Starting phenix.real_space_refine
on Tue Mar 11 18:05:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8geg_29969/03_2025/8geg_29969.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8geg_29969/03_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_29969/03_2025/8geg_29969.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8geg_29969/03_2025/8geg_29969.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8geg_29969/03_2025/8geg_29969.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8geg_29969/03_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-5624/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: 4.63, per 1000 atoms: 0.71
  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: 1.71
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.82
  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: 1.83

  Time building geometry restraints manager: 2.01 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:             1.360
  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:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     20.150
  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:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.100
-------------------------------------------------------------------------------
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= 0.216
  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 

*********************** 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  : 0.738 
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: 0.1207
  time to fit residues: 17.4667
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  : 0.737 
-------------------------------------------------------------------------------
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 = 45)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.099355 restraints weight = 15509.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.101772 restraints weight = 8929.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.103351 restraints weight = 6088.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
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= 0.168
  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 

*********************** 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  : 0.651 
Fit side-chains
REVERT: B  333 ASP cc_start: 0.8259 (p0) cc_final: 0.7982 (p0)
REVERT: G   48 ASP cc_start: 0.7596 (t0) cc_final: 0.7080 (t70)
REVERT: R  169 ILE cc_start: 0.9055 (mm) cc_final: 0.8682 (mt)
  outliers start: 14
  outliers final: 12
  residues processed: 84
  average time/residue: 0.1129
  time to fit residues: 14.5204
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  : 0.664 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 18 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 82 optimal weight:    0.7980
   chunk 50 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   chunk 75 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9990
   chunk 26 optimal weight:   10.0000
   chunk 90 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3794 r_free = 0.3794 target = 0.115364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.098508 restraints weight = 15614.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.100929 restraints weight = 9041.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.102612 restraints weight = 6186.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.1558

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= 0.177
  Angle     :  0.486   5.370   9089  Z= 0.266
  Chirality :  0.040   0.173   1105
  Planarity :  0.003   0.032   1169
  Dihedral  :  4.171  27.364   1027
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 13.67 %
    Favored  : 82.65 %
  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:  2.94 (0.24), residues: 454
  sheet: -0.04 (0.36), residues: 193
  loop : -0.57 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.010   0.001   PHE B 235 
 TYR   0.018   0.001   TYR B  59 
 ARG   0.003   0.000   ARG G  27 

*********************** 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
  94 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.666 
Fit side-chains
   revert: symmetry clash
REVERT: B  333 ASP cc_start: 0.8389 (p0) cc_final: 0.7886 (p0)
REVERT: G   48 ASP cc_start: 0.7634 (t0) cc_final: 0.7107 (t70)
REVERT: R  174 TYR cc_start: 0.7173 (p90) cc_final: 0.6924 (p90)
  outliers start: 17
  outliers final: 12
  residues processed: 85
  average time/residue: 0.1140
  time to fit residues: 14.8225
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  : 0.635 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 41 optimal weight:    0.0770
   chunk 86 optimal weight:    0.8980
   chunk 73 optimal weight:    3.9990
   chunk 75 optimal weight:    0.5980
   chunk 77 optimal weight:    0.5980
   chunk 30 optimal weight:    9.9990
   chunk 31 optimal weight:    7.9990
   chunk 78 optimal weight:    0.0270
   chunk 45 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.4396

-------------------------------------------------------------------------------
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 = 0.3820 r_free = 0.3820 target = 0.116998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.101144 restraints weight = 15614.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.103315 restraints weight = 9609.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.104633 restraints weight = 6755.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.1814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6614  Z= 0.138
  Angle     :  0.454   5.404   9089  Z= 0.248
  Chirality :  0.039   0.145   1105
  Planarity :  0.003   0.030   1169
  Dihedral  :  3.944  26.692   1027
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 16.92 %
    Favored  : 78.96 %
  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:  1.91 (0.28), residues: 948
  helix:  3.04 (0.24), residues: 454
  sheet: -0.07 (0.36), residues: 189
  loop : -0.63 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 234 
 HIS   0.003   0.001   HIS B  54 
 PHE   0.010   0.001   PHE R 282 
 TYR   0.014   0.001   TYR R 141 
 ARG   0.001   0.000   ARG A 380 

*********************** 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
  101 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.703 
Fit side-chains
REVERT: B  333 ASP cc_start: 0.8281 (p0) cc_final: 0.7789 (p0)
REVERT: G   48 ASP cc_start: 0.7655 (t0) cc_final: 0.6990 (t70)
REVERT: R  174 TYR cc_start: 0.7093 (p90) cc_final: 0.6868 (p90)
  outliers start: 19
  outliers final: 13
  residues processed: 92
  average time/residue: 0.1267
  time to fit residues: 17.3500
Evaluate side-chains
  85 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
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  168 LEU
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain G residue   38 MET
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  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:    7.9990
   chunk 36 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9990
   chunk 93 optimal weight:    0.0770
   chunk 31 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.9544

