Starting phenix.real_space_refine
on Sat Jul 26 12:23:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j0b_61052/07_2025/9j0b_61052.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j0b_61052/07_2025/9j0b_61052.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j0b_61052/07_2025/9j0b_61052.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j0b_61052/07_2025/9j0b_61052.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j0b_61052/07_2025/9j0b_61052.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j0b_61052/07_2025/9j0b_61052.cif"
  }
  resolution = 2.88
  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=   0.071
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      57      5.16       5
     C    5533      2.51       5
     N    1446      2.21       5
     O    1561      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8599
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1620
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1620
          Classifications: {'peptide': 219}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 46}
          Link IDs: {'PTRANS': 2, 'TRANS': 216}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 143
          Unresolved non-hydrogen angles: 176
          Unresolved non-hydrogen dihedrals: 110
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 12, 'ARG:plan': 2, 'ASP:plan': 9}
          Unresolved non-hydrogen planarities: 89
    Chain: "B"
      Number of atoms: 2484
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2484
          Classifications: {'peptide': 337}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 107
          Unresolved non-hydrogen angles: 130
          Unresolved non-hydrogen dihedrals: 84
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 83
    Chain: "G"
      Number of atoms: 373
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 373
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 65
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 32
    Chain: "R"
      Number of atoms: 2313
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 295, 2313
          Classifications: {'peptide': 295}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 10, 'TRANS': 284}
          Unresolved non-hydrogen bonds: 113
          Unresolved non-hydrogen angles: 142
          Unresolved non-hydrogen dihedrals: 95
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 67
    Chain: "S"
      Number of atoms: 1773
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1773
          Classifications: {'peptide': 234}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 10, 'TRANS': 223}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 12
    Chain: "R"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 36
          Unusual residues: {'UPG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.97, per 1000 atoms: 0.69
  Number of scatterers: 8599
  At special positions: 0
  Unit cell: (85.696, 120.64, 120.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      57     16.00
     P       2     15.00
     O    1561      8.00
     N    1446      7.00
     C    5533      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  94 " - pdb=" SG  CYS R 172 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03

  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: 2.33
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2142

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 12 sheets defined
      40.0% alpha, 22.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.808A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.339A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.609A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 232
      removed outlier: 3.877A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.522A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 4.219A  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
    Processing helix  chain 'A' and resid 329 through 351
      removed outlier: 4.160A  pdb=" N   GLN A 333 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 8 through 24
      removed outlier: 3.532A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.547A  pdb=" N   ALA G  35 " --> pdb=" O   SER G  31 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'R' and resid 23 through 48
      removed outlier: 3.772A  pdb=" N   VAL R  27 " --> pdb=" O   GLN R  23 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   LEU R  38 " --> pdb=" O   ILE R  34 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 54 through 82
      removed outlier: 3.506A  pdb=" N   ILE R  58 " --> pdb=" O   LYS R  54 " (cutoff:3.500A)
      Proline residue:  R  75  - end of helix
    Processing helix  chain 'R' and resid 89 through 96
    Processing helix  chain 'R' and resid 96 through 125
    Processing helix  chain 'R' and resid 134 through 154
      removed outlier: 4.464A  pdb=" N   LYS R 139 " --> pdb=" O   VAL R 135 " (cutoff:3.500A)
      removed outlier: 5.414A  pdb=" N   LEU R 140 " --> pdb=" O   SER R 136 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 154 through 159
    Processing helix  chain 'R' and resid 171 through 176
      removed outlier: 3.770A  pdb=" N   LYS R 176 " --> pdb=" O   ILE R 173 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 177 through 215
    Processing helix  chain 'R' and resid 222 through 262
      Proline residue:  R 248  - end of helix
      removed outlier: 4.998A  pdb=" N   ILE R 254 " --> pdb=" O   HIS R 250 " (cutoff:3.500A)
      Proline residue:  R 255  - end of helix
    Processing helix  chain 'R' and resid 266 through 291
      removed outlier: 3.885A  pdb=" N   VAL R 288 " --> pdb=" O   SER R 284 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   CYS R 289 " --> pdb=" O   ALA R 285 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 292 through 294
      No H-bonds generated for 'chain 'R' and resid 292 through 294'
    Processing helix  chain 'R' and resid 299 through 308
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 4.100A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.563A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 3.683A  pdb=" N   ASP S 223 " --> pdb=" O   GLU S 220 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 220 through 224'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.269A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.367A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 5.855A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.493A  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 52
      removed outlier: 3.505A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.654A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.521A  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: 4.269A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 152
      removed outlier: 3.849A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.014A  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: 6.982A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.227A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.843A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.569A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 5.866A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12
      removed outlier: 5.910A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 4.849A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 142
    Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148
      removed outlier: 6.513A  pdb=" N   LEU S 174 " --> pdb=" O   TYR S 190 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   TYR S 190 " --> pdb=" O   LEU S 174 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)

    469 hydrogen bonds defined for protein.
