Starting phenix.real_space_refine
on Thu Mar 13 02:33:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ykx_39375/03_2025/8ykx_39375_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ykx_39375/03_2025/8ykx_39375.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ykx_39375/03_2025/8ykx_39375.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ykx_39375/03_2025/8ykx_39375.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ykx_39375/03_2025/8ykx_39375_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ykx_39375/03_2025/8ykx_39375_neut.cif"
  }
  resolution = 2.69
  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=   0.079
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      56      5.16       5
     C    5576      2.51       5
     N    1472      2.21       5
     O    1606      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8710
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2276
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2276
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 12, 'TRANS': 268}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "A"
      Number of atoms: 1699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1699
          Classifications: {'peptide': 213}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 2, 'TRANS': 210}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 21
    Chain: "B"
      Number of atoms: 2558
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2558
          Classifications: {'peptide': 337}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "E"
      Number of atoms: 1728
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1728
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 72
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 46
    Chain: "G"
      Number of atoms: 441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 441
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "R"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Unusual residues: {'MAE': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.25, per 1000 atoms: 0.60
  Number of scatterers: 8710
  At special positions: 0
  Unit cell: (86.87, 119.72, 132.13, 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      56     16.00
     O    1606      8.00
     N    1472      7.00
     C    5576      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " distance=2.61

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.50
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2102

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 13 sheets defined
      39.4% alpha, 23.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.19
  Creating SS restraints...
    Processing helix  chain 'R' and resid 11 through 49
      removed outlier: 4.065A  pdb=" N   ALA R  19 " --> pdb=" O   LEU R  15 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ALA R  20 " --> pdb=" O   ALA R  16 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   LEU R  21 " --> pdb=" O   ALA R  17 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   GLU R  22 " --> pdb=" O   GLU R  18 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   LEU R  26 " --> pdb=" O   GLU R  22 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   SER R  27 " --> pdb=" O   LYS R  23 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 56 through 74
    Processing helix  chain 'R' and resid 75 through 86
      removed outlier: 4.231A  pdb=" N   LEU R  79 " --> pdb=" O   THR R  75 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 91 through 126
    Processing helix  chain 'R' and resid 131 through 134
    Processing helix  chain 'R' and resid 135 through 155
    Processing helix  chain 'R' and resid 156 through 158
      No H-bonds generated for 'chain 'R' and resid 156 through 158'
    Processing helix  chain 'R' and resid 180 through 196
    Processing helix  chain 'R' and resid 196 through 217
    Processing helix  chain 'R' and resid 227 through 259
      removed outlier: 3.577A  pdb=" N   VAL R 238 " --> pdb=" O   VAL R 234 " (cutoff:3.500A)
      Proline residue:  R 247  - end of helix
      removed outlier: 3.564A  pdb=" N   ARG R 259 " --> pdb=" O   ARG R 255 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 270 through 286
      Proline residue:  R 282  - end of helix
    Processing helix  chain 'R' and resid 286 through 297
      Proline residue:  R 292  - end of helix
    Processing helix  chain 'R' and resid 299 through 309
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.649A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 50
    Processing helix  chain 'A' and resid 51 through 53
      No H-bonds generated for 'chain 'A' and resid 51 through 53'
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 3.971A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 4.026A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.582A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.790A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 5 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'G' and resid 8 through 25
      removed outlier: 3.862A  pdb=" N   ILE G  25 " --> pdb=" O   MET G  21 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.204A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.594A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 8.940A  pdb=" N   ALA A 220 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.687A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.157A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.594A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.659A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.598A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.684A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.783A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.987A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.724A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 5.887A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.188A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.893A  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: 3.997A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.059A  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: 6.498A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.743A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.125A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.125A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
      removed outlier: 6.348A  pdb=" N   LEU E 174 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   TYR E 190 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)

    459 hydrogen bonds defined for protein.
    1287 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.59

