Starting phenix.real_space_refine
on Wed Mar 12 04:13:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x9b_33070/03_2025/7x9b_33070.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x9b_33070/03_2025/7x9b_33070.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x9b_33070/03_2025/7x9b_33070.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x9b_33070/03_2025/7x9b_33070.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x9b_33070/03_2025/7x9b_33070.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x9b_33070/03_2025/7x9b_33070.cif"
  }
  resolution = 3.4
  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=   0.003 sd=   0.053
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      45      5.16       5
     C    4634      2.51       5
     N    1242      2.21       5
     O    1321      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7242
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1684
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1684
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 74
          Unresolved non-hydrogen angles: 88
          Unresolved non-hydrogen dihedrals: 60
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 39
    Chain: "B"
      Number of atoms: 2523
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2523
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 72
          Unresolved non-hydrogen dihedrals: 50
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 45
    Chain: "C"
      Number of atoms: 391
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 391
          Classifications: {'peptide': 54}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "R"
      Number of atoms: 2362
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 302, 2362
          Classifications: {'peptide': 302}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 10, 'TRANS': 291}
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 33
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4}
          Unresolved non-hydrogen planarities: 20
    Chain: "P"
      Number of atoms: 282
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 282
          Classifications: {'peptide': 36}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 31}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 13
  Time building chain proxies: 5.12, per 1000 atoms: 0.71
  Number of scatterers: 7242
  At special positions: 0
  Unit cell: (111.52, 125.46, 84.46, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      45     16.00
     O    1321      8.00
     N    1242      7.00
     C    4634      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 123 " - pdb=" SG  CYS R 203 " 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: 1.94
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1794

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 8 sheets defined
      44.6% alpha, 12.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 33
      removed outlier: 4.226A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   GLU A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 50
      removed outlier: 3.763A  pdb=" N   VAL A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.461A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 232
      removed outlier: 3.609A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 255
      removed outlier: 3.623A  pdb=" N   LEU A 249 " --> pdb=" O   ALA A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 280
      removed outlier: 3.636A  pdb=" N   GLU A 275 " --> pdb=" O   LYS A 271 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 4.048A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 308
      removed outlier: 3.740A  pdb=" N   PHE A 307 " --> pdb=" O   ILE A 303 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLU A 308 " --> pdb=" O   GLN A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 349
      removed outlier: 3.796A  pdb=" N   ILE A 344 " --> pdb=" O   THR A 340 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LYS A 345 " --> pdb=" O   ASP A 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 25
      removed outlier: 4.420A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 37
      removed outlier: 3.703A  pdb=" N   ASN B  36 " --> pdb=" O   ILE B  33 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ILE B  37 " --> pdb=" O   THR B  34 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 33 through 37'
    Processing helix  chain 'C' and resid 10 through 24
      removed outlier: 4.291A  pdb=" N   LYS C  14 " --> pdb=" O   ALA C  10 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   LEU C  15 " --> pdb=" O   GLN C  11 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.611A  pdb=" N   ASP C  36 " --> pdb=" O   LYS C  32 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 46 through 78
    Processing helix  chain 'R' and resid 83 through 104
      removed outlier: 4.285A  pdb=" N   LEU R 104 " --> pdb=" O   ASN R 100 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 104 through 112
      removed outlier: 3.882A  pdb=" N   TYR R 110 " --> pdb=" O   PHE R 106 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 121 through 124
    Processing helix  chain 'R' and resid 125 through 153
    Processing helix  chain 'R' and resid 161 through 180
    Processing helix  chain 'R' and resid 181 through 184
    Processing helix  chain 'R' and resid 213 through 249
      Proline residue:  R 231  - end of helix
    Processing helix  chain 'R' and resid 259 through 294
      removed outlier: 3.648A  pdb=" N   PHE R 277 " --> pdb=" O   VAL R 273 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ALA R 278 " --> pdb=" O   VAL R 274 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   TRP R 281 " --> pdb=" O   PHE R 277 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   LEU R 282 " --> pdb=" O   ALA R 278 " (cutoff:3.500A)
      Proline residue:  R 283  - end of helix
    Processing helix  chain 'R' and resid 302 through 328
      removed outlier: 4.474A  pdb=" N   SER R 317 " --> pdb=" O   ILE R 313 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   THR R 318 " --> pdb=" O   ALA R 314 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   PHE R 319 " --> pdb=" O   MET R 315 " (cutoff:3.500A)
      Proline residue:  R 322  - end of helix
    Processing helix  chain 'R' and resid 329 through 340
      removed outlier: 3.764A  pdb=" N   LEU R 337 " --> pdb=" O   ARG R 333 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 13 through 32
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.697A  pdb=" N   PHE A 189 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 8.062A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.718A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 9.051A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 4.090A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.374A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.494A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.495A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   SER B  72 " --> pdb=" O   ILE B  80 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   ILE B  80 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 112
      removed outlier: 5.833A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.741A  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 149
      removed outlier: 6.776A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.954A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 7.305A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ALA B 167 " --> pdb=" O   THR B 159 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.651A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 5.148A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.427A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   SER B 201 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 233 through 234
      removed outlier: 6.635A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.785A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ASP B 254 " --> pdb=" O   GLN B 259 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 284 through 285
      removed outlier: 3.580A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)

    337 hydrogen bonds defined for protein.
    963 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.98