    1302 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: 2.69

  Time building geometry restraints manager: 2.71 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2710
        1.34 -     1.46: 1930
        1.46 -     1.58: 4064
        1.58 -     1.69: 4
        1.69 -     1.81: 82
  Bond restraints: 8790
  Sorted by residual:
  bond pdb=" C4  UPG R 401 "
       pdb=" C5  UPG R 401 "
    ideal  model  delta    sigma   weight residual
    1.441  1.389  0.052 2.00e-02 2.50e+03 6.79e+00
  bond pdb=" C4  UPG R 401 "
       pdb=" N3  UPG R 401 "
    ideal  model  delta    sigma   weight residual
    1.388  1.337  0.051 2.00e-02 2.50e+03 6.45e+00
  bond pdb=" C5  UPG R 401 "
       pdb=" C6  UPG R 401 "
    ideal  model  delta    sigma   weight residual
    1.342  1.388 -0.046 2.00e-02 2.50e+03 5.33e+00
  bond pdb=" O3B UPG R 401 "
       pdb=" PB  UPG R 401 "
    ideal  model  delta    sigma   weight residual
    1.652  1.611  0.041 2.00e-02 2.50e+03 4.18e+00
  bond pdb=" O3A UPG R 401 "
       pdb=" PB  UPG R 401 "
    ideal  model  delta    sigma   weight residual
    1.648  1.608  0.040 2.00e-02 2.50e+03 4.06e+00
  ... (remaining 8785 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 11724
        1.52 -     3.05: 186
        3.05 -     4.57: 27
        4.57 -     6.10: 11
        6.10 -     7.62: 5
  Bond angle restraints: 11953
  Sorted by residual:
  angle pdb=" N   ILE R 132 "
        pdb=" CA  ILE R 132 "
        pdb=" C   ILE R 132 "
      ideal   model   delta    sigma   weight residual
     110.21  103.46    6.75 1.13e+00 7.83e-01 3.57e+01
  angle pdb=" N   SER R 134 "
        pdb=" CA  SER R 134 "
        pdb=" C   SER R 134 "
      ideal   model   delta    sigma   weight residual
     110.50  105.24    5.26 1.41e+00 5.03e-01 1.39e+01
  angle pdb=" CA  ILE R 132 "
        pdb=" C   ILE R 132 "
        pdb=" N   GLN R 133 "
      ideal   model   delta    sigma   weight residual
     115.26  118.87   -3.61 1.11e+00 8.12e-01 1.06e+01
  angle pdb=" C   ILE R 132 "
        pdb=" N   GLN R 133 "
        pdb=" CA  GLN R 133 "
      ideal   model   delta    sigma   weight residual
     122.19  117.90    4.29 1.41e+00 5.03e-01 9.27e+00
  angle pdb=" N   THR R 129 "
        pdb=" CA  THR R 129 "
        pdb=" C   THR R 129 "
      ideal   model   delta    sigma   weight residual
     111.28  114.45   -3.17 1.09e+00 8.42e-01 8.45e+00
  ... (remaining 11948 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.73: 4693
       16.73 -    33.46: 386
       33.46 -    50.19: 83
       50.19 -    66.91: 12
       66.91 -    83.64: 6
  Dihedral angle restraints: 5180
    sinusoidal: 1861
      harmonic: 3319
  Sorted by residual:
  dihedral pdb=" CA  TRP B  82 "
           pdb=" C   TRP B  82 "
           pdb=" N   ASP B  83 "
           pdb=" CA  ASP B  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.29   19.71     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  HIS R 250 "
           pdb=" C   HIS R 250 "
           pdb=" N   ILE R 251 "
           pdb=" CA  ILE R 251 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.90   17.10     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CA  ARG S 191 "
           pdb=" C   ARG S 191 "
           pdb=" N   MET S 192 "
           pdb=" CA  MET S 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.49   16.51     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 5177 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1061
       0.044 -    0.087: 249
       0.087 -    0.131: 77
       0.131 -    0.175: 2
       0.175 -    0.218: 3
  Chirality restraints: 1392
  Sorted by residual:
  chirality pdb=" C1' UPG R 401 "
            pdb=" C2' UPG R 401 "
            pdb=" O3B UPG R 401 "
            pdb=" O5' UPG R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.23   -2.45    0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CA  ILE R 132 "
            pdb=" N   ILE R 132 "
            pdb=" C   ILE R 132 "
            pdb=" CB  ILE R 132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.65e-01
  chirality pdb=" CB  ILE A 265 "
            pdb=" CA  ILE A 265 "
            pdb=" CG1 ILE A 265 "
            pdb=" CG2 ILE A 265 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.70e-01
  ... (remaining 1389 not shown)

  Planarity restraints: 1490
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 132 "    0.012 2.00e-02 2.50e+03   2.45e-02 6.01e+00
        pdb=" C   ILE R 132 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   ILE R 132 "    0.016 2.00e-02 2.50e+03
        pdb=" N   GLN R 133 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 191 "   -0.011 2.00e-02 2.50e+03   1.25e-02 2.73e+00
        pdb=" CG  PHE R 191 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 191 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 191 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 191 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 191 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 191 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.022 5.00e-02 4.00e+02   3.37e-02 1.82e+00
        pdb=" N   PRO B 236 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.019 5.00e-02 4.00e+02