  Time building geometry restraints manager: 2.86 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2190
        1.33 -     1.45: 1820
        1.45 -     1.58: 4796
        1.58 -     1.70: 0
        1.70 -     1.82: 82
  Bond restraints: 8888
  Sorted by residual:
  bond pdb=" C   LEU R 214 "
       pdb=" N   LYS R 215 "
    ideal  model  delta    sigma   weight residual
    1.335  1.431 -0.097 1.36e-02 5.41e+03 5.05e+01
  bond pdb=" C   PHE R 296 "
       pdb=" N   LEU R 297 "
    ideal  model  delta    sigma   weight residual
    1.334  1.410 -0.076 1.43e-02 4.89e+03 2.83e+01
  bond pdb=" CA  ARG R 281 "
       pdb=" C   ARG R 281 "
    ideal  model  delta    sigma   weight residual
    1.521  1.571 -0.049 1.17e-02 7.31e+03 1.78e+01
  bond pdb=" C   ARG R 281 "
       pdb=" N   PRO R 282 "
    ideal  model  delta    sigma   weight residual
    1.335  1.382 -0.047 1.28e-02 6.10e+03 1.36e+01
  bond pdb=" N   THR R 269 "
       pdb=" CA  THR R 269 "
    ideal  model  delta    sigma   weight residual
    1.458  1.411  0.047 1.90e-02 2.77e+03 6.15e+00
  ... (remaining 8883 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.18: 11882
        2.18 -     4.37: 150
        4.37 -     6.55: 11
        6.55 -     8.73: 3
        8.73 -    10.92: 1
  Bond angle restraints: 12047
  Sorted by residual:
  angle pdb=" N   LEU R 231 "
        pdb=" CA  LEU R 231 "
        pdb=" C   LEU R 231 "
      ideal   model   delta    sigma   weight residual
     111.28  105.84    5.44 1.09e+00 8.42e-01 2.50e+01
  angle pdb=" N   THR R 269 "
        pdb=" CA  THR R 269 "
        pdb=" C   THR R 269 "
      ideal   model   delta    sigma   weight residual
     111.00  100.08   10.92 2.80e+00 1.28e-01 1.52e+01
  angle pdb=" C   ARG E 191 "
        pdb=" N   MET E 192 "
        pdb=" CA  MET E 192 "
      ideal   model   delta    sigma   weight residual
     121.54  128.04   -6.50 1.91e+00 2.74e-01 1.16e+01
  angle pdb=" N   VAL A 201 "
        pdb=" CA  VAL A 201 "
        pdb=" C   VAL A 201 "
      ideal   model   delta    sigma   weight residual
     111.91  109.26    2.65 8.90e-01 1.26e+00 8.89e+00
  angle pdb=" N   ASP A 251 "
        pdb=" CA  ASP A 251 "
        pdb=" C   ASP A 251 "
      ideal   model   delta    sigma   weight residual
     111.07  108.12    2.95 1.07e+00 8.73e-01 7.59e+00
  ... (remaining 12042 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.53: 4721
       17.53 -    35.07: 400
       35.07 -    52.60: 110
       52.60 -    70.13: 17
       70.13 -    87.66: 12
  Dihedral angle restraints: 5260
    sinusoidal: 2003
      harmonic: 3257
  Sorted by residual:
  dihedral pdb=" CB  CYS E 159 "
           pdb=" SG  CYS E 159 "
           pdb=" SG  CYS E 229 "
           pdb=" CB  CYS E 229 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   50.10   42.90     1      1.00e+01 1.00e-02 2.57e+01
  dihedral pdb=" CA  LYS B  78 "
           pdb=" C   LYS B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.03   20.97     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" CA  ILE R  89 "
           pdb=" C   ILE R  89 "
           pdb=" N   TYR R  90 "
           pdb=" CA  TYR R  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.51  -18.49     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 5257 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 951
       0.035 -    0.070: 286
       0.070 -    0.105: 101
       0.105 -    0.140: 40
       0.140 -    0.175: 4
  Chirality restraints: 1382
  Sorted by residual:
  chirality pdb=" CA  LYS R 135 "
            pdb=" N   LYS R 135 "
            pdb=" C   LYS R 135 "
            pdb=" CB  LYS R 135 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.69e-01
  chirality pdb=" CA  THR R 269 "
            pdb=" N   THR R 269 "
            pdb=" C   THR R 269 "
            pdb=" CB  THR R 269 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.70   -0.17 2.00e-01 2.50e+01 7.22e-01
  chirality pdb=" CB  THR R 280 "
            pdb=" CA  THR R 280 "
            pdb=" OG1 THR R 280 "
            pdb=" CG2 THR R 280 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 5.83e-01
  ... (remaining 1379 not shown)