  Time building geometry restraints manager: 2.27 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: 2338
        1.34 -     1.46: 1525
        1.46 -     1.58: 3466
        1.58 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 7391
  Sorted by residual:
  bond pdb=" CB  TYC P  36 "
       pdb=" CG  TYC P  36 "
    ideal  model  delta    sigma   weight residual
    1.501  1.389  0.112 2.00e-02 2.50e+03 3.14e+01
  bond pdb=" C   LEU R 230 "
       pdb=" N   PRO R 231 "
    ideal  model  delta    sigma   weight residual
    1.335  1.352 -0.016 1.30e-02 5.92e+03 1.60e+00
  bond pdb=" N   TYC P  36 "
       pdb=" CA  TYC P  36 "
    ideal  model  delta    sigma   weight residual
    1.458  1.479 -0.021 1.90e-02 2.77e+03 1.17e+00
  bond pdb=" N   THR B  87 "
       pdb=" CA  THR B  87 "
    ideal  model  delta    sigma   weight residual
    1.460  1.473 -0.014 1.54e-02 4.22e+03 7.97e-01
  bond pdb=" C   LYS P   4 "
       pdb=" N   PRO P   5 "
    ideal  model  delta    sigma   weight residual
    1.334  1.353 -0.019 2.34e-02 1.83e+03 6.42e-01
  ... (remaining 7386 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 9889
        1.54 -     3.07: 121
        3.07 -     4.61: 21
        4.61 -     6.15: 17
        6.15 -     7.68: 2
  Bond angle restraints: 10050
  Sorted by residual:
  angle pdb=" N   ILE B 270 "
        pdb=" CA  ILE B 270 "
        pdb=" C   ILE B 270 "
      ideal   model   delta    sigma   weight residual
     113.20  109.50    3.70 9.60e-01 1.09e+00 1.48e+01
  angle pdb=" N   THR B 164 "
        pdb=" CA  THR B 164 "
        pdb=" CB  THR B 164 "
      ideal   model   delta    sigma   weight residual
     113.65  109.47    4.18 1.47e+00 4.63e-01 8.07e+00
  angle pdb=" C   GLU R 210 "
        pdb=" N   GLU R 211 "
        pdb=" CA  GLU R 211 "
      ideal   model   delta    sigma   weight residual
     121.54  126.72   -5.18 1.91e+00 2.74e-01 7.37e+00
  angle pdb=" CA  LEU R  55 "
        pdb=" CB  LEU R  55 "
        pdb=" CG  LEU R  55 "
      ideal   model   delta    sigma   weight residual
     116.30  123.98   -7.68 3.50e+00 8.16e-02 4.82e+00
  angle pdb=" N   ALA R 202 "
        pdb=" CA  ALA R 202 "
        pdb=" C   ALA R 202 "
      ideal   model   delta    sigma   weight residual
     108.46  111.51   -3.05 1.51e+00 4.39e-01 4.08e+00
  ... (remaining 10045 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 4054
       17.96 -    35.92: 261
       35.92 -    53.88: 49
       53.88 -    71.84: 8
       71.84 -    89.80: 2
  Dihedral angle restraints: 4374
    sinusoidal: 1609
      harmonic: 2765
  Sorted by residual:
  dihedral pdb=" CB  CYS R 123 "
           pdb=" SG  CYS R 123 "
           pdb=" SG  CYS R 203 "
           pdb=" CB  CYS R 203 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -153.21   67.21     1      1.00e+01 1.00e-02 5.88e+01
  dihedral pdb=" CA  ASP B 298 "
           pdb=" CB  ASP B 298 "
           pdb=" CG  ASP B 298 "
           pdb=" OD1 ASP B 298 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.31   58.31     1      2.00e+01 2.50e-03 1.14e+01
  dihedral pdb=" CA  SER A 326 "
           pdb=" C   SER A 326 "
           pdb=" N   THR A 327 "
           pdb=" CA  THR A 327 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.58  -15.42     0      5.00e+00 4.00e-02 9.51e+00
  ... (remaining 4371 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 691
       0.027 -    0.054: 310
       0.054 -    0.081: 108
       0.081 -    0.109: 54
       0.109 -    0.136: 20
  Chirality restraints: 1183
  Sorted by residual:
  chirality pdb=" CB  ILE R  66 "
            pdb=" CA  ILE R  66 "
            pdb=" CG1 ILE R  66 "
            pdb=" CG2 ILE R  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.14 2.00e-01 2.50e+01 4.60e-01
  chirality pdb=" CA  ILE R 194 "
            pdb=" N   ILE R 194 "
            pdb=" C   ILE R 194 "
            pdb=" CB  ILE R 194 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.14e-01
  chirality pdb=" CA  ILE B  81 "
            pdb=" N   ILE B  81 "
            pdb=" C   ILE B  81 "
            pdb=" CB  ILE B  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.05e-01
  ... (remaining 1180 not shown)