  ... (remaining 1487 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 292
        2.72 -     3.26: 8547
        3.26 -     3.81: 15013
        3.81 -     4.35: 18611
        4.35 -     4.90: 31793
  Nonbonded interactions: 74256
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 175 "
     model   vdw
     2.171 3.040
  nonbonded pdb=" OD1 ASN R 188 "
            pdb=" OG1 THR R 257 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OH  TYR A 230 "
            pdb=" O   SER A 281 "
     model   vdw
     2.266 3.040
  ... (remaining 74251 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.560
  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:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     25.220
  Find NCS groups from input model:        0.120
  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:11.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
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   0.052   8792  Z= 0.141
  Angle     :  0.516   7.619  11957  Z= 0.281
  Chirality :  0.041   0.218   1392
  Planarity :  0.003   0.034   1490
  Dihedral  : 13.126  83.644   3032
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.58 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.26), residues: 1125
  helix:  2.15 (0.26), residues: 410
  sheet:  0.34 (0.29), residues: 299
  loop :  0.07 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.029   0.001   PHE R 191 
 TYR   0.010   0.001   TYR S 190 
 ARG   0.004   0.000   ARG S  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12644 (  469)
  hydrogen bonds       : angle       5.42834 ( 1302)
  SS BOND              : bond        0.00295 (    2)
  SS BOND              : angle       0.87800 (    4)
  covalent geometry    : bond        0.00267 ( 8790)
  covalent geometry    : angle       0.51625 (11953)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 203
  time to evaluate  : 0.953 
Fit side-chains
REVERT: R  210 THR cc_start: 0.8345 (m) cc_final: 0.8139 (m)
REVERT: S  204 SER cc_start: 0.8184 (p) cc_final: 0.7950 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 204
  average time/residue: 1.0792
  time to fit residues: 238.4676
Evaluate side-chains
  137 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.8980
   chunk 84 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 87 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 52 optimal weight:    3.9990
   chunk 64 optimal weight:    0.4980
   chunk 100 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN
B 125 ASN
B 293 ASN
S  82 GLN
S 194 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.185434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.151601 restraints weight = 10393.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3850 rms_B_bonded: 1.89
r_work: 0.3686 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3541 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.1887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8792  Z= 0.158
  Angle     :  0.572  17.028  11957  Z= 0.293
  Chirality :  0.043   0.178   1392
  Planarity :  0.004   0.032   1490
  Dihedral  :  6.192  68.853   1273
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.38 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 13.38 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.25), residues: 1125
  helix:  2.11 (0.26), residues: 404
  sheet:  0.23 (0.28), residues: 289
  loop :  0.07 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 211 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.024   0.001   PHE R 191 
 TYR   0.018   0.001   TYR S 190 
 ARG   0.006   0.001   ARG R 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03785 (  469)
  hydrogen bonds       : angle       4.71540 ( 1302)
  SS BOND              : bond        0.00622 (    2)
  SS BOND              : angle       1.03788 (    4)
  covalent geometry    : bond        0.00355 ( 8790)
  covalent geometry    : angle       0.57168 (11953)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 151
  time to evaluate  : 1.067 
Fit side-chains
   revert: symmetry clash
REVERT: B  254 ASP cc_start: 0.7493 (t0) cc_final: 0.7285 (t0)
REVERT: R   46 ILE cc_start: 0.8446 (mm) cc_final: 0.8135 (mp)
REVERT: R  236 PHE cc_start: 0.7227 (m-10) cc_final: 0.5914 (t80)
REVERT: S  204 SER cc_start: 0.8080 (p) cc_final: 0.7836 (t)
  outliers start: 21
  outliers final: 11
  residues processed: 160
  average time/residue: 1.0245
  time to fit residues: 176.7459
Evaluate side-chains
  148 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 137
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  293 ASN
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  224 SER
Chi-restraints excluded: chain S residue  138 ILE
Chi-restraints excluded: chain S residue  162 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0980
   chunk 86 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0370
   chunk 54 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 44 optimal weight:    0.5980
   overall best weight:    0.4658

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

