.43 %
  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:  1.87 (0.28), residues: 948
  helix:  2.98 (0.24), residues: 448
  sheet: -0.05 (0.36), residues: 193
  loop : -0.56 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.010   0.001   PHE B 235 
 TYR   0.017   0.001   TYR B  59 
 ARG   0.003   0.000   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03233 (  422)
  hydrogen bonds       : angle       4.28795 ( 1218)
  covalent geometry    : bond        0.00274 ( 6614)
  covalent geometry    : angle       0.48940 ( 9089)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.708 
Fit side-chains
REVERT: B  333 ASP cc_start: 0.8389 (p0) cc_final: 0.7890 (p0)
REVERT: G   48 ASP cc_start: 0.7609 (t0) cc_final: 0.7070 (t70)
REVERT: R  169 ILE cc_start: 0.9102 (mm) cc_final: 0.8757 (mt)
  outliers start: 17
  outliers final: 12
  residues processed: 84
  average time/residue: 0.1205
  time to fit residues: 15.5840
Evaluate side-chains
  84 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  129 VAL
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  183 ASN
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain R residue  311 LEU
Chi-restraints excluded: chain R residue  321 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 64 optimal weight:    7.9990
   chunk 41 optimal weight:    2.9990
   chunk 86 optimal weight:    0.8980
   chunk 73 optimal weight:    3.9990
   chunk 75 optimal weight:    0.6980
   chunk 77 optimal weight:    0.7980
   chunk 30 optimal weight:    9.9990
   chunk 31 optimal weight:    5.9990
   chunk 78 optimal weight:    0.0070
   chunk 45 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.0800

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

Flipped N/Q/H residues before XYZ refinement:
B  62 HIS
** R 296 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 = 0.3761 r_free = 0.3761 target = 0.113382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.096788 restraints weight = 15786.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.099055 restraints weight = 9496.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.100431 restraints weight = 6619.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6614  Z= 0.142
  Angle     :  0.488   5.374   9089  Z= 0.269
  Chirality :  0.040   0.156   1105
  Planarity :  0.003   0.030   1169
  Dihedral  :  4.121  25.838   1027
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 17.14 %
    Favored  : 78.31 %
  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:  1.85 (0.28), residues: 948
  helix:  2.97 (0.24), residues: 453
  sheet: -0.03 (0.36), residues: 185
  loop : -0.64 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 234 
 HIS   0.004   0.001   HIS A 362 
 PHE   0.013   0.001   PHE B 235 
 TYR   0.016   0.001   TYR R 141 
 ARG   0.002   0.000   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03210 (  422)
  hydrogen bonds       : angle       4.10895 ( 1218)
  covalent geometry    : bond        0.00317 ( 6614)
  covalent geometry    : angle       0.48841 ( 9089)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.657 
Fit side-chains
REVERT: B  333 ASP cc_start: 0.8403 (p0) cc_final: 0.7869 (p0)
REVERT: R  174 TYR cc_start: 0.7303 (p90) cc_final: 0.6883 (p90)
  outliers start: 21
  outliers final: 15
  residues processed: 86
  average time/residue: 0.1196
  time to fit residues: 15.7990
Evaluate side-chains
  81 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  129 VAL
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  183 ASN
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain R residue  311 LEU
Chi-restraints excluded: chain R residue  321 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 14 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 56 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 93 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.114357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.098058 restraints weight = 15510.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.100148 restraints weight = 9655.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.101416 restraints weight = 6875.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.1931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6614  Z= 0.121
  Angle     :  0.486   5.797   9089  Z= 0.264
  Chirality :  0.040   0.151   1105
  Planarity :  0.003   0.029   1169
  Dihedral  :  4.072  27.440   1027
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 18.66 %
    Favored  : 76.36 %
  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:  1.84 (0.28), residues: 948
  helix:  3.03 (0.24), residues: 453
  sheet: -0.17 (0.36), residues: 187
  loop : -0.68 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 234 