  Planarity restraints: 1262
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS P   4 "    0.042 5.00e-02 4.00e+02   6.41e-02 6.57e+00
        pdb=" N   PRO P   5 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO P   5 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO P   5 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 226 "    0.008 2.00e-02 2.50e+03   1.53e-02 2.34e+00
        pdb=" C   ILE R 226 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   ILE R 226 "    0.010 2.00e-02 2.50e+03
        pdb=" N   LEU R 227 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER R 238 "    0.006 2.00e-02 2.50e+03   1.28e-02 1.63e+00
        pdb=" C   SER R 238 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   SER R 238 "    0.008 2.00e-02 2.50e+03
        pdb=" N   TYR R 239 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1259 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 2110
        2.81 -     3.33: 6960
        3.33 -     3.85: 12021
        3.85 -     4.38: 13502
        4.38 -     4.90: 23546
  Nonbonded interactions: 58139
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 290 "
            pdb=" OE2 GLU A 298 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" OD1 ASP A 341 "
            pdb=" NE2 HIS R 249 "
     model   vdw
     2.323 3.120
  nonbonded pdb=" O   ARG P  25 "
            pdb=" ND2 ASN P  29 "
     model   vdw
     2.324 3.120
  ... (remaining 58134 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.600
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  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:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
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      :  0.002   0.112   7391  Z= 0.135
  Angle     :  0.510   7.682  10050  Z= 0.275
  Chirality :  0.040   0.136   1183
  Planarity :  0.003   0.064   1262
  Dihedral  : 12.290  89.805   2577
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.17 %
    Favored  : 96.70 %
  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: -3.52 (0.23), residues: 931
  helix: -0.99 (0.23), residues: 398
  sheet: -3.11 (0.39), residues: 137
  loop : -3.48 (0.23), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP B  82 
 HIS   0.002   0.000   HIS B 142 
 PHE   0.010   0.001   PHE R 340 
 TYR   0.005   0.001   TYR R 228 
 ARG   0.001   0.000   ARG C  27 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 248
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8761 (tm-30)
REVERT: A   25 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8419 (tm-30)
REVERT: A   33 GLU cc_start: 0.9020 (pp20) cc_final: 0.8485 (pp20)
REVERT: A  191 PHE cc_start: 0.8324 (t80) cc_final: 0.8011 (t80)
REVERT: A  195 HIS cc_start: 0.8167 (m-70) cc_final: 0.7646 (m-70)
REVERT: A  224 CYS cc_start: 0.7098 (t) cc_final: 0.6577 (t)
REVERT: A  261 ASP cc_start: 0.7874 (t0) cc_final: 0.7586 (t0)
REVERT: A  276 GLU cc_start: 0.9229 (mp0) cc_final: 0.8954 (mp0)
REVERT: A  337 ASP cc_start: 0.8219 (m-30) cc_final: 0.7875 (m-30)
REVERT: B  266 HIS cc_start: 0.7811 (t-170) cc_final: 0.7355 (t-170)
REVERT: B  339 TRP cc_start: 0.8625 (m100) cc_final: 0.7954 (m-10)
REVERT: B  340 ASN cc_start: 0.7249 (t0) cc_final: 0.6573 (t0)
REVERT: C   40 TYR cc_start: 0.8674 (t80) cc_final: 0.8463 (t80)
REVERT: R   86 ASN cc_start: 0.8522 (m-40) cc_final: 0.8255 (m-40)
REVERT: R  262 ARG cc_start: 0.7373 (mtp85) cc_final: 0.7040 (mtm180)
REVERT: R  301 LYS cc_start: 0.8392 (tttt) cc_final: 0.8121 (ttmm)
REVERT: P   34 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7421 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 248
  average time/residue: 0.2187
  time to fit residues: 69.4058
Evaluate side-chains
  166 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 38 optimal weight:    9.9990
   chunk 23 optimal weight:    0.1980
   chunk 47 optimal weight:    0.9990
   chunk 37 optimal weight:    8.9990
   chunk 72 optimal weight:    1.9990
   chunk 27 optimal weight:   10.0000
   chunk 43 optimal weight:    5.9990
   chunk 53 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 244 HIS
B  62 HIS
B 176 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 295 ASN
R  73 HIS
R 100 ASN
R 155 HIS
** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 260 HIS
R 261 GLN
R 288 GLN
R 311 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.124110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.100055 restraints weight = 16531.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3591 rms_B_bonded: 3.91
r_work: 0.3447 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7391  Z= 0.187
  Angle     :  0.624   9.329  10050  Z= 0.313
  Chirality :  0.043   0.275   1183
  Planarity :  0.004   0.050   1262
  Dihedral  :  4.951  58.239   1022
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 13.61 %
    Favored  : 83.22 %
  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: -2.31 (0.26), residues: 931
  helix:  0.28 (0.26), residues: 396
  sheet: -2.89 (0.34), residues: 173
  loop : -2.88 (0.27), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP R 116 
 HIS   0.009   0.001   HIS R  73 
 PHE   0.019   0.001   PHE R 340 
 TYR   0.030   0.001   TYR P  21 
 ARG   0.007   0.001   ARG B 251 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 187
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.9232 (tm-30) cc_final: 0.9028 (tm-30)
REVERT: A   33 GLU cc_start: 0.9099 (pp20) cc_final: 0.8091 (pp20)
REVERT: A   35 LYS cc_start: 0.8970 (mppt) cc_final: 0.8698 (mptt)
REVERT: A  191 PHE cc_start: 0.8490 (t80) cc_final: 0.7990 (t80)
REVERT: A  195 HIS cc_start: 0.8489 (m-70) cc_final: 0.7650 (m-70)
REVERT: A  261 ASP cc_start: 0.8394 (t0) cc_final: 0.8034 (t0)
REVERT: A  276 GLU cc_start: 0.9393 (mp0) cc_final: 0.9077 (mp0)
REVERT: A  337 ASP cc_start: 0.8543 (m-30) cc_final: 0.8015 (m-30)
REVERT: A  341 ASP cc_start: 0.8474 (t70) cc_final: 0.8263 (t0)
REVERT: B   45 MET cc_start: 0.8128 (mmt) cc_final: 0.7893 (mmt)
REVERT: B   58 ILE cc_start: 0.8416 (pt) cc_final: 0.8212 (mp)
REVERT: B   72 SER cc_start: 0.8298 (m) cc_final: 0.7986 (p)
REVERT: B  209 LYS cc_start: 0.7479 (mttt) cc_final: 0.6999 (mttm)
REVERT: B  211 TRP cc_start: 0.7156 (m100) cc_final: 0.6029 (m100)
REVERT: B  215 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8207 (pt0)
REVERT: B  266 HIS cc_start: 0.8417 (t-170) cc_final: 0.7895 (t70)
REVERT: B  339 TRP cc_start: 0.8736 (m100) cc_final: 0.8270 (m100)
REVERT: C   40 TYR cc_start: 0.8753 (t80) cc_final: 0.8512 (t80)
REVERT: R  146 LEU cc_start: 0.8691 (mt) cc_final: 0.8477 (mm)
REVERT: R  262 ARG cc_start: 0.7582 (mtp85) cc_final: 0.7095 (mtm180)
REVERT: R  301 LYS cc_start: 0.8606 (tttt) cc_final: 0.8339 (ttmm)
REVERT: P   15 GLU cc_start: 0.8712 (pm20) cc_final: 0.8377 (pm20)
  outliers start: 24
  outliers final: 16
  residues processed: 203
  average time/residue: 0.2116
  time to fit residues: 56.1038
Evaluate side-chains
  176 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 160
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 ASP
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain R residue   62 LEU
Chi-restraints excluded: chain R residue   63 LEU
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  102 LEU
Chi-restraints excluded: chain R residue  225 LEU
Chi-restraints excluded: chain R residue  232 LEU
Chi-restraints excluded: chain R residue  259 TYR
Chi-restraints excluded: chain R residue  263 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 59 optimal weight:    9.9990
   chunk 24 optimal weight:    0.0040
   chunk 41 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 81 optimal weight:    8.9990
   chunk 9 optimal weight:    3.9990
   chunk 13 optimal weight:    7.9990
   chunk 70 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0970
   overall best weight:    0.7794