Flipped N/Q/H residues before XYZ refinement:
A 241 ASN
B 125 ASN
B 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.185850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.148929 restraints weight = 10595.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3814 rms_B_bonded: 1.94
r_work: 0.3691 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3547 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8792  Z= 0.116
  Angle     :  0.505  11.537  11957  Z= 0.264
  Chirality :  0.041   0.194   1392
  Planarity :  0.003   0.032   1490
  Dihedral  :  6.011  68.301   1273
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.76 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 16.26 %
    Favored  : 81.08 %
  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:  1.22 (0.25), residues: 1125
  helix:  2.21 (0.26), residues: 404
  sheet:  0.07 (0.28), residues: 293
  loop :  0.11 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 211 
 HIS   0.002   0.001   HIS B 142 
 PHE   0.017   0.001   PHE R 195 
 TYR   0.016   0.001   TYR S 190 
 ARG   0.004   0.000   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03477 (  469)
  hydrogen bonds       : angle       4.50527 ( 1302)
  SS BOND              : bond        0.00375 (    2)
  SS BOND              : angle       0.82177 (    4)
  covalent geometry    : bond        0.00253 ( 8790)
  covalent geometry    : angle       0.50501 (11953)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 147
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  247 MET cc_start: 0.8258 (mtp) cc_final: 0.8017 (mtp)
REVERT: R   46 ILE cc_start: 0.8504 (mm) cc_final: 0.8200 (mp)
REVERT: R   93 VAL cc_start: 0.7691 (OUTLIER) cc_final: 0.7476 (p)
REVERT: R  214 PHE cc_start: 0.7640 (m-10) cc_final: 0.7347 (m-10)
REVERT: R  236 PHE cc_start: 0.7269 (m-10) cc_final: 0.6002 (t80)
REVERT: S  193 SER cc_start: 0.7738 (OUTLIER) cc_final: 0.7528 (p)
REVERT: S  204 SER cc_start: 0.8128 (p) cc_final: 0.7855 (t)
  outliers start: 23
  outliers final: 11
  residues processed: 161
  average time/residue: 1.0058
  time to fit residues: 174.5153
Evaluate side-chains
  144 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 131
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain S residue   76 LYS
Chi-restraints excluded: chain S residue  138 ILE
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain S residue  193 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 47 optimal weight:    0.0770
   chunk 16 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 90 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 106 optimal weight:    2.9990
   overall best weight:    1.4146

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

Flipped N/Q/H residues before XYZ refinement:
A 241 ASN
B 125 ASN
B 156 GLN
B 293 ASN
S 194 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.184783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.149022 restraints weight = 10065.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3700 rms_B_bonded: 1.96
r_work: 0.3574 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3433 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.2863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   8792  Z= 0.217
  Angle     :  0.585  12.678  11957  Z= 0.306
  Chirality :  0.045   0.218   1392
  Planarity :  0.004   0.029   1490
  Dihedral  :  6.279  65.904   1273
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.47 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 16.72 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.25), residues: 1125
  helix:  1.83 (0.26), residues: 410
  sheet: -0.11 (0.28), residues: 293
  loop : -0.22 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  82 
 HIS   0.004   0.001   HIS R 250 
 PHE   0.023   0.002   PHE R 191 
 TYR   0.017   0.002   TYR R 121 
 ARG   0.005   0.001   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04053 (  469)
  hydrogen bonds       : angle       4.75447 ( 1302)
  SS BOND              : bond        0.00670 (    2)
  SS BOND              : angle       1.01872 (    4)
  covalent geometry    : bond        0.00509 ( 8790)
  covalent geometry    : angle       0.58476 (11953)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 148
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
REVERT: A  318 GLU cc_start: 0.8276 (tp30) cc_final: 0.7992 (tt0)
REVERT: B  134 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7332 (ppt170)
REVERT: B  189 SER cc_start: 0.9204 (p) cc_final: 0.8999 (t)
REVERT: B  337 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8172 (mttm)
REVERT: S   98 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7206 (ttm170)
REVERT: S  204 SER cc_start: 0.8299 (p) cc_final: 0.7999 (t)
  outliers start: 39
  outliers final: 17
  residues processed: 172
  average time/residue: 0.9805
  time to fit residues: 182.2446
Evaluate side-chains
  146 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 126
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  337 LYS
Chi-restraints excluded: chain R residue   54 LYS
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  270 LYS
Chi-restraints excluded: chain S residue   18 ARG