 HIS   0.003   0.001   HIS A 362 
 PHE   0.012   0.001   PHE B 199 
 TYR   0.015   0.001   TYR R 141 
 ARG   0.001   0.000   ARG A 380 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03099 (  422)
  hydrogen bonds       : angle       3.98681 ( 1218)
  covalent geometry    : bond        0.00270 ( 6614)
  covalent geometry    : angle       0.48579 ( 9089)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 76
  time to evaluate  : 0.761 
Fit side-chains
REVERT: B  333 ASP cc_start: 0.8405 (p0) cc_final: 0.7843 (p0)
REVERT: G   48 ASP cc_start: 0.7550 (t0) cc_final: 0.6944 (t70)
REVERT: R  174 TYR cc_start: 0.7146 (p90) cc_final: 0.6784 (p90)
  outliers start: 23
  outliers final: 18
  residues processed: 89
  average time/residue: 0.1295
  time to fit residues: 17.0495
Evaluate side-chains
  88 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 70
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  129 VAL
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  183 ASN
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain R residue  311 LEU
Chi-restraints excluded: chain R residue  321 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 72 optimal weight:    0.7980
   chunk 46 optimal weight:    5.9990
   chunk 3 optimal weight:    6.9990
   chunk 7 optimal weight:   20.0000
   chunk 84 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 76 optimal weight:    0.6980
   chunk 44 optimal weight:    0.8980
   chunk 70 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 183 HIS
R 296 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.112605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.095814 restraints weight = 15499.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.098054 restraints weight = 9529.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.099391 restraints weight = 6737.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.2088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6614  Z= 0.137
  Angle     :  0.493   5.372   9089  Z= 0.269
  Chirality :  0.040   0.155   1105
  Planarity :  0.003   0.029   1169
  Dihedral  :  4.069  27.050   1027
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 19.74 %
    Favored  : 75.49 %
  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:  1.80 (0.28), residues: 948
  helix:  3.02 (0.24), residues: 453
  sheet: -0.32 (0.36), residues: 189
  loop : -0.63 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 277 
 HIS   0.003   0.001   HIS A 362 
 PHE   0.013   0.001   PHE B 235 
 TYR   0.017   0.001   TYR R 141 
 ARG   0.002   0.000   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03117 (  422)
  hydrogen bonds       : angle       3.94965 ( 1218)
  covalent geometry    : bond        0.00308 ( 6614)
  covalent geometry    : angle       0.49253 ( 9089)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 75
  time to evaluate  : 0.761 
Fit side-chains
REVERT: A  255 MET cc_start: 0.7651 (mmm) cc_final: 0.7322 (tpp)
REVERT: B  333 ASP cc_start: 0.8470 (p0) cc_final: 0.7900 (p0)
REVERT: R  174 TYR cc_start: 0.7181 (p90) cc_final: 0.6800 (p90)
  outliers start: 22
  outliers final: 17
  residues processed: 87
  average time/residue: 0.1438
  time to fit residues: 17.9972
Evaluate side-chains
  86 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  129 VAL
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  183 ASN
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain R residue  311 LEU
Chi-restraints excluded: chain R residue  321 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    0.0970
   chunk 13 optimal weight:    0.5980
   chunk 43 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 12 optimal weight:    0.4980
   chunk 32 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 30 optimal weight:   10.0000
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
B 183 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.114461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.098196 restraints weight = 15316.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.100289 restraints weight = 9495.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.101321 restraints weight = 6802.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6614  Z= 0.109
  Angle     :  0.487   7.414   9089  Z= 0.262
  Chirality :  0.040   0.148   1105
  Planarity :  0.003   0.029   1169
  Dihedral  :  3.996  26.653   1027
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 20.17 %
    Favored  : 75.05 %
  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:  1.83 (0.28), residues: 948
  helix:  3.09 (0.24), residues: 452
  sheet: -0.35 (0.36), residues: 191
  loop : -0.64 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 277 
 HIS   0.007   0.001   HIS B 183 