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

Flipped N/Q/H residues before XYZ refinement:
A 244 HIS
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 119 ASN
B 156 GLN
B 259 GLN
R 135 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.123903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.099692 restraints weight = 16474.908|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 3.91
r_work: 0.3442 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.2542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7391  Z= 0.160
  Angle     :  0.598   7.629  10050  Z= 0.297
  Chirality :  0.042   0.212   1183
  Planarity :  0.004   0.049   1262
  Dihedral  :  4.828  53.278   1022
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 15.32 %
    Favored  : 81.24 %
  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: -1.82 (0.27), residues: 931
  helix:  0.75 (0.27), residues: 396
  sheet: -2.66 (0.38), residues: 157
  loop : -2.72 (0.27), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 297 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.019   0.001   PHE B 292 
 TYR   0.016   0.001   TYR P  20 
 ARG   0.006   0.001   ARG A  21 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 175
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.8671 (tpp) cc_final: 0.8326 (tpp)
REVERT: A   33 GLU cc_start: 0.9101 (pp20) cc_final: 0.8572 (pp20)
REVERT: A  190 THR cc_start: 0.8017 (m) cc_final: 0.7562 (m)
REVERT: A  191 PHE cc_start: 0.8473 (t80) cc_final: 0.8013 (t80)
REVERT: A  195 HIS cc_start: 0.8503 (m-70) cc_final: 0.7658 (m-70)
REVERT: A  231 ASP cc_start: 0.8958 (OUTLIER) cc_final: 0.8745 (m-30)
REVERT: A  243 MET cc_start: 0.8824 (ttm) cc_final: 0.8557 (ttm)
REVERT: A  261 ASP cc_start: 0.8440 (t0) cc_final: 0.8066 (t0)
REVERT: A  276 GLU cc_start: 0.9397 (mp0) cc_final: 0.9047 (mp0)
REVERT: A  315 ASP cc_start: 0.8098 (p0) cc_final: 0.7832 (p0)
REVERT: A  337 ASP cc_start: 0.8596 (m-30) cc_final: 0.7972 (m-30)
REVERT: A  341 ASP cc_start: 0.8435 (t70) cc_final: 0.8226 (t0)
REVERT: B   45 MET cc_start: 0.8231 (mmt) cc_final: 0.7957 (mmt)
REVERT: B   59 TYR cc_start: 0.8187 (m-80) cc_final: 0.7865 (m-80)
REVERT: B   72 SER cc_start: 0.8286 (OUTLIER) cc_final: 0.8043 (p)
REVERT: B  209 LYS cc_start: 0.7475 (mttt) cc_final: 0.6802 (mttm)
REVERT: B  211 TRP cc_start: 0.7146 (m100) cc_final: 0.6000 (m100)
REVERT: B  215 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8092 (tm-30)
REVERT: B  266 HIS cc_start: 0.8371 (t-170) cc_final: 0.7882 (t70)
REVERT: B  292 PHE cc_start: 0.7907 (m-10) cc_final: 0.7364 (m-10)
REVERT: B  339 TRP cc_start: 0.8758 (m100) cc_final: 0.8285 (m100)
REVERT: C   40 TYR cc_start: 0.8743 (t80) cc_final: 0.8508 (t80)
REVERT: R  185 ILE cc_start: 0.8694 (tp) cc_final: 0.8369 (mm)
REVERT: R  262 ARG cc_start: 0.7605 (mtp85) cc_final: 0.7062 (mtm180)
REVERT: R  301 LYS cc_start: 0.8623 (tttt) cc_final: 0.8300 (ttmm)
REVERT: P   21 TYR cc_start: 0.8089 (m-80) cc_final: 0.7519 (m-80)
  outliers start: 26
  outliers final: 13
  residues processed: 192
  average time/residue: 0.2009
  time to fit residues: 50.8376
Evaluate side-chains
  182 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 167
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 ASP
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain R residue   62 LEU
Chi-restraints excluded: chain R residue  102 LEU
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  225 LEU
Chi-restraints excluded: chain R residue  232 LEU
Chi-restraints excluded: chain R residue  259 TYR
Chi-restraints excluded: chain R residue  263 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 49 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 89 optimal weight:    8.9990
   chunk 12 optimal weight:    4.9990
   chunk 48 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 77 optimal weight:    0.8980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 244 HIS
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
R 288 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.121347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.096431 restraints weight = 16844.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 3.96
r_work: 0.3384 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.2888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7391  Z= 0.191
  Angle     :  0.600   8.140  10050  Z= 0.300
  Chirality :  0.043   0.180   1183
  Planarity :  0.004   0.048   1262
  Dihedral  :  4.677  47.952   1022
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 16.38 %
    Favored  : 79.79 %
  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: -1.59 (0.27), residues: 931
  helix:  0.86 (0.27), residues: 396
  sheet: -2.40 (0.38), residues: 162
  loop : -2.55 (0.28), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP B 297 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.015   0.001   PHE B 292 
 TYR   0.021   0.001   TYR R 110 
 ARG   0.004   0.000   ARG A  21 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 169
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8615 (pp20)
REVERT: A   18 MET cc_start: 0.8834 (tpp) cc_final: 0.8620 (tpp)
REVERT: A   33 GLU cc_start: 0.9070 (pp20) cc_final: 0.8535 (pp20)
REVERT: A  191 PHE cc_start: 0.8493 (t80) cc_final: 0.8071 (t80)
REVERT: A  243 MET cc_start: 0.8765 (ttm) cc_final: 0.8539 (ttm)
REVERT: A  261 ASP cc_start: 0.8476 (t0) cc_final: 0.8103 (t0)
REVERT: A  276 GLU cc_start: 0.9401 (mp0) cc_final: 0.9036 (mp0)
REVERT: A  315 ASP cc_start: 0.8058 (p0) cc_final: 0.7761 (p0)
REVERT: A  337 ASP cc_start: 0.8691 (m-30) cc_final: 0.8001 (m-30)
REVERT: A  341 ASP cc_start: 0.8515 (t70) cc_final: 0.8301 (t0)
REVERT: B   45 MET cc_start: 0.8309 (mmt) cc_final: 0.8031 (mmt)
REVERT: B   59 TYR cc_start: 0.8443 (m-80) cc_final: 0.8134 (m-80)
REVERT: B  215 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8112 (tm-30)
REVERT: B  266 HIS cc_start: 0.8328 (t-170) cc_final: 0.7957 (t70)
REVERT: B  292 PHE cc_start: 0.8010 (m-10) cc_final: 0.7433 (m-10)
REVERT: B  339 TRP cc_start: 0.8792 (m100) cc_final: 0.8343 (m100)
REVERT: C   40 TYR cc_start: 0.8755 (t80) cc_final: 0.8511 (t80)
REVERT: R  107 THR cc_start: 0.9334 (m) cc_final: 0.9121 (m)
REVERT: R  215 TYR cc_start: 0.7117 (m-80) cc_final: 0.6400 (t80)
REVERT: R  262 ARG cc_start: 0.7758 (mtp85) cc_final: 0.7305 (mtm180)
REVERT: R  301 LYS cc_start: 0.8669 (tttt) cc_final: 0.8300 (ttmm)
REVERT: P   15 GLU cc_start: 0.8647 (pm20) cc_final: 0.8367 (pm20)
REVERT: P   21 TYR cc_start: 0.8154 (m-80) cc_final: 0.7614 (m-80)
  outliers start: 29
  outliers final: 17
  residues processed: 185
  average time/residue: 0.1987
  time to fit residues: 48.9118
Evaluate side-chains
  174 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 157
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  194 ILE
Chi-restraints excluded: chain R residue  225 LEU
Chi-restraints excluded: chain R residue  227 LEU
Chi-restraints excluded: chain R residue  259 TYR
Chi-restraints excluded: chain R residue  263 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 55 optimal weight:   30.0000
   chunk 26 optimal weight:    5.9990
   chunk 16 optimal weight:    7.9990
   chunk 61 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 6 optimal weight:    9.9990
   chunk 7 optimal weight:    1.9990
   chunk 22 optimal weight:    7.9990
   chunk 24 optimal weight:    0.0170
   chunk 43 optimal weight:    0.5980
   chunk 36 optimal weight:    9.9990
   overall best weight:    0.9222