Chi-restraints excluded: chain S residue   64 VAL
Chi-restraints excluded: chain S residue   76 LYS
Chi-restraints excluded: chain S residue   98 ARG
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  138 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 93 optimal weight:    0.4980
   chunk 11 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 8 optimal weight:    0.4980
   chunk 59 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 79 optimal weight:    7.9990
   chunk 99 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B  16 ASN
B 125 ASN
B 293 ASN
R 260 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.188245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.153554 restraints weight = 10038.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3755 rms_B_bonded: 1.95
r_work: 0.3636 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3494 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.2958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8792  Z= 0.126
  Angle     :  0.515  11.005  11957  Z= 0.270
  Chirality :  0.042   0.221   1392
  Planarity :  0.003   0.040   1490
  Dihedral  :  5.850  68.276   1273
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.76 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 18.34 %
    Favored  : 77.97 %
  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:  0.81 (0.25), residues: 1125
  helix:  1.87 (0.26), residues: 417
  sheet: -0.16 (0.28), residues: 287
  loop : -0.21 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 211 
 HIS   0.002   0.001   HIS R 250 
 PHE   0.018   0.001   PHE R 195 
 TYR   0.015   0.001   TYR R 121 
 ARG   0.009   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03536 (  469)
  hydrogen bonds       : angle       4.57378 ( 1302)
  SS BOND              : bond        0.00333 (    2)
  SS BOND              : angle       0.84723 (    4)
  covalent geometry    : bond        0.00285 ( 8790)
  covalent geometry    : angle       0.51450 (11953)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 142
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
REVERT: A  209 LYS cc_start: 0.8313 (pttm) cc_final: 0.8070 (tmmt)
REVERT: A  318 GLU cc_start: 0.8178 (tp30) cc_final: 0.7875 (tt0)
REVERT: B  189 SER cc_start: 0.9191 (p) cc_final: 0.8963 (t)
REVERT: B  337 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8208 (mttm)
REVERT: R   46 ILE cc_start: 0.8604 (mm) cc_final: 0.8305 (mp)
REVERT: R  214 PHE cc_start: 0.7697 (m-10) cc_final: 0.7447 (m-10)
REVERT: S   98 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7270 (ttm170)
REVERT: S  204 SER cc_start: 0.8304 (p) cc_final: 0.7960 (t)
  outliers start: 32
  outliers final: 19
  residues processed: 165
  average time/residue: 0.9198
  time to fit residues: 164.8308
Evaluate side-chains
  152 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  337 LYS
Chi-restraints excluded: chain R residue   65 ILE
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  241 VAL
Chi-restraints excluded: chain R residue  244 VAL
Chi-restraints excluded: chain R residue  270 LYS
Chi-restraints excluded: chain S residue   18 ARG
Chi-restraints excluded: chain S residue   76 LYS
Chi-restraints excluded: chain S residue   98 ARG
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  138 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 101 optimal weight:    0.4980
   chunk 79 optimal weight:    8.9990
   chunk 90 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 14 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN
B 293 ASN
S 194 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.178123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.139205 restraints weight = 10393.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.3727 rms_B_bonded: 2.01
r_work: 0.3607 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3464 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.3251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   8792  Z= 0.226
  Angle     :  0.592  12.889  11957  Z= 0.308
  Chirality :  0.045   0.233   1392
  Planarity :  0.004   0.030   1490
  Dihedral  :  6.163  68.499   1273
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.91 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 18.92 %
    Favored  : 76.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.25), residues: 1125
  helix:  1.66 (0.26), residues: 417
  sheet: -0.24 (0.28), residues: 288
  loop : -0.31 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP R 128 
 HIS   0.004   0.001   HIS R 250 
 PHE   0.024   0.002   PHE A 274 
 TYR   0.014   0.002   TYR R 121 
 ARG   0.009   0.001   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04042 (  469)
  hydrogen bonds       : angle       4.80686 ( 1302)
  SS BOND              : bond        0.00662 (    2)
  SS BOND              : angle       1.03003 (    4)
  covalent geometry    : bond        0.00538 ( 8790)
  covalent geometry    : angle       0.59196 (11953)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 131
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
REVERT: A  318 GLU cc_start: 0.8227 (tp30) cc_final: 0.7987 (tt0)