  Planarity restraints: 1518
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R 296 "   -0.014 2.00e-02 2.50e+03   2.74e-02 7.51e+00
        pdb=" C   PHE R 296 "    0.047 2.00e-02 2.50e+03
        pdb=" O   PHE R 296 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   LEU R 297 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 134 "    0.166 9.50e-02 1.11e+02   7.47e-02 3.75e+00
        pdb=" NE  ARG B 134 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 134 "    0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 134 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 134 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R 280 "   -0.009 2.00e-02 2.50e+03   1.81e-02 3.29e+00
        pdb=" C   THR R 280 "    0.031 2.00e-02 2.50e+03
        pdb=" O   THR R 280 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ARG R 281 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1515 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1408
        2.76 -     3.29: 8515
        3.29 -     3.83: 14726
        3.83 -     4.36: 18273
        4.36 -     4.90: 31851
  Nonbonded interactions: 74773
  Sorted by model distance:
  nonbonded pdb=" O   THR B  86 "
            pdb=" OG1 THR B  87 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   VAL B 187 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OG1 THR B 321 "
            pdb=" OD1 ASP B 323 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" O   ASP B 333 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" O   GLY R  37 "
            pdb=" ND2 ASN R  41 "
     model   vdw
     2.351 3.120
  ... (remaining 74768 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.660
  Find NCS groups from input model:        0.080
  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:12.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.097   8888  Z= 0.244
  Angle     :  0.609  10.915  12047  Z= 0.337
  Chirality :  0.042   0.175   1382
  Planarity :  0.004   0.075   1518
  Dihedral  : 14.755  87.663   3155
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 13.73 %
    Favored  : 85.84 %
  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:  1.26 (0.26), residues: 1097
  helix:  2.06 (0.27), residues: 388
  sheet:  0.55 (0.31), residues: 277
  loop : -0.01 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  99 
 HIS   0.003   0.001   HIS R 103 
 PHE   0.009   0.001   PHE R 205 
 TYR   0.013   0.001   TYR E 103 
 ARG   0.010   0.001   ARG B 134 

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 151
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  203 MET cc_start: 0.8417 (ttm) cc_final: 0.8195 (mtp)
REVERT: R  281 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7163 (ttm170)
REVERT: A   29 LYS cc_start: 0.7862 (tttt) cc_final: 0.7484 (tmmt)
REVERT: A  242 ARG cc_start: 0.7933 (mtt180) cc_final: 0.7579 (mtm180)
REVERT: A  333 GLN cc_start: 0.7529 (tp40) cc_final: 0.7121 (tp-100)
REVERT: B  212 ASP cc_start: 0.7579 (t70) cc_final: 0.7157 (t70)
REVERT: B  259 GLN cc_start: 0.8066 (pt0) cc_final: 0.7608 (pt0)
  outliers start: 4
  outliers final: 1
  residues processed: 154
  average time/residue: 1.5691
  time to fit residues: 254.4146
Evaluate side-chains
  141 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 139
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  275 SER
Chi-restraints excluded: chain R residue  281 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.6980
   chunk 83 optimal weight:    8.9990
   chunk 46 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 56 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 52 optimal weight:   20.0000
   chunk 64 optimal weight:    5.9990
   chunk 99 optimal weight:    0.2980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
R 220 GLN
R 301 HIS
A 188 HIS
A 269 ASN
A 306 GLN
A 331 ASN
E   3 GLN
E  77 ASN
G  24 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.158962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.114012 restraints weight = 10805.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 2.36
r_work: 0.3336 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3230 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.1189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8888  Z= 0.171
  Angle     :  0.536   7.914  12047  Z= 0.287
  Chirality :  0.042   0.145   1382
  Planarity :  0.004   0.058   1518
  Dihedral  :  4.938  64.138   1214
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 12.77 %
    Favored  : 84.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.26), residues: 1097
  helix:  2.20 (0.26), residues: 394
  sheet:  0.49 (0.30), residues: 280
  loop :  0.19 (0.32), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 339 
 HIS   0.005   0.001   HIS R 301 
 PHE   0.011   0.001   PHE R  72 
 TYR   0.014   0.001   TYR E 190 
 ARG   0.007   0.000   ARG B 134 

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 159
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
REVERT: R  288 SER cc_start: 0.8904 (OUTLIER) cc_final: 0.8480 (p)
REVERT: A   29 LYS cc_start: 0.8230 (tttt) cc_final: 0.7813 (tmmt)
REVERT: A  251 ASP cc_start: 0.8452 (t70) cc_final: 0.8189 (t0)
REVERT: A  333 GLN cc_start: 0.7844 (tp40) cc_final: 0.7349 (tp-100)
REVERT: B  212 ASP cc_start: 0.7611 (t70) cc_final: 0.7279 (OUTLIER)
REVERT: B  259 GLN cc_start: 0.8098 (pt0) cc_final: 0.7840 (pt0)
REVERT: E   82 GLN cc_start: 0.8467 (mm-40) cc_final: 0.8207 (tp40)
REVERT: E  157 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8273 (mp)
REVERT: E  160 ARG cc_start: 0.7502 (mtm-85) cc_final: 0.6763 (mtm110)
REVERT: E  213 THR cc_start: 0.8031 (OUTLIER) cc_final: 0.7785 (t)
  outliers start: 22
  outliers final: 6
  residues processed: 166
  average time/residue: 1.4601
  time to fit residues: 257.9373
Evaluate side-chains
  152 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 144
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue  236 MET
Chi-restraints excluded: chain R residue  272 VAL
Chi-restraints excluded: chain R residue  288 SER
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain E residue  157 ILE
Chi-restraints excluded: chain E residue  213 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 81 optimal weight:    6.9990
   chunk 82 optimal weight:    2.9990
   chunk 90 optimal weight:   10.0000
   chunk 36 optimal weight:    4.9990
   chunk 94 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 68 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9990
   chunk 79 optimal weight:    6.9990
   chunk 73 optimal weight:    0.7980
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A  52 GLN
A 188 HIS
A 306 GLN
A 331 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.155742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.109935 restraints weight = 11110.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 2.40
r_work: 0.3301 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3194 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.1475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8888  Z= 0.288
  Angle     :  0.574   7.487  12047  Z= 0.300
  Chirality :  0.044   0.141   1382
  Planarity :  0.004   0.050   1518
  Dihedral  :  4.776  56.317   1209
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 13.84 %
    Favored  : 82.94 %
  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:  1.30 (0.26), residues: 1097
  helix:  2.13 (0.26), residues: 393
  sheet:  0.33 (0.30), residues: 278
  loop :  0.14 (0.32), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  82 
 HIS   0.005   0.001   HIS R 103 
 PHE   0.012   0.002   PHE A 196 
 TYR   0.015   0.001   TYR R 107 
 ARG   0.008   0.000   ARG B 134 