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

Flipped N/Q/H residues before XYZ refinement:
A 244 HIS
B  75 GLN
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
R 100 ASN
R 288 GLN
** P  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.120967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.095831 restraints weight = 16442.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 3.93
r_work: 0.3390 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.3021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7391  Z= 0.173
  Angle     :  0.593   8.741  10050  Z= 0.294
  Chirality :  0.043   0.285   1183
  Planarity :  0.004   0.046   1262
  Dihedral  :  4.540  43.977   1022
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 19.15 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.27), residues: 931
  helix:  0.95 (0.27), residues: 397
  sheet: -2.40 (0.38), residues: 162
  loop : -2.45 (0.28), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP R 116 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.011   0.001   PHE R 319 
 TYR   0.020   0.001   TYR R 303 
 ARG   0.005   0.000   ARG A  21 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 165
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8654 (pp20)
REVERT: A   18 MET cc_start: 0.8821 (tpp) cc_final: 0.8616 (tpp)
REVERT: A   33 GLU cc_start: 0.9094 (pp20) cc_final: 0.8255 (pp20)
REVERT: A   35 LYS cc_start: 0.9080 (mppt) cc_final: 0.8757 (mptt)
REVERT: A  191 PHE cc_start: 0.8451 (t80) cc_final: 0.7978 (t80)
REVERT: A  195 HIS cc_start: 0.8558 (m-70) cc_final: 0.7496 (m-70)
REVERT: A  261 ASP cc_start: 0.8507 (t0) cc_final: 0.8145 (t0)
REVERT: A  276 GLU cc_start: 0.9396 (mp0) cc_final: 0.9018 (mp0)
REVERT: A  315 ASP cc_start: 0.8030 (p0) cc_final: 0.7726 (p0)
REVERT: A  337 ASP cc_start: 0.8753 (m-30) cc_final: 0.8027 (m-30)
REVERT: B   45 MET cc_start: 0.8318 (mmt) cc_final: 0.8021 (mmp)
REVERT: B   59 TYR cc_start: 0.8440 (m-80) cc_final: 0.8164 (m-80)
REVERT: B  215 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8143 (tm-30)
REVERT: B  259 GLN cc_start: 0.6893 (OUTLIER) cc_final: 0.6676 (pt0)
REVERT: B  266 HIS cc_start: 0.8346 (t-170) cc_final: 0.7970 (t70)
REVERT: B  292 PHE cc_start: 0.8008 (m-10) cc_final: 0.7746 (m-80)
REVERT: B  339 TRP cc_start: 0.8782 (m100) cc_final: 0.8395 (m100)
REVERT: C   40 TYR cc_start: 0.8743 (t80) cc_final: 0.8534 (t80)
REVERT: R  107 THR cc_start: 0.8977 (m) cc_final: 0.8704 (m)
REVERT: R  116 TRP cc_start: 0.7900 (t-100) cc_final: 0.7570 (t-100)
REVERT: R  215 TYR cc_start: 0.7144 (m-80) cc_final: 0.6443 (t80)
REVERT: R  256 ASN cc_start: 0.8468 (t0) cc_final: 0.8250 (t0)
REVERT: R  262 ARG cc_start: 0.7784 (mtp85) cc_final: 0.7276 (mtm180)
REVERT: R  301 LYS cc_start: 0.8647 (tttt) cc_final: 0.8292 (ttmm)
REVERT: P   21 TYR cc_start: 0.8207 (m-80) cc_final: 0.7711 (m-80)
REVERT: P   34 GLN cc_start: 0.8331 (tt0) cc_final: 0.7967 (tt0)
  outliers start: 25
  outliers final: 15
  residues processed: 181
  average time/residue: 0.1847
  time to fit residues: 44.7594
Evaluate side-chains
  169 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 153
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain R residue   63 LEU
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  194 ILE
Chi-restraints excluded: chain R residue  225 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 21 optimal weight:    7.9990
   chunk 70 optimal weight:    0.0370
   chunk 45 optimal weight:    7.9990
   chunk 13 optimal weight:    7.9990
   chunk 87 optimal weight:    4.9990
   chunk 56 optimal weight:    5.9990
   chunk 82 optimal weight:    0.7980
   chunk 42 optimal weight:   10.0000
   chunk 60 optimal weight:    0.5980
   chunk 14 optimal weight:    8.9990
   chunk 47 optimal weight:    0.0470
   overall best weight:    1.2958