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** 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 = 0.3782 r_free = 0.3782 target = 0.114535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.097982 restraints weight = 15638.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.100270 restraints weight = 9343.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.101677 restraints weight = 6507.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.1948

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= 0.201
  Angle     :  0.495   5.369   9089  Z= 0.269
  Chirality :  0.040   0.155   1105
  Planarity :  0.003   0.029   1169
  Dihedral  :  4.015  26.619   1027
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 19.31 %
    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:  1.93 (0.28), residues: 948
  helix:  3.08 (0.24), residues: 454
  sheet: -0.08 (0.36), residues: 187
  loop : -0.63 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 234 
 HIS   0.003   0.001   HIS A 362 
 PHE   0.024   0.001   PHE B 292 
 TYR   0.015   0.001   TYR B  59 
 ARG   0.002   0.000   ARG B 150 

*********************** 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
  96 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 76
  time to evaluate  : 0.691 
Fit side-chains
   revert: symmetry clash
REVERT: B  333 ASP cc_start: 0.8454 (p0) cc_final: 0.7879 (p0)
  outliers start: 20
  outliers final: 17
  residues processed: 85
  average time/residue: 0.1328
  time to fit residues: 16.6864
Evaluate side-chains
  90 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
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  161 SER
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  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:    3.9990
   chunk 72 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 7 optimal weight:   20.0000
   chunk 84 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 76 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   chunk 70 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
R 296 HIS
** R 312 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 = 0.3747 r_free = 0.3747 target = 0.112293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.095768 restraints weight = 15379.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.097777 restraints weight = 9650.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.099040 restraints weight = 6964.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6614  Z= 0.245
  Angle     :  0.513   5.470   9089  Z= 0.281
  Chirality :  0.040   0.155   1105
  Planarity :  0.003   0.028   1169
  Dihedral  :  4.158  26.447   1027
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  5.42 %
    Allowed  : 18.66 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.86 (0.28), residues: 948
  helix:  3.02 (0.24), residues: 453
  sheet: -0.02 (0.37), residues: 179
  loop : -0.71 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 277 
 HIS   0.004   0.001   HIS A 362 
 PHE   0.025   0.001   PHE B 292 
 TYR   0.016   0.001   TYR R 141 
 ARG   0.002   0.000   ARG G  27 

*********************** 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
  101 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 76
  time to evaluate  : 0.747 
Fit side-chains
REVERT: A  255 MET cc_start: 0.7654 (mmm) cc_final: 0.7359 (tpp)
REVERT: B  333 ASP cc_start: 0.8442 (p0) cc_final: 0.7871 (p0)
REVERT: G   48 ASP cc_start: 0.7482 (t0) cc_final: 0.6790 (t70)
  outliers start: 25
  outliers final: 18
  residues processed: 91
  average time/residue: 0.1420
  time to fit residues: 18.6074
Evaluate side-chains
  87 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
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  161 SER
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  210 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 48 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 30 optimal weight:   10.0000
   chunk 21 optimal weight:    2.9990
   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 183 HIS
** B 259 GLN ** 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 = 0.3764 r_free = 0.3764 target = 0.113372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.096781 restraints weight = 15355.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.098910 restraints weight = 9323.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.100395 restraints weight = 6616.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.2160

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= 0.183
  Angle     :  0.492   7.066   9089  Z= 0.265
  Chirality :  0.040   0.149   1105
  Planarity :  0.003   0.029   1169
  Dihedral  :  4.093  27.958   1027
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  5.42 %
    Allowed  : 19.74 %
    Favored  : 74.84 %
  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:  3.08 (0.24), residues: 452
  sheet: -0.08 (0.37), residues: 181
  loop : -0.75 (0.34), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  63 
 HIS   0.005   0.001   HIS B  54 
 PHE   0.013   0.001   PHE B 292 
 TYR   0.017   0.001   TYR R 141 
 ARG   0.002   0.000   ARG A 265 

*********************** 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
  99 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 74
  time to evaluate  : 0.748 
Fit side-chains
REVERT: B  333 ASP cc_start: 0.8444 (p0) cc_final: 0.7887 (p0)
REVERT: G   48 ASP cc_start: 0.7525 (t0) cc_final: 0.6768 (t70)
REVERT: R  174 TYR cc_start: 0.7089 (p90) cc_final: 0.6673 (p90)
  outliers start: 25
  outliers final: 18
  residues processed: 90
  average time/residue: 0.1269
  time to fit residues: 17.4413
Evaluate side-chains
  89 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
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   93 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  263 THR
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   38 MET
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 11 optimal weight:   20.0000
   chunk 15 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 30 optimal weight:    9.9990
   chunk 35 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 83 optimal weight:    7.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.111251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.094355 restraints weight = 15650.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.096561 restraints weight = 9617.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.097997 restraints weight = 6830.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6614  Z= 0.253
  Angle     :  0.524   7.121   9089  Z= 0.283
  Chirality :  0.041   0.153   1105
  Planarity :  0.003   0.028   1169
  Dihedral  :  4.196  29.335   1027
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 20.17 %
    Favored  : 74.62 %
  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:  1.81 (0.28), residues: 948
  helix:  3.04 (0.24), residues: 451
  sheet: -0.08 (0.37), residues: 179
  loop : -0.80 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 339 
 HIS   0.005   0.001   HIS B  54 
 PHE   0.015   0.001   PHE B 235 
 TYR   0.019   0.001   TYR R 141 
 ARG   0.002   0.000   ARG G  27 