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 137
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
REVERT: R   79 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8197 (mm)
REVERT: R  288 SER cc_start: 0.8977 (OUTLIER) cc_final: 0.8581 (p)
REVERT: A   29 LYS cc_start: 0.8240 (tttt) cc_final: 0.7805 (tmmt)
REVERT: A  242 ARG cc_start: 0.8100 (mtt180) cc_final: 0.7858 (mtm180)
REVERT: A  333 GLN cc_start: 0.7910 (tp40) cc_final: 0.7482 (tp-100)
REVERT: B  212 ASP cc_start: 0.7538 (t70) cc_final: 0.7143 (OUTLIER)
REVERT: B  259 GLN cc_start: 0.8066 (pt0) cc_final: 0.7696 (pt0)
REVERT: E  157 ILE cc_start: 0.8615 (mm) cc_final: 0.8252 (mp)
  outliers start: 30
  outliers final: 10
  residues processed: 151
  average time/residue: 1.3824
  time to fit residues: 222.3597
Evaluate side-chains
  138 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 127
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  151 THR
Chi-restraints excluded: chain R residue  183 TYR
Chi-restraints excluded: chain R residue  288 SER
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain E residue  215 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 89 optimal weight:    0.1980
   chunk 90 optimal weight:    0.9990
   chunk 67 optimal weight:    6.9990
   chunk 83 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 104 optimal weight:    0.4980
   chunk 105 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 86 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
R 287 ASN
A  22 ASN
A 269 ASN
A 306 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.159017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.113871 restraints weight = 10868.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 2.38
r_work: 0.3345 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.1748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8888  Z= 0.157
  Angle     :  0.518   7.802  12047  Z= 0.272
  Chirality :  0.042   0.169   1382
  Planarity :  0.004   0.041   1518
  Dihedral  :  4.416  49.318   1209
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 15.45 %
    Favored  : 82.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.26), residues: 1097
  helix:  2.22 (0.26), residues: 394
  sheet:  0.36 (0.29), residues: 287
  loop :  0.10 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 339 
 HIS   0.002   0.001   HIS E  35 
 PHE   0.010   0.001   PHE R  72 
 TYR   0.014   0.001   TYR R 183 
 ARG   0.010   0.000   ARG B 134 

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 142
  time to evaluate  : 1.000 
Fit side-chains
REVERT: R   79 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8208 (mm)
REVERT: R  288 SER cc_start: 0.8931 (OUTLIER) cc_final: 0.8548 (p)
REVERT: A   21 ARG cc_start: 0.8322 (ttm110) cc_final: 0.8064 (ttm110)
REVERT: A   29 LYS cc_start: 0.8194 (tttt) cc_final: 0.7778 (tmmt)
REVERT: A  242 ARG cc_start: 0.8131 (mtt180) cc_final: 0.7893 (mtm180)
REVERT: A  333 GLN cc_start: 0.7922 (tp40) cc_final: 0.7479 (tp-100)
REVERT: B  212 ASP cc_start: 0.7440 (t70) cc_final: 0.7106 (t0)
REVERT: B  259 GLN cc_start: 0.8071 (pt0) cc_final: 0.7830 (pt0)
REVERT: E   18 ARG cc_start: 0.7608 (ttm170) cc_final: 0.7394 (ttt90)
REVERT: E  157 ILE cc_start: 0.8588 (mm) cc_final: 0.8318 (mp)
REVERT: G   21 MET cc_start: 0.6275 (tmm) cc_final: 0.5961 (tpt)
  outliers start: 19
  outliers final: 4
  residues processed: 149
  average time/residue: 1.3653
  time to fit residues: 215.4260
Evaluate side-chains
  142 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 136
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue  288 SER
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  263 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 95 optimal weight:    8.9990
   chunk 10 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 78 optimal weight:    4.9990
   chunk 31 optimal weight:    0.4980
   chunk 101 optimal weight:    9.9990
   chunk 68 optimal weight:    0.0980
   chunk 43 optimal weight:    0.0770
   chunk 14 optimal weight:    0.0870
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.3518