REVERT: B  134 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7359 (ppt170)
REVERT: R   29 TYR cc_start: 0.8101 (OUTLIER) cc_final: 0.7476 (m-80)
REVERT: S   19 LYS cc_start: 0.8034 (tttm) cc_final: 0.7717 (tttp)
REVERT: S   98 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7134 (ttm170)
REVERT: S  204 SER cc_start: 0.8385 (p) cc_final: 0.8055 (t)
  outliers start: 37
  outliers final: 20
  residues processed: 155
  average time/residue: 0.9926
  time to fit residues: 166.0858
Evaluate side-chains
  145 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 122
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  293 ASN
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain R residue   29 TYR
Chi-restraints excluded: chain R residue   65 ILE
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  241 VAL
Chi-restraints excluded: chain R residue  244 VAL
Chi-restraints excluded: chain R residue  270 LYS
Chi-restraints excluded: chain S residue   18 ARG
Chi-restraints excluded: chain S residue   76 LYS
Chi-restraints excluded: chain S residue   98 ARG
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  138 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 109 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 47 optimal weight:    0.3980
   chunk 89 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN
B 293 ASN
S 194 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.185745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.150522 restraints weight = 10128.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3727 rms_B_bonded: 1.95
r_work: 0.3608 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3466 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.3286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8792  Z= 0.169
  Angle     :  0.550  11.099  11957  Z= 0.288
  Chirality :  0.043   0.245   1392
  Planarity :  0.004   0.029   1490
  Dihedral  :  5.952  71.243   1273
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 19.26 %
    Favored  : 76.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.25), residues: 1125
  helix:  1.81 (0.26), residues: 411
  sheet: -0.28 (0.28), residues: 287
  loop : -0.34 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 211 
 HIS   0.003   0.001   HIS R 250 
 PHE   0.028   0.002   PHE A 274 
 TYR   0.015   0.002   TYR S 190 
 ARG   0.007   0.000   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03791 (  469)
  hydrogen bonds       : angle       4.69827 ( 1302)
  SS BOND              : bond        0.00517 (    2)
  SS BOND              : angle       0.93446 (    4)
  covalent geometry    : bond        0.00393 ( 8790)
  covalent geometry    : angle       0.54953 (11953)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 133
  time to evaluate  : 0.951 
Fit side-chains
   revert: symmetry clash
REVERT: A  209 LYS cc_start: 0.8391 (pttm) cc_final: 0.8145 (tmmt)
REVERT: A  318 GLU cc_start: 0.8114 (tp30) cc_final: 0.7858 (tt0)
REVERT: B  134 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7340 (ppt170)
REVERT: R   29 TYR cc_start: 0.7984 (OUTLIER) cc_final: 0.7277 (m-80)
REVERT: R  214 PHE cc_start: 0.7771 (m-10) cc_final: 0.7520 (m-10)
REVERT: S   98 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7200 (ttm170)
REVERT: S  204 SER cc_start: 0.8332 (p) cc_final: 0.7981 (t)
  outliers start: 34
  outliers final: 19
  residues processed: 154
  average time/residue: 1.0367
  time to fit residues: 172.6504
Evaluate side-chains
  145 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain R residue   29 TYR
Chi-restraints excluded: chain R residue   65 ILE
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  241 VAL
Chi-restraints excluded: chain R residue  244 VAL
Chi-restraints excluded: chain R residue  270 LYS
Chi-restraints excluded: chain S residue   18 ARG
Chi-restraints excluded: chain S residue   98 ARG
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  138 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 87 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   chunk 103 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0870
   chunk 1 optimal weight:    0.7980
   chunk 5 optimal weight:    7.9990
   chunk 80 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   overall best weight:    1.1562

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

Flipped N/Q/H residues before XYZ refinement:
B 293 ASN
S 194 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.179551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.140802 restraints weight = 10533.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3743 rms_B_bonded: 2.03
r_work: 0.3625 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3483 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.3363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8792  Z= 0.185
  Angle     :  0.560  10.234  11957  Z= 0.293
  Chirality :  0.043   0.251   1392
  Planarity :  0.004   0.029   1490
  Dihedral  :  5.921  71.535   1273
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 19.84 %
    Favored  : 76.47 %
  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:  0.60 (0.25), residues: 1125