*********************** 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
  95 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 71
  time to evaluate  : 0.685 
Fit side-chains
REVERT: B  333 ASP cc_start: 0.8457 (p0) cc_final: 0.8092 (p0)
  outliers start: 24
  outliers final: 22
  residues processed: 85
  average time/residue: 0.1358
  time to fit residues: 17.4123
Evaluate side-chains
  88 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 66
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue   93 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  210 LEU
Chi-restraints excluded: chain B residue  339 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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    0.3980
   chunk 78 optimal weight:    0.1980
   chunk 39 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 93 optimal weight:    0.0020
   chunk 73 optimal weight:    0.4980
   chunk 46 optimal weight:    3.9990
   overall best weight:    0.3788

-------------------------------------------------------------------------------
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 = 0.3784 r_free = 0.3784 target = 0.114897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.098624 restraints weight = 15620.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.100716 restraints weight = 9662.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.102199 restraints weight = 6881.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.2271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6614  Z= 0.144
  Angle     :  0.497   7.154   9089  Z= 0.263
  Chirality :  0.040   0.145   1105
  Planarity :  0.003   0.029   1169
  Dihedral  :  4.075  29.869   1027
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 21.69 %
    Favored  : 74.19 %
  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:  3.08 (0.24), residues: 452
  sheet: -0.15 (0.37), residues: 183
  loop : -0.73 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 277 
 HIS   0.010   0.001   HIS B 183 
 PHE   0.011   0.001   PHE R 289 
 TYR   0.019   0.001   TYR R 141 
 ARG   0.001   0.000   ARG A 380 

*********************** 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
  99 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 80
  time to evaluate  : 0.702 
Fit side-chains
REVERT: B  333 ASP cc_start: 0.8540 (p0) cc_final: 0.8172 (p0)
  outliers start: 19
  outliers final: 14
  residues processed: 91
  average time/residue: 0.1261
  time to fit residues: 17.5359
Evaluate side-chains
  89 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
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  169 TRP
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   38 MET
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:    7.9990
   chunk 66 optimal weight:    0.5980
   chunk 54 optimal weight:    0.6980
   chunk 71 optimal weight:    8.9990
   chunk 79 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 78 optimal weight:    0.4980
   chunk 17 optimal weight:    0.7980
   chunk 70 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
B 183 HIS
** 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 = 0.3776 r_free = 0.3776 target = 0.114306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.097682 restraints weight = 15608.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.099911 restraints weight = 9529.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.101397 restraints weight = 6680.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.2404

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= 0.181
  Angle     :  0.517   6.814   9089  Z= 0.274
  Chirality :  0.040   0.158   1105
  Planarity :  0.003   0.029   1169
  Dihedral  :  4.084  30.019   1027
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 22.13 %
    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:  1.84 (0.28), residues: 948
  helix:  3.10 (0.24), residues: 452
  sheet: -0.32 (0.37), residues: 191
  loop : -0.67 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B  63 
 HIS   0.005   0.001   HIS B  54 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.023   0.001   TYR R 174 
 ARG   0.002   0.000   ARG G  27 

********************** 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
  91 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.722 
Fit side-chains
REVERT: B  333 ASP cc_start: 0.8581 (p0) cc_final: 0.8011 (p0)
  outliers start: 18
  outliers final: 17
  residues processed: 83
  average time/residue: 0.1217
  time to fit residues: 15.3753
Evaluate side-chains
  89 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
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  210 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   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 89 optimal weight:    0.0060
   chunk 60 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   chunk 94 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    1.1198

-------------------------------------------------------------------------------
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 = 0.3753 r_free = 0.3753 target = 0.112986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.096573 restraints weight = 15827.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.098664 restraints weight = 9828.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.100115 restraints weight = 7020.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.2407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6614  Z= 0.224
  Angle     :  0.528   6.889   9089  Z= 0.282
  Chirality :  0.040   0.152   1105
  Planarity :  0.003   0.029   1169
  Dihedral  :  4.112  30.764   1027
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 22.13 %
    Favored  : 74.19 %
  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:  1.86 (0.28), residues: 948
  helix:  3.09 (0.24), residues: 451
  sheet: -0.11 (0.38), residues: 183
  loop : -0.75 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 339 
 HIS   0.007   0.001   HIS B  54 
 PHE   0.013   0.001   PHE B 235 
 TYR   0.023   0.001   TYR R 174 
 ARG   0.002   0.000   ARG G  27 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2013.76 seconds
wall clock time: 35 minutes 46.56 seconds (2146.56 seconds total)