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

Flipped N/Q/H residues before XYZ refinement:
** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 287 ASN
A  22 ASN
A 306 GLN
E 179 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.161613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.117082 restraints weight = 10896.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 2.38
r_work: 0.3377 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3271 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8888  Z= 0.134
  Angle     :  0.487   6.764  12047  Z= 0.258
  Chirality :  0.041   0.180   1382
  Planarity :  0.004   0.036   1518
  Dihedral  :  4.112  42.090   1209
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 16.09 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.26), residues: 1097
  helix:  2.31 (0.26), residues: 402
  sheet:  0.36 (0.29), residues: 280
  loop :  0.08 (0.32), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 339 
 HIS   0.005   0.001   HIS R 301 
 PHE   0.030   0.001   PHE R 175 
 TYR   0.025   0.001   TYR R 183 
 ARG   0.007   0.000   ARG B 134 

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 154
  time to evaluate  : 1.008 
Fit side-chains
REVERT: R   79 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8212 (mm)
REVERT: R  219 ARG cc_start: 0.7620 (mtt-85) cc_final: 0.7356 (mtt-85)
REVERT: A   29 LYS cc_start: 0.8141 (tttt) cc_final: 0.7727 (tmmt)
REVERT: A  242 ARG cc_start: 0.8121 (mtt180) cc_final: 0.7688 (mtm-85)
REVERT: A  251 ASP cc_start: 0.8479 (t70) cc_final: 0.8253 (t0)
REVERT: A  333 GLN cc_start: 0.7922 (tp40) cc_final: 0.7389 (tp-100)
REVERT: B  137 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7122 (ttp-170)
REVERT: B  176 GLN cc_start: 0.8682 (pt0) cc_final: 0.8299 (pt0)
REVERT: B  197 ARG cc_start: 0.7965 (mtm110) cc_final: 0.7371 (mtt90)
REVERT: B  212 ASP cc_start: 0.7441 (t70) cc_final: 0.7083 (t0)
REVERT: B  259 GLN cc_start: 0.8024 (pt0) cc_final: 0.7770 (pt0)
REVERT: E    6 GLU cc_start: 0.8158 (mp0) cc_final: 0.7871 (mp0)
REVERT: E   18 ARG cc_start: 0.7530 (ttm170) cc_final: 0.7318 (ttt90)
REVERT: E  113 GLN cc_start: 0.7308 (mm-40) cc_final: 0.6860 (mp10)
REVERT: E  157 ILE cc_start: 0.8517 (mm) cc_final: 0.8265 (mp)
REVERT: E  178 LEU cc_start: 0.8509 (tp) cc_final: 0.8181 (tp)
REVERT: G   21 MET cc_start: 0.6191 (tmm) cc_final: 0.5910 (tpt)
REVERT: G   47 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7334 (mp0)
REVERT: G   59 ASN cc_start: 0.7847 (t0) cc_final: 0.7643 (t0)
  outliers start: 17
  outliers final: 7
  residues processed: 160
  average time/residue: 1.2515
  time to fit residues: 213.0826
Evaluate side-chains
  147 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 138
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  306 LEU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  263 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0030
   chunk 6 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 85 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 100 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.6792

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

Flipped N/Q/H residues before XYZ refinement:
** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 184 ASN
R 287 ASN
A  22 ASN
A 269 ASN
A 306 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.160940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.116309 restraints weight = 10796.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 2.38
r_work: 0.3379 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3274 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8888  Z= 0.157
  Angle     :  0.508   8.285  12047  Z= 0.266
  Chirality :  0.041   0.161   1382
  Planarity :  0.004   0.036   1518
  Dihedral  :  4.085  41.728   1209
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 17.17 %
    Favored  : 81.33 %
  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:  1.51 (0.26), residues: 1097
  helix:  2.38 (0.26), residues: 402
  sheet:  0.35 (0.29), residues: 283
  loop :  0.19 (0.32), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 339 
 HIS   0.004   0.001   HIS R 301 
 PHE   0.016   0.001   PHE R 175 
 TYR   0.014   0.001   TYR R  30 
 ARG   0.008   0.000   ARG B 134 