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

Flipped N/Q/H residues before XYZ refinement:
A 244 HIS
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
R 135 GLN
R 288 GLN
** P  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.120850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.095659 restraints weight = 16578.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 3.94
r_work: 0.3368 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.3159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7391  Z= 0.195
  Angle     :  0.608  12.362  10050  Z= 0.305
  Chirality :  0.044   0.393   1183
  Planarity :  0.004   0.046   1262
  Dihedral  :  4.406  37.724   1022
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.95 %
    Favored  : 76.88 %
  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: -1.34 (0.27), residues: 931
  helix:  1.01 (0.27), residues: 396
  sheet: -2.16 (0.39), residues: 159
  loop : -2.40 (0.28), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R 116 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.012   0.001   PHE B 222 
 TYR   0.010   0.001   TYR R 303 
 ARG   0.005   0.000   ARG A  21 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 163
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.8811 (tpp) cc_final: 0.8580 (tpp)
REVERT: A   33 GLU cc_start: 0.9078 (pp20) cc_final: 0.8575 (pp20)
REVERT: A   35 LYS cc_start: 0.9073 (mppt) cc_final: 0.8651 (mptt)
REVERT: A  191 PHE cc_start: 0.8431 (t80) cc_final: 0.7970 (t80)
REVERT: A  195 HIS cc_start: 0.8567 (m-70) cc_final: 0.7815 (m-70)
REVERT: A  261 ASP cc_start: 0.8544 (t0) cc_final: 0.8135 (t0)
REVERT: A  276 GLU cc_start: 0.9404 (mp0) cc_final: 0.9013 (mp0)
REVERT: A  315 ASP cc_start: 0.8051 (p0) cc_final: 0.7708 (p0)
REVERT: A  337 ASP cc_start: 0.8787 (m-30) cc_final: 0.8043 (m-30)
REVERT: B   45 MET cc_start: 0.8409 (mmt) cc_final: 0.8066 (mmp)
REVERT: B   59 TYR cc_start: 0.8417 (m-80) cc_final: 0.8216 (m-80)
REVERT: B   78 LYS cc_start: 0.8170 (mmmt) cc_final: 0.7799 (mmmt)
REVERT: B  196 THR cc_start: 0.6720 (OUTLIER) cc_final: 0.6509 (p)
REVERT: B  215 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8129 (tm-30)
REVERT: B  266 HIS cc_start: 0.8341 (t-170) cc_final: 0.7964 (t70)
REVERT: B  292 PHE cc_start: 0.8140 (m-10) cc_final: 0.7936 (m-80)
REVERT: B  325 MET cc_start: 0.7114 (tpp) cc_final: 0.6811 (tpp)
REVERT: B  339 TRP cc_start: 0.8792 (m100) cc_final: 0.8409 (m100)
REVERT: C   40 TYR cc_start: 0.8761 (t80) cc_final: 0.8536 (t80)
REVERT: R  107 THR cc_start: 0.9003 (m) cc_final: 0.8678 (m)
REVERT: R  116 TRP cc_start: 0.7934 (t-100) cc_final: 0.7678 (t60)
REVERT: R  135 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8463 (mm-40)
REVERT: R  188 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6578 (pp20)
REVERT: R  256 ASN cc_start: 0.8480 (t0) cc_final: 0.8243 (t0)
REVERT: R  262 ARG cc_start: 0.7842 (mtp85) cc_final: 0.7319 (mtm180)
REVERT: R  301 LYS cc_start: 0.8638 (tttt) cc_final: 0.8288 (ttmm)
REVERT: P   21 TYR cc_start: 0.8203 (m-10) cc_final: 0.7700 (m-80)
REVERT: P   34 GLN cc_start: 0.8358 (tt0) cc_final: 0.7884 (tt0)
  outliers start: 24
  outliers final: 18
  residues processed: 178
  average time/residue: 0.1995
  time to fit residues: 47.0542
Evaluate side-chains
  174 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 153
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain R residue   63 LEU
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  135 GLN
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  188 GLU
Chi-restraints excluded: chain R residue  194 ILE
Chi-restraints excluded: chain R residue  225 LEU
Chi-restraints excluded: chain R residue  259 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 32 optimal weight:    6.9990
   chunk 23 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0470
   chunk 11 optimal weight:    0.5980
   chunk 77 optimal weight:    7.9990
   chunk 63 optimal weight:    0.8980
   chunk 10 optimal weight:    6.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
A 244 HIS
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 GLN
B 259 GLN
R 288 GLN
P  26 HIS
** P  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.123319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.098184 restraints weight = 16461.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 4.01
r_work: 0.3388 rms_B_bonded: 4.84 restraints_weight: 0.5000
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.3264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7391  Z= 0.167
  Angle     :  0.611  13.915  10050  Z= 0.302
  Chirality :  0.043   0.421   1183
  Planarity :  0.004   0.048   1262
  Dihedral  :  4.160  29.913   1022
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 20.74 %
    Favored  : 76.09 %
  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: -1.20 (0.27), residues: 931
  helix:  1.09 (0.27), residues: 397
  sheet: -2.12 (0.40), residues: 154
  loop : -2.29 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 116 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.015   0.001   PHE B 222 
 TYR   0.011   0.001   TYR R 303 
 ARG   0.006   0.000   ARG A  21 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 162
  time to evaluate  : 0.800 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8624 (pp20)
REVERT: A   18 MET cc_start: 0.8815 (tpp) cc_final: 0.8562 (tpp)
REVERT: A   33 GLU cc_start: 0.9066 (pp20) cc_final: 0.8225 (pp20)
REVERT: A   35 LYS cc_start: 0.9064 (mppt) cc_final: 0.8719 (mptt)
REVERT: A  191 PHE cc_start: 0.8424 (t80) cc_final: 0.7984 (t80)
REVERT: A  195 HIS cc_start: 0.8580 (m-70) cc_final: 0.7592 (m-70)
REVERT: A  261 ASP cc_start: 0.8537 (t0) cc_final: 0.8190 (t0)
REVERT: A  275 GLU cc_start: 0.8970 (tp30) cc_final: 0.8685 (mm-30)
REVERT: A  276 GLU cc_start: 0.9391 (mp0) cc_final: 0.9008 (mp0)
REVERT: A  315 ASP cc_start: 0.8061 (p0) cc_final: 0.7683 (p0)
REVERT: A  337 ASP cc_start: 0.8790 (m-30) cc_final: 0.8045 (m-30)
REVERT: B   45 MET cc_start: 0.8371 (mmt) cc_final: 0.8035 (mmp)
REVERT: B   78 LYS cc_start: 0.8173 (mmmt) cc_final: 0.7780 (mmmt)
REVERT: B  196 THR cc_start: 0.6690 (OUTLIER) cc_final: 0.6470 (p)
REVERT: B  215 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8193 (tm-30)
REVERT: B  266 HIS cc_start: 0.8362 (t-170) cc_final: 0.7959 (t70)
REVERT: B  292 PHE cc_start: 0.8155 (m-10) cc_final: 0.7945 (m-80)
REVERT: B  325 MET cc_start: 0.7070 (tpp) cc_final: 0.6812 (tpp)
REVERT: B  339 TRP cc_start: 0.8790 (m100) cc_final: 0.8446 (m100)
REVERT: C   40 TYR cc_start: 0.8752 (t80) cc_final: 0.8525 (t80)
REVERT: C   46 LYS cc_start: 0.7895 (ptpp) cc_final: 0.7520 (tptt)
REVERT: R  107 THR cc_start: 0.8980 (m) cc_final: 0.8697 (m)
REVERT: R  116 TRP cc_start: 0.7938 (t-100) cc_final: 0.7689 (t60)
REVERT: R  256 ASN cc_start: 0.8447 (t0) cc_final: 0.8246 (t0)
REVERT: R  262 ARG cc_start: 0.7811 (mtp85) cc_final: 0.7296 (mtm180)
REVERT: R  301 LYS cc_start: 0.8562 (tttt) cc_final: 0.8227 (ttmm)
REVERT: P   21 TYR cc_start: 0.8248 (m-10) cc_final: 0.7768 (m-80)
REVERT: P   34 GLN cc_start: 0.8317 (tt0) cc_final: 0.7949 (tt0)
  outliers start: 24
  outliers final: 19
  residues processed: 178
  average time/residue: 0.1885
  time to fit residues: 45.0691
Evaluate side-chains
  178 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 158
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain R residue   63 LEU
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  194 ILE
Chi-restraints excluded: chain R residue  213 SER
Chi-restraints excluded: chain R residue  225 LEU
Chi-restraints excluded: chain R residue  259 TYR
Chi-restraints excluded: chain R residue  263 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 80 optimal weight:    0.6980
   chunk 39 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   chunk 26 optimal weight:    0.0270
   chunk 6 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 54 optimal weight:   20.0000
   chunk 16 optimal weight:    6.9990
   chunk 59 optimal weight:    9.9990
   chunk 64 optimal weight:    0.8980
   overall best weight:    1.1240