  helix:  1.78 (0.26), residues: 411
  sheet: -0.30 (0.28), residues: 287
  loop : -0.35 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 211 
 HIS   0.003   0.001   HIS R 250 
 PHE   0.025   0.002   PHE A 274 
 TYR   0.017   0.002   TYR S 190 
 ARG   0.008   0.001   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03812 (  469)
  hydrogen bonds       : angle       4.70824 ( 1302)
  SS BOND              : bond        0.00568 (    2)
  SS BOND              : angle       0.97717 (    4)
  covalent geometry    : bond        0.00434 ( 8790)
  covalent geometry    : angle       0.55968 (11953)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 126
  time to evaluate  : 0.954 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  209 LYS cc_start: 0.8390 (pttm) cc_final: 0.8143 (tmmt)
REVERT: A  318 GLU cc_start: 0.8125 (tp30) cc_final: 0.7867 (tt0)
REVERT: B  134 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7342 (ppt170)
REVERT: B  234 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.9078 (m-80)
REVERT: R   29 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7359 (m-80)
REVERT: R  214 PHE cc_start: 0.7748 (m-10) cc_final: 0.7446 (m-10)
REVERT: S   98 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7157 (ttm170)
REVERT: S  204 SER cc_start: 0.8359 (p) cc_final: 0.8014 (t)
  outliers start: 32
  outliers final: 22
  residues processed: 147
  average time/residue: 0.9895
  time to fit residues: 157.2513
Evaluate side-chains
  151 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 125
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  293 ASN
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain R residue   29 TYR
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue   65 ILE
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  241 VAL
Chi-restraints excluded: chain R residue  244 VAL
Chi-restraints excluded: chain R residue  270 LYS
Chi-restraints excluded: chain S residue   18 ARG
Chi-restraints excluded: chain S residue   64 VAL
Chi-restraints excluded: chain S residue   98 ARG
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  138 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 99 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 104 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 79 optimal weight:    8.9990
   chunk 48 optimal weight:    0.8980
   chunk 103 optimal weight:    0.7980
   chunk 94 optimal weight:    0.0170
   chunk 61 optimal weight:   10.0000
   chunk 51 optimal weight:    6.9990
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
B 293 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.187071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.152325 restraints weight = 10146.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3781 rms_B_bonded: 1.95
r_work: 0.3660 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3517 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.3369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8792  Z= 0.128
  Angle     :  0.540  14.238  11957  Z= 0.279
  Chirality :  0.042   0.243   1392
  Planarity :  0.003   0.029   1490
  Dihedral  :  5.741  73.327   1273
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 20.42 %
    Favored  : 76.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.26), residues: 1125
  helix:  1.91 (0.26), residues: 412
  sheet: -0.29 (0.29), residues: 294
  loop : -0.27 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 211 
 HIS   0.004   0.001   HIS A 244 
 PHE   0.023   0.001   PHE A 274 
 TYR   0.017   0.001   TYR S 190 
 ARG   0.007   0.000   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03527 (  469)
  hydrogen bonds       : angle       4.58474 ( 1302)
  SS BOND              : bond        0.00404 (    2)
  SS BOND              : angle       0.84379 (    4)
  covalent geometry    : bond        0.00291 ( 8790)
  covalent geometry    : angle       0.54006 (11953)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 137
  time to evaluate  : 1.051 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  318 GLU cc_start: 0.8146 (tp30) cc_final: 0.7876 (tt0)
REVERT: B  134 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7345 (ppt170)
REVERT: B  234 PHE cc_start: 0.9291 (OUTLIER) cc_final: 0.9067 (m-80)
REVERT: R   46 ILE cc_start: 0.8674 (mm) cc_final: 0.8369 (mp)
REVERT: R  214 PHE cc_start: 0.7732 (m-10) cc_final: 0.7429 (m-10)
REVERT: S   21 SER cc_start: 0.8490 (t) cc_final: 0.8231 (m)
REVERT: S   98 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7205 (ttm170)
REVERT: S  204 SER cc_start: 0.8377 (p) cc_final: 0.8025 (t)
  outliers start: 25
  outliers final: 19
  residues processed: 155
  average time/residue: 0.9889
  time to fit residues: 165.7554
Evaluate side-chains
  153 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 131
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  293 ASN
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  241 VAL
Chi-restraints excluded: chain R residue  244 VAL
Chi-restraints excluded: chain S residue   18 ARG
Chi-restraints excluded: chain S residue   98 ARG