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 135
  time to evaluate  : 0.990 
Fit side-chains
REVERT: R   79 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8171 (mm)
REVERT: R  219 ARG cc_start: 0.7606 (mtt-85) cc_final: 0.7289 (mtt-85)
REVERT: A    9 ASP cc_start: 0.8206 (m-30) cc_final: 0.7904 (m-30)
REVERT: A   29 LYS cc_start: 0.8161 (tttt) cc_final: 0.7732 (tmmt)
REVERT: A  242 ARG cc_start: 0.8167 (mtt180) cc_final: 0.7942 (mtm180)
REVERT: A  302 TYR cc_start: 0.8045 (t80) cc_final: 0.7774 (t80)
REVERT: A  333 GLN cc_start: 0.7903 (tp40) cc_final: 0.7456 (tp-100)
REVERT: B  137 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7215 (ttp-170)
REVERT: B  197 ARG cc_start: 0.7968 (mtm110) cc_final: 0.7366 (mtt90)
REVERT: B  212 ASP cc_start: 0.7421 (t70) cc_final: 0.7036 (t0)
REVERT: B  259 GLN cc_start: 0.8030 (pt0) cc_final: 0.7770 (pt0)
REVERT: E   18 ARG cc_start: 0.7568 (ttm170) cc_final: 0.7290 (ttt90)
REVERT: E   95 TYR cc_start: 0.8830 (m-80) cc_final: 0.8584 (m-80)
REVERT: E  157 ILE cc_start: 0.8520 (mm) cc_final: 0.8276 (mp)
REVERT: E  178 LEU cc_start: 0.8507 (tp) cc_final: 0.8160 (tp)
REVERT: G   21 MET cc_start: 0.6244 (tmm) cc_final: 0.5949 (tpt)
REVERT: G   47 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7304 (mp0)
REVERT: G   59 ASN cc_start: 0.7867 (t0) cc_final: 0.7657 (t0)
  outliers start: 14
  outliers final: 6
  residues processed: 140
  average time/residue: 1.3335
  time to fit residues: 198.2220
Evaluate side-chains
  138 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 130
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue  236 MET
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  263 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 80 optimal weight:    0.8980
   chunk 63 optimal weight:    4.9990
   chunk 79 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 96 optimal weight:    9.9990
   chunk 53 optimal weight:    4.9990
   chunk 99 optimal weight:    0.4980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 269 ASN
A 306 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.160674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.116053 restraints weight = 10963.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 2.39
r_work: 0.3374 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3268 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8888  Z= 0.166
  Angle     :  0.509   8.495  12047  Z= 0.267
  Chirality :  0.041   0.176   1382
  Planarity :  0.004   0.038   1518
  Dihedral  :  4.054  40.037   1209
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.70 %
    Favored  : 80.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.26), residues: 1097
  helix:  2.35 (0.26), residues: 404
  sheet:  0.41 (0.29), residues: 288
  loop :  0.17 (0.33), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 301 
 PHE   0.012   0.001   PHE R 175 
 TYR   0.018   0.001   TYR R  30 
 ARG   0.009   0.000   ARG R 217 

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 133
  time to evaluate  : 0.903 
Fit side-chains
REVERT: R   79 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8253 (mm)
REVERT: R  219 ARG cc_start: 0.7631 (mtt-85) cc_final: 0.7310 (mtt-85)
REVERT: A    9 ASP cc_start: 0.8236 (m-30) cc_final: 0.7930 (m-30)
REVERT: A   29 LYS cc_start: 0.8172 (tttt) cc_final: 0.7742 (tmmt)
REVERT: A  242 ARG cc_start: 0.8187 (mtt180) cc_final: 0.7952 (mtm180)
REVERT: A  333 GLN cc_start: 0.7927 (tp40) cc_final: 0.7521 (tp-100)
REVERT: B  212 ASP cc_start: 0.7419 (t70) cc_final: 0.7005 (t0)
REVERT: B  259 GLN cc_start: 0.8059 (pt0) cc_final: 0.7789 (pt0)
REVERT: E  157 ILE cc_start: 0.8505 (mm) cc_final: 0.8271 (mp)
REVERT: E  178 LEU cc_start: 0.8508 (tp) cc_final: 0.8161 (tp)
REVERT: G   21 MET cc_start: 0.6250 (tmm) cc_final: 0.5995 (tpt)
REVERT: G   47 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7362 (mp0)
  outliers start: 17
  outliers final: 9
  residues processed: 142
  average time/residue: 1.4729
  time to fit residues: 221.2625
Evaluate side-chains
  136 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  236 MET
Chi-restraints excluded: chain R residue  306 LEU
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  263 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9990
   chunk 13 optimal weight:    6.9990
   chunk 107 optimal weight:   20.0000
   chunk 51 optimal weight:    8.9990
   chunk 106 optimal weight:    6.9990
   chunk 94 optimal weight:    0.6980
   chunk 84 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 67 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 269 ASN
A 306 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.160471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.115553 restraints weight = 11055.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 2.41
r_work: 0.3369 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3263 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.2334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8888  Z= 0.168
  Angle     :  0.510   6.094  12047  Z= 0.268
  Chirality :  0.041   0.176   1382
  Planarity :  0.004   0.037   1518
  Dihedral  :  4.020  36.640   1209
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.81 %
    Favored  : 80.36 %
  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:  1.52 (0.26), residues: 1097
  helix:  2.36 (0.26), residues: 405
  sheet:  0.40 (0.29), residues: 283
  loop :  0.17 (0.33), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 301 
 PHE   0.011   0.001   PHE R 175 
 TYR   0.025   0.001   TYR R 183 
 ARG   0.009   0.000   ARG B 134 