 PHE   0.027   0.001   PHE B 292 
 TYR   0.017   0.001   TYR R 141 
 ARG   0.002   0.000   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03019 (  422)
  hydrogen bonds       : angle       3.87516 ( 1218)
  covalent geometry    : bond        0.00237 ( 6614)
  covalent geometry    : angle       0.48750 ( 9089)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 76
  time to evaluate  : 0.679 
Fit side-chains
REVERT: B  333 ASP cc_start: 0.8445 (p0) cc_final: 0.8115 (p0)
REVERT: R  174 TYR cc_start: 0.7011 (p90) cc_final: 0.6701 (p90)
  outliers start: 22
  outliers final: 15
  residues processed: 89
  average time/residue: 0.1273
  time to fit residues: 16.7808
Evaluate side-chains
  87 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  129 VAL
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  183 ASN
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  311 LEU
Chi-restraints excluded: chain R residue  321 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 11 optimal weight:    0.4980
   chunk 15 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 30 optimal weight:   10.0000
   chunk 35 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 72 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 83 optimal weight:    6.9990
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** 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 = 0.3777 r_free = 0.3777 target = 0.114697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.098287 restraints weight = 15368.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.100361 restraints weight = 9638.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.101789 restraints weight = 6933.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.2268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6614  Z= 0.133
  Angle     :  0.520   7.644   9089  Z= 0.277
  Chirality :  0.040   0.150   1105
  Planarity :  0.003   0.029   1169
  Dihedral  :  4.084  26.360   1027
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 20.39 %
    Favored  : 75.05 %
  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:  1.84 (0.28), residues: 948
  helix:  3.07 (0.23), residues: 452
  sheet: -0.15 (0.37), residues: 181
  loop : -0.75 (0.34), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 339 
 HIS   0.009   0.001   HIS B 183 
 PHE   0.021   0.001   PHE B 292 
 TYR   0.019   0.001   TYR R 141 
 ARG   0.002   0.000   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03084 (  422)
  hydrogen bonds       : angle       3.94806 ( 1218)
  covalent geometry    : bond        0.00299 ( 6614)
  covalent geometry    : angle       0.52017 ( 9089)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 72
  time to evaluate  : 0.733 
Fit side-chains
REVERT: A  255 MET cc_start: 0.7367 (mmm) cc_final: 0.7112 (tpp)
REVERT: B  333 ASP cc_start: 0.8482 (p0) cc_final: 0.8106 (p0)
REVERT: R  174 TYR cc_start: 0.6981 (p90) cc_final: 0.6682 (p90)
  outliers start: 21
  outliers final: 17
  residues processed: 84
  average time/residue: 0.1209
  time to fit residues: 15.5165
Evaluate side-chains
  85 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  129 VAL
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  183 ASN
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  311 LEU
Chi-restraints excluded: chain R residue  321 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 64 optimal weight:    4.9990
   chunk 93 optimal weight:    1.9990
   chunk 73 optimal weight:    0.6980
   chunk 46 optimal weight:    3.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** 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 = 0.3760 r_free = 0.3760 target = 0.113359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.096084 restraints weight = 15594.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.098479 restraints weight = 9012.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.100146 restraints weight = 6181.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.2320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6614  Z= 0.129
  Angle     :  0.519   7.002   9089  Z= 0.276
  Chirality :  0.040   0.150   1105
  Planarity :  0.003   0.029   1169
  Dihedral  :  4.110  28.622   1027
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 21.91 %
    Favored  : 73.97 %
  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:  1.85 (0.28), residues: 948
  helix:  3.07 (0.24), residues: 452
  sheet: -0.11 (0.37), residues: 179
  loop : -0.75 (0.34), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  63 
 HIS   0.008   0.001   HIS B 183 
 PHE   0.028   0.001   PHE B 292 
 TYR   0.020   0.001   TYR R 141 
 ARG   0.002   0.000   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03057 (  422)