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  138 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 105 optimal weight:    0.9990
   chunk 106 optimal weight:    5.9990
   chunk 37 optimal weight:    0.4980
   chunk 72 optimal weight:    0.4980
   chunk 66 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   chunk 103 optimal weight:    0.4980
   chunk 9 optimal weight:    0.5980
   chunk 68 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0970
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
B 293 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.188591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.154314 restraints weight = 10044.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3810 rms_B_bonded: 1.92
r_work: 0.3682 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3541 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.3398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8792  Z= 0.116
  Angle     :  0.533  13.487  11957  Z= 0.274
  Chirality :  0.042   0.263   1392
  Planarity :  0.003   0.030   1490
  Dihedral  :  5.628  73.986   1273
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 20.99 %
    Favored  : 76.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.26), residues: 1125
  helix:  2.02 (0.26), residues: 411
  sheet: -0.27 (0.29), residues: 300
  loop : -0.19 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 211 
 HIS   0.004   0.001   HIS A 244 
 PHE   0.022   0.001   PHE A 274 
 TYR   0.018   0.001   TYR S 190 
 ARG   0.008   0.000   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03403 (  469)
  hydrogen bonds       : angle       4.50229 ( 1302)
  SS BOND              : bond        0.00346 (    2)
  SS BOND              : angle       0.81570 (    4)
  covalent geometry    : bond        0.00256 ( 8790)
  covalent geometry    : angle       0.53253 (11953)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 138
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 ARG cc_start: 0.8071 (mtm110) cc_final: 0.7851 (mtp180)
REVERT: A  318 GLU cc_start: 0.8113 (tp30) cc_final: 0.7850 (tt0)
REVERT: B  134 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7315 (ppt170)
REVERT: B  234 PHE cc_start: 0.9279 (OUTLIER) cc_final: 0.9053 (m-80)
REVERT: R   46 ILE cc_start: 0.8647 (mm) cc_final: 0.8351 (mp)
REVERT: R  140 LEU cc_start: 0.8059 (tt) cc_final: 0.7656 (tm)
REVERT: R  214 PHE cc_start: 0.7677 (m-10) cc_final: 0.7380 (m-10)
REVERT: S   18 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7907 (ttm110)
REVERT: S   21 SER cc_start: 0.8385 (t) cc_final: 0.8134 (m)
REVERT: S   98 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7197 (ttm170)
REVERT: S  204 SER cc_start: 0.8344 (p) cc_final: 0.8019 (t)
  outliers start: 24
  outliers final: 17
  residues processed: 156
  average time/residue: 0.9172
  time to fit residues: 155.2863
Evaluate side-chains
  154 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 133
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  243 MET
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  241 VAL
Chi-restraints excluded: chain R residue  244 VAL
Chi-restraints excluded: chain S residue   18 ARG
Chi-restraints excluded: chain S residue   98 ARG
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  138 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 83 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   chunk 100 optimal weight:    3.9990
   chunk 65 optimal weight:    0.0370
   chunk 110 optimal weight:    0.3980
   chunk 76 optimal weight:    0.9980
   chunk 59 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.4858

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

Flipped N/Q/H residues before XYZ refinement:
B 293 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.188673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.154391 restraints weight = 10168.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3814 rms_B_bonded: 1.94
r_work: 0.3690 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3545 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.3434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8792  Z= 0.118
  Angle     :  0.533  12.887  11957  Z= 0.274
  Chirality :  0.042   0.265   1392
  Planarity :  0.003   0.049   1490
  Dihedral  :  5.534  74.322   1273
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 21.57 %
    Favored  : 75.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.26), residues: 1125
  helix:  2.04 (0.26), residues: 414
  sheet: -0.21 (0.29), residues: 299
  loop : -0.20 (0.32), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 211 
 HIS   0.002   0.001   HIS B 142 
 PHE   0.021   0.001   PHE A 274 
 TYR   0.016   0.001   TYR S 190 
 ARG   0.015   0.001   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03396 (  469)
  hydrogen bonds       : angle       4.45745 ( 1302)
  SS BOND              : bond        0.00347 (    2)
  SS BOND              : angle       0.81809 (    4)
  covalent geometry    : bond        0.00264 ( 8790)
  covalent geometry    : angle       0.53322 (11953)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6981.60 seconds
wall clock time: 120 minutes 24.71 seconds (7224.71 seconds total)