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 1.021 
Fit side-chains
REVERT: R   79 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8256 (mm)
REVERT: R  189 MET cc_start: 0.8335 (tpp) cc_final: 0.8123 (mmm)
REVERT: R  219 ARG cc_start: 0.7655 (mtt-85) cc_final: 0.7327 (mtt-85)
REVERT: A   29 LYS cc_start: 0.8174 (tttt) cc_final: 0.7735 (tmmt)
REVERT: A  242 ARG cc_start: 0.8188 (mtt180) cc_final: 0.7978 (mtm180)
REVERT: A  302 TYR cc_start: 0.7973 (t80) cc_final: 0.7716 (t80)
REVERT: A  306 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.7375 (mt0)
REVERT: A  333 GLN cc_start: 0.7901 (tp40) cc_final: 0.7433 (tp-100)
REVERT: A  344 ILE cc_start: 0.7869 (mt) cc_final: 0.7531 (mt)
REVERT: B  197 ARG cc_start: 0.8296 (mtt90) cc_final: 0.7986 (mtm110)
REVERT: B  212 ASP cc_start: 0.7432 (t70) cc_final: 0.7074 (t0)
REVERT: B  217 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.6593 (ptt)
REVERT: B  259 GLN cc_start: 0.8063 (pt0) cc_final: 0.7786 (pt0)
REVERT: E   19 LYS cc_start: 0.8539 (tttp) cc_final: 0.8291 (tptt)
REVERT: E   93 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8102 (ttm)
REVERT: E  157 ILE cc_start: 0.8443 (mm) cc_final: 0.8202 (mp)
REVERT: E  178 LEU cc_start: 0.8504 (tp) cc_final: 0.8130 (tp)
REVERT: G   21 MET cc_start: 0.6195 (tmm) cc_final: 0.5895 (tpt)
REVERT: G   47 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7305 (mp0)
  outliers start: 17
  outliers final: 8
  residues processed: 139
  average time/residue: 1.2548
  time to fit residues: 185.7106
Evaluate side-chains
  136 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 124
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  236 MET
Chi-restraints excluded: chain R residue  306 LEU
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  306 GLN
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain E residue   93 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 85 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 73 optimal weight:    0.6980
   chunk 13 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
R 287 ASN
A  22 ASN
A 269 ASN
A 306 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.159685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.114684 restraints weight = 11024.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 2.41
r_work: 0.3361 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.2318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8888  Z= 0.189
  Angle     :  0.522   8.527  12047  Z= 0.274
  Chirality :  0.042   0.178   1382
  Planarity :  0.004   0.037   1518
  Dihedral  :  4.050  36.024   1209
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.81 %
    Favored  : 80.36 %
  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:  1.54 (0.26), residues: 1097
  helix:  2.41 (0.26), residues: 403
  sheet:  0.40 (0.29), residues: 283
  loop :  0.17 (0.32), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 301 
 PHE   0.010   0.001   PHE R  72 
 TYR   0.012   0.001   TYR R 107 
 ARG   0.009   0.000   ARG B 134 