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

Flipped N/Q/H residues before XYZ refinement:
A 244 HIS
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 288 GLN
** P  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.121389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.095946 restraints weight = 16522.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 3.97
r_work: 0.3369 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.3416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7391  Z= 0.190
  Angle     :  0.625  14.467  10050  Z= 0.309
  Chirality :  0.044   0.427   1183
  Planarity :  0.004   0.046   1262
  Dihedral  :  3.987  20.552   1022
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 20.87 %
    Favored  : 75.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.28), residues: 931
  helix:  1.15 (0.27), residues: 396
  sheet: -1.98 (0.41), residues: 159
  loop : -2.24 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 116 
 HIS   0.006   0.001   HIS P  26 
 PHE   0.010   0.001   PHE R 340 
 TYR   0.017   0.001   TYR R 110 
 ARG   0.007   0.000   ARG A  21 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 160
  time to evaluate  : 0.804 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8692 (pp20)
REVERT: A   18 MET cc_start: 0.8812 (tpp) cc_final: 0.8564 (tpp)
REVERT: A   33 GLU cc_start: 0.9055 (pp20) cc_final: 0.8223 (pp20)
REVERT: A   35 LYS cc_start: 0.9078 (mppt) cc_final: 0.8736 (mptt)
REVERT: A  191 PHE cc_start: 0.8422 (t80) cc_final: 0.7948 (t80)
REVERT: A  195 HIS cc_start: 0.8580 (m-70) cc_final: 0.7603 (m-70)
REVERT: A  261 ASP cc_start: 0.8533 (t0) cc_final: 0.8136 (t0)
REVERT: A  275 GLU cc_start: 0.8964 (tp30) cc_final: 0.8674 (mm-30)
REVERT: A  276 GLU cc_start: 0.9386 (mp0) cc_final: 0.9013 (mp0)
REVERT: A  315 ASP cc_start: 0.8066 (p0) cc_final: 0.7665 (p0)
REVERT: A  337 ASP cc_start: 0.8822 (m-30) cc_final: 0.8072 (m-30)
REVERT: B  196 THR cc_start: 0.6743 (OUTLIER) cc_final: 0.6534 (p)
REVERT: B  215 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8276 (tm-30)
REVERT: B  266 HIS cc_start: 0.8336 (t-170) cc_final: 0.7911 (t70)
REVERT: B  325 MET cc_start: 0.7091 (tpp) cc_final: 0.6885 (tpp)
REVERT: B  339 TRP cc_start: 0.8796 (m100) cc_final: 0.8452 (m100)
REVERT: C   40 TYR cc_start: 0.8762 (t80) cc_final: 0.8534 (t80)
REVERT: R   82 ARG cc_start: 0.8265 (mtp85) cc_final: 0.8028 (mtp85)
REVERT: R  107 THR cc_start: 0.8999 (m) cc_final: 0.8685 (m)
REVERT: R  116 TRP cc_start: 0.8035 (t-100) cc_final: 0.7684 (t60)
REVERT: R  188 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6673 (pp20)
REVERT: R  262 ARG cc_start: 0.7873 (mtp85) cc_final: 0.7338 (mtm180)
REVERT: R  301 LYS cc_start: 0.8547 (tttt) cc_final: 0.8307 (ttmm)
REVERT: P   21 TYR cc_start: 0.8239 (m-10) cc_final: 0.7731 (m-80)
REVERT: P   34 GLN cc_start: 0.8284 (tt0) cc_final: 0.7947 (tt0)
  outliers start: 24
  outliers final: 18
  residues processed: 177
  average time/residue: 0.1979
  time to fit residues: 46.9810
Evaluate side-chains
  171 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 151
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain R residue   63 LEU
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  188 GLU
Chi-restraints excluded: chain R residue  194 ILE
Chi-restraints excluded: chain R residue  213 SER
Chi-restraints excluded: chain R residue  225 LEU
Chi-restraints excluded: chain R residue  298 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 22 optimal weight:   10.0000
   chunk 25 optimal weight:    0.4980
   chunk 69 optimal weight:    3.9990
   chunk 60 optimal weight:    0.7980
   chunk 45 optimal weight:    8.9990
   chunk 79 optimal weight:    4.9990
   chunk 31 optimal weight:    0.0980
   chunk 85 optimal weight:    0.9990
   chunk 86 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0070
   overall best weight:    0.4198

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

Flipped N/Q/H residues before XYZ refinement:
A 244 HIS
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 288 GLN
** P  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.124017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.098998 restraints weight = 16514.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.3569 rms_B_bonded: 4.03
r_work: 0.3423 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.3525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7391  Z= 0.163
  Angle     :  0.630  14.798  10050  Z= 0.309
  Chirality :  0.044   0.441   1183
  Planarity :  0.004   0.047   1262
  Dihedral  :  3.859  20.113   1022
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 22.59 %
    Favored  : 75.03 %
  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: -1.05 (0.28), residues: 931
  helix:  1.14 (0.27), residues: 395
  sheet: -1.90 (0.41), residues: 154
  loop : -2.18 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 116 
 HIS   0.005   0.001   HIS P  26 
 PHE   0.014   0.001   PHE R 287 
 TYR   0.013   0.001   TYR B 124 
 ARG   0.009   0.000   ARG A  21 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 160
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.9153 (tm-30) cc_final: 0.8676 (pp20)
REVERT: A   18 MET cc_start: 0.8775 (tpp) cc_final: 0.8535 (tpp)
REVERT: A   33 GLU cc_start: 0.9035 (pp20) cc_final: 0.8213 (pp20)
REVERT: A   35 LYS cc_start: 0.9051 (mppt) cc_final: 0.8692 (mptt)
REVERT: A  191 PHE cc_start: 0.8426 (t80) cc_final: 0.7921 (t80)
REVERT: A  195 HIS cc_start: 0.8563 (m-70) cc_final: 0.7584 (m-70)
REVERT: A  261 ASP cc_start: 0.8545 (t0) cc_final: 0.8207 (t0)
REVERT: A  275 GLU cc_start: 0.8979 (tp30) cc_final: 0.8723 (mm-30)
REVERT: A  276 GLU cc_start: 0.9358 (mp0) cc_final: 0.8971 (mp0)
REVERT: A  315 ASP cc_start: 0.8047 (p0) cc_final: 0.7658 (p0)
REVERT: A  337 ASP cc_start: 0.8752 (m-30) cc_final: 0.7986 (m-30)
REVERT: B   59 TYR cc_start: 0.8032 (m-80) cc_final: 0.7661 (m-80)
REVERT: B   78 LYS cc_start: 0.7907 (mmmt) cc_final: 0.7526 (mmmt)
REVERT: B  169 TRP cc_start: 0.8264 (m100) cc_final: 0.7552 (m100)
REVERT: B  196 THR cc_start: 0.6624 (OUTLIER) cc_final: 0.6411 (p)
REVERT: B  215 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8442 (tt0)
REVERT: B  266 HIS cc_start: 0.8384 (t-170) cc_final: 0.7923 (t70)
REVERT: B  292 PHE cc_start: 0.8086 (m-80) cc_final: 0.7581 (m-80)
REVERT: B  325 MET cc_start: 0.7118 (tpp) cc_final: 0.6903 (tpp)
REVERT: B  339 TRP cc_start: 0.8750 (m100) cc_final: 0.8491 (m100)
REVERT: C   40 TYR cc_start: 0.8745 (t80) cc_final: 0.8507 (t80)
REVERT: R  107 THR cc_start: 0.8894 (m) cc_final: 0.8612 (m)
REVERT: R  116 TRP cc_start: 0.7883 (t-100) cc_final: 0.7614 (t-100)
REVERT: R  262 ARG cc_start: 0.7823 (mtp85) cc_final: 0.7295 (mtm180)
REVERT: P   21 TYR cc_start: 0.8202 (m-10) cc_final: 0.7678 (m-80)
  outliers start: 18
  outliers final: 13
  residues processed: 172
  average time/residue: 0.2169
  time to fit residues: 50.8140
Evaluate side-chains
  167 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 153
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue   63 LEU
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  194 ILE
Chi-restraints excluded: chain R residue  225 LEU
Chi-restraints excluded: chain R residue  298 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 76 optimal weight:    0.0170
   chunk 26 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0670
   overall best weight:    0.7758