  hydrogen bonds       : angle       3.95003 ( 1218)
  covalent geometry    : bond        0.00291 ( 6614)
  covalent geometry    : angle       0.51896 ( 9089)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.772 
Fit side-chains
REVERT: B  333 ASP cc_start: 0.8491 (p0) cc_final: 0.7917 (p0)
REVERT: R  174 TYR cc_start: 0.6976 (p90) cc_final: 0.6678 (p90)
  outliers start: 19
  outliers final: 18
  residues processed: 80
  average time/residue: 0.1306
  time to fit residues: 16.0585
Evaluate side-chains
  85 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 67
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  129 VAL
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  183 ASN
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  311 LEU
Chi-restraints excluded: chain R residue  321 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 66 optimal weight:    0.7980
   chunk 54 optimal weight:    0.2980
   chunk 71 optimal weight:   10.0000
   chunk 79 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 78 optimal weight:    0.7980
   chunk 17 optimal weight:    6.9990
   chunk 70 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 322 ASN ** 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 = 0.3760 r_free = 0.3760 target = 0.113736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.097227 restraints weight = 15663.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.099381 restraints weight = 9875.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.100803 restraints weight = 7071.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6614  Z= 0.149
  Angle     :  0.531   6.970   9089  Z= 0.286
  Chirality :  0.041   0.154   1105
  Planarity :  0.003   0.029   1169
  Dihedral  :  4.190  28.578   1027
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 21.48 %
    Favored  : 73.97 %
  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:  1.85 (0.28), residues: 948
  helix:  3.05 (0.24), residues: 452
  sheet: -0.12 (0.37), residues: 179
  loop : -0.72 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 339 
 HIS   0.009   0.001   HIS B 183 
 PHE   0.028   0.001   PHE B 292 
 TYR   0.021   0.001   TYR R 141 
 ARG   0.002   0.000   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03159 (  422)
  hydrogen bonds       : angle       3.99084 ( 1218)
  covalent geometry    : bond        0.00340 ( 6614)
  covalent geometry    : angle       0.53087 ( 9089)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 67
  time to evaluate  : 0.770 
Fit side-chains
REVERT: B  333 ASP cc_start: 0.8591 (p0) cc_final: 0.8070 (p0)
REVERT: R  174 TYR cc_start: 0.6999 (p90) cc_final: 0.6639 (p90)
  outliers start: 21
  outliers final: 20
  residues processed: 80
  average time/residue: 0.1348
  time to fit residues: 16.5931
Evaluate side-chains
  85 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 65
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  129 VAL
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  183 ASN
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain R residue  311 LEU
Chi-restraints excluded: chain R residue  321 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 89 optimal weight:    0.5980
   chunk 60 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 322 ASN ** 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 = 0.3756 r_free = 0.3756 target = 0.113734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.096392 restraints weight = 15896.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.098852 restraints weight = 9071.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.100512 restraints weight = 6164.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.2424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6614  Z= 0.127
  Angle     :  0.519   6.953   9089  Z= 0.277
  Chirality :  0.040   0.151   1105
  Planarity :  0.003   0.029   1169
  Dihedral  :  4.145  29.217   1027
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 21.91 %
    Favored  : 73.54 %
  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:  1.84 (0.28), residues: 948
  helix:  3.06 (0.24), residues: 452
  sheet: -0.12 (0.37), residues: 179
  loop : -0.74 (0.34), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B  63 
 HIS   0.008   0.001   HIS B 183 
 PHE   0.025   0.001   PHE B 292 
 TYR   0.020   0.001   TYR R 141 
 ARG   0.002   0.000   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03051 (  422)
  hydrogen bonds       : angle       3.93816 ( 1218)
  covalent geometry    : bond        0.00285 ( 6614)
  covalent geometry    : angle       0.51861 ( 9089)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2004.62 seconds
wall clock time: 35 minutes 46.34 seconds (2146.34 seconds total)