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 1.020 
Fit side-chains
REVERT: R   79 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8279 (mm)
REVERT: R  219 ARG cc_start: 0.7671 (mtt-85) cc_final: 0.7342 (mtt-85)
REVERT: A   29 LYS cc_start: 0.8177 (tttt) cc_final: 0.7747 (tmmt)
REVERT: A  242 ARG cc_start: 0.8174 (mtt180) cc_final: 0.7943 (mtm180)
REVERT: A  269 ASN cc_start: 0.8956 (m-40) cc_final: 0.8750 (m110)
REVERT: A  333 GLN cc_start: 0.7927 (tp40) cc_final: 0.7466 (tp-100)
REVERT: A  344 ILE cc_start: 0.7853 (mt) cc_final: 0.7509 (mt)
REVERT: B  197 ARG cc_start: 0.8315 (mtt90) cc_final: 0.7853 (mtt90)
REVERT: B  212 ASP cc_start: 0.7455 (t70) cc_final: 0.7099 (t0)
REVERT: B  259 GLN cc_start: 0.8051 (pt0) cc_final: 0.7766 (pt0)
REVERT: E  178 LEU cc_start: 0.8511 (tp) cc_final: 0.8143 (tp)
REVERT: G   47 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7338 (mp0)
  outliers start: 17
  outliers final: 8
  residues processed: 130
  average time/residue: 1.3658
  time to fit residues: 188.2125
Evaluate side-chains
  130 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  236 MET
Chi-restraints excluded: chain R residue  306 LEU
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  263 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 0 optimal weight:   30.0000
   chunk 56 optimal weight:    2.9990
   chunk 65 optimal weight:    7.9990
   chunk 97 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9980
   chunk 58 optimal weight:    4.9990
   chunk 84 optimal weight:    4.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
R 287 ASN
A  22 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.159370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.114158 restraints weight = 10987.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 2.41
r_work: 0.3356 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3249 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.2345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8888  Z= 0.192
  Angle     :  0.526   6.594  12047  Z= 0.277
  Chirality :  0.042   0.183   1382
  Planarity :  0.004   0.038   1518
  Dihedral  :  4.070  35.757   1209
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 18.99 %
    Favored  : 79.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.26), residues: 1097
  helix:  2.43 (0.26), residues: 403
  sheet:  0.36 (0.29), residues: 283
  loop :  0.17 (0.32), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 301 
 PHE   0.010   0.001   PHE R  72 
 TYR   0.012   0.001   TYR R 107 
 ARG   0.009   0.000   ARG B 134 

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 123
  time to evaluate  : 0.978 
Fit side-chains
   revert: symmetry clash
REVERT: R   79 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8268 (mm)
REVERT: R  189 MET cc_start: 0.8335 (tpp) cc_final: 0.8119 (mmm)
REVERT: R  219 ARG cc_start: 0.7671 (mtt-85) cc_final: 0.7454 (mtt-85)
REVERT: A   29 LYS cc_start: 0.8171 (tttt) cc_final: 0.7728 (tmmt)
REVERT: A  242 ARG cc_start: 0.8161 (mtt180) cc_final: 0.7925 (mtm180)
REVERT: A  333 GLN cc_start: 0.7911 (tp40) cc_final: 0.7525 (tp-100)
REVERT: A  344 ILE cc_start: 0.7853 (mt) cc_final: 0.7506 (mt)
REVERT: B  153 ASP cc_start: 0.7390 (m-30) cc_final: 0.6804 (p0)
REVERT: B  197 ARG cc_start: 0.8305 (mtt90) cc_final: 0.7970 (mtm110)
REVERT: B  212 ASP cc_start: 0.7440 (t70) cc_final: 0.7047 (t0)
REVERT: B  259 GLN cc_start: 0.8036 (pt0) cc_final: 0.7671 (pt0)
REVERT: B  304 ARG cc_start: 0.8126 (ttm170) cc_final: 0.7547 (ttm170)
REVERT: E   93 MET cc_start: 0.8478 (ttp) cc_final: 0.8057 (ttm)
  outliers start: 10
  outliers final: 8
  residues processed: 129
  average time/residue: 1.4260
  time to fit residues: 194.5160
Evaluate side-chains
  129 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 120
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  236 MET
Chi-restraints excluded: chain R residue  306 LEU
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  263 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 7 optimal weight:    6.9990
   chunk 49 optimal weight:    4.9990
   chunk 4 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9990
   chunk 63 optimal weight:    4.9990
   chunk 108 optimal weight:    6.9990
   chunk 13 optimal weight:    0.8980
   chunk 106 optimal weight:   10.0000
   chunk 97 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 269 ASN
A 306 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.157901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.113136 restraints weight = 10885.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 2.35
r_work: 0.3335 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3228 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.2285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8888  Z= 0.230
  Angle     :  0.545   7.466  12047  Z= 0.286
  Chirality :  0.043   0.180   1382
  Planarity :  0.004   0.038   1518
  Dihedral  :  4.200  37.516   1209
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 18.56 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.26), residues: 1097
  helix:  2.38 (0.26), residues: 404
  sheet:  0.34 (0.29), residues: 285
  loop :  0.17 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 301 
 PHE   0.011   0.002   PHE B 199 
 TYR   0.014   0.001   TYR R 107 
 ARG   0.009   0.001   ARG B 134 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8821.91 seconds
wall clock time: 152 minutes 15.08 seconds (9135.08 seconds total)