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

Flipped N/Q/H residues before XYZ refinement:
A 244 HIS
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 135 GLN
** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.122872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.097621 restraints weight = 16710.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 4.03
r_work: 0.3419 rms_B_bonded: 4.81 restraints_weight: 0.5000
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.3594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7391  Z= 0.174
  Angle     :  0.678  17.298  10050  Z= 0.325
  Chirality :  0.045   0.445   1183
  Planarity :  0.004   0.044   1262
  Dihedral  :  3.858  19.787   1022
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 22.99 %
    Favored  : 74.37 %
  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: -1.05 (0.28), residues: 931
  helix:  1.11 (0.27), residues: 395
  sheet: -1.98 (0.39), residues: 166
  loop : -2.07 (0.30), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 339 
 HIS   0.005   0.001   HIS P  26 
 PHE   0.021   0.001   PHE B 222 
 TYR   0.017   0.001   TYR P  20 
 ARG   0.009   0.000   ARG A  21 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 155
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8682 (pp20)
REVERT: A   18 MET cc_start: 0.8778 (tpp) cc_final: 0.8556 (tpp)
REVERT: A   33 GLU cc_start: 0.9043 (pp20) cc_final: 0.8213 (pp20)
REVERT: A   35 LYS cc_start: 0.9070 (mppt) cc_final: 0.8714 (mptt)
REVERT: A  191 PHE cc_start: 0.8413 (t80) cc_final: 0.7904 (t80)
REVERT: A  195 HIS cc_start: 0.8571 (m-70) cc_final: 0.7617 (m-70)
REVERT: A  205 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.8162 (mtm-85)
REVERT: A  261 ASP cc_start: 0.8550 (t0) cc_final: 0.8163 (t0)
REVERT: A  275 GLU cc_start: 0.8971 (tp30) cc_final: 0.8711 (mm-30)
REVERT: A  276 GLU cc_start: 0.9369 (mp0) cc_final: 0.8983 (mp0)
REVERT: A  315 ASP cc_start: 0.8098 (p0) cc_final: 0.7719 (p0)
REVERT: A  337 ASP cc_start: 0.8787 (m-30) cc_final: 0.8032 (m-30)
REVERT: B   59 TYR cc_start: 0.8123 (m-80) cc_final: 0.7652 (m-80)
REVERT: B   78 LYS cc_start: 0.7865 (mmmt) cc_final: 0.7531 (mmmt)
REVERT: B  169 TRP cc_start: 0.8295 (m100) cc_final: 0.7499 (m100)
REVERT: B  196 THR cc_start: 0.6696 (OUTLIER) cc_final: 0.6475 (p)
REVERT: B  215 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8491 (tt0)
REVERT: B  266 HIS cc_start: 0.8386 (t-170) cc_final: 0.7923 (t70)
REVERT: B  292 PHE cc_start: 0.8047 (m-80) cc_final: 0.7573 (m-80)
REVERT: B  325 MET cc_start: 0.7018 (tpp) cc_final: 0.6816 (tpp)
REVERT: B  339 TRP cc_start: 0.8765 (m100) cc_final: 0.8517 (m100)
REVERT: C   40 TYR cc_start: 0.8735 (t80) cc_final: 0.8506 (t80)
REVERT: R  215 TYR cc_start: 0.7135 (m-80) cc_final: 0.6492 (t80)
REVERT: R  262 ARG cc_start: 0.7864 (mtp85) cc_final: 0.7316 (mtm180)
REVERT: P   21 TYR cc_start: 0.8264 (m-10) cc_final: 0.7743 (m-80)
  outliers start: 20
  outliers final: 18
  residues processed: 168
  average time/residue: 0.2315
  time to fit residues: 52.7264
Evaluate side-chains
  173 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 154
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue   63 LEU
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  123 CYS
Chi-restraints excluded: chain R residue  135 GLN
Chi-restraints excluded: chain R residue  194 ILE
Chi-restraints excluded: chain R residue  213 SER
Chi-restraints excluded: chain R residue  225 LEU
Chi-restraints excluded: chain R residue  259 TYR
Chi-restraints excluded: chain R residue  298 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 7 optimal weight:    5.9990
   chunk 9 optimal weight:    0.3980
   chunk 36 optimal weight:    8.9990
   chunk 8 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   chunk 1 optimal weight:    6.9990
   chunk 81 optimal weight:    7.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 244 HIS
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.123774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.098738 restraints weight = 16603.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 4.02
r_work: 0.3400 rms_B_bonded: 4.84 restraints_weight: 0.5000
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.3626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.171   7391  Z= 0.290
  Angle     :  1.025  59.197  10050  Z= 0.577
  Chirality :  0.046   0.437   1183
  Planarity :  0.004   0.044   1262
  Dihedral  :  3.857  19.699   1022
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 23.65 %
    Favored  : 73.84 %
  Cbeta Deviations :  0.11 %
  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: -1.06 (0.28), residues: 931
  helix:  1.09 (0.27), residues: 395
  sheet: -1.97 (0.39), residues: 166
  loop : -2.06 (0.30), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP R 116 
 HIS   0.005   0.001   HIS P  26 
 PHE   0.015   0.001   PHE B 222 
 TYR   0.011   0.001   TYR B 124 
 ARG   0.006   0.000   ARG A  21 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4040.58 seconds
wall clock time: 71 minutes 12.35 seconds (4272.35 seconds total)