Starting phenix.real_space_refine
on Wed Feb 12 04:34:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x9b_33070/02_2025/7x9b_33070.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x9b_33070/02_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_33070/02_2025/7x9b_33070.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x9b_33070/02_2025/7x9b_33070.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x9b_33070/02_2025/7x9b_33070.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x9b_33070/02_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-5592/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: 4.70, per 1000 atoms: 0.65
  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: 1.73
  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: 0.69
  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: 2.07

  Time building geometry restraints manager: 1.98 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:             1.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.740
  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:3.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.260
-------------------------------------------------------------------------------
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  : 0.851 
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: 0.2334
  time to fit residues: 74.3071
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  : 0.803 
-------------------------------------------------------------------------------
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 = 0.124111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.100050 restraints weight = 16531.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.3591 rms_B_bonded: 3.91
r_work: 0.3446 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
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 (0.35), 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  : 0.872 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.9238 (tm-30) cc_final: 0.9034 (tm-30)
REVERT: A   33 GLU cc_start: 0.9097 (pp20) cc_final: 0.8088 (pp20)
REVERT: A   35 LYS cc_start: 0.8969 (mppt) cc_final: 0.8698 (mptt)
REVERT: A  191 PHE cc_start: 0.8490 (t80) cc_final: 0.7992 (t80)
REVERT: A  195 HIS cc_start: 0.8492 (m-70) cc_final: 0.7654 (m-70)
REVERT: A  261 ASP cc_start: 0.8397 (t0) cc_final: 0.8039 (t0)
REVERT: A  276 GLU cc_start: 0.9393 (mp0) cc_final: 0.9075 (mp0)
REVERT: A  337 ASP cc_start: 0.8547 (m-30) cc_final: 0.8021 (m-30)
REVERT: A  341 ASP cc_start: 0.8474 (t70) cc_final: 0.8265 (t0)
REVERT: B   45 MET cc_start: 0.8133 (mmt) cc_final: 0.7901 (mmt)
REVERT: B   58 ILE cc_start: 0.8418 (pt) cc_final: 0.8215 (mp)
REVERT: B   72 SER cc_start: 0.8299 (m) cc_final: 0.7987 (p)
REVERT: B  209 LYS cc_start: 0.7476 (mttt) cc_final: 0.6993 (mttm)
REVERT: B  211 TRP cc_start: 0.7159 (m100) cc_final: 0.6027 (m100)
REVERT: B  215 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8207 (pt0)
REVERT: B  266 HIS cc_start: 0.8419 (t-170) cc_final: 0.7899 (t70)
REVERT: B  339 TRP cc_start: 0.8738 (m100) cc_final: 0.8271 (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: 0.8475 (mm)
REVERT: R  262 ARG cc_start: 0.7582 (mtp85) cc_final: 0.7097 (mtm180)
REVERT: R  301 LYS cc_start: 0.8610 (tttt) cc_final: 0.8344 (ttmm)
REVERT: P   15 GLU cc_start: 0.8718 (pm20) cc_final: 0.8383 (pm20)
  outliers start: 24
  outliers final: 16
  residues processed: 203
  average time/residue: 0.2114
  time to fit residues: 55.8040
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  : 0.772 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 24 optimal weight:    0.0050
   chunk 41 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 81 optimal weight:    7.9990
   chunk 9 optimal weight:    3.9990
   chunk 13 optimal weight:    8.9990
   chunk 70 optimal weight:    0.0040
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.7408

-------------------------------------------------------------------------------
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 = 0.3941 r_free = 0.3941 target = 0.124186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.099636 restraints weight = 16554.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 3.96
r_work: 0.3441 rms_B_bonded: 4.82 restraints_weight: 0.5000
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.2547

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= 0.158
  Angle     :  0.597   7.771  10050  Z= 0.296
  Chirality :  0.042   0.207   1183
  Planarity :  0.004   0.049   1262
  Dihedral  :  4.814  52.941   1022
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 15.19 %
    Favored  : 81.37 %
  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: -1.81 (0.27), residues: 931
  helix:  0.76 (0.27), residues: 396
  sheet: -2.66 (0.38), residues: 157
  loop : -2.71 (0.27), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 297 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.020   0.001   PHE B 292 
 TYR   0.015   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  : 0.818 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.8691 (tpp) cc_final: 0.8350 (tpp)
REVERT: A   33 GLU cc_start: 0.9097 (pp20) cc_final: 0.8566 (pp20)
REVERT: A  190 THR cc_start: 0.8021 (m) cc_final: 0.7569 (m)
REVERT: A  191 PHE cc_start: 0.8472 (t80) cc_final: 0.8011 (t80)
REVERT: A  195 HIS cc_start: 0.8506 (m-70) cc_final: 0.7662 (m-70)
REVERT: A  231 ASP cc_start: 0.8960 (OUTLIER) cc_final: 0.8751 (m-30)
REVERT: A  243 MET cc_start: 0.8827 (ttm) cc_final: 0.8568 (ttm)
REVERT: A  261 ASP cc_start: 0.8439 (t0) cc_final: 0.8065 (t0)
REVERT: A  276 GLU cc_start: 0.9397 (mp0) cc_final: 0.9046 (mp0)
REVERT: A  315 ASP cc_start: 0.8097 (p0) cc_final: 0.7829 (p0)
REVERT: A  337 ASP cc_start: 0.8594 (m-30) cc_final: 0.7969 (m-30)
REVERT: B   45 MET cc_start: 0.8227 (mmt) cc_final: 0.7955 (mmt)
REVERT: B   59 TYR cc_start: 0.8185 (m-80) cc_final: 0.7935 (m-80)
REVERT: B   72 SER cc_start: 0.8274 (OUTLIER) cc_final: 0.8036 (p)
REVERT: B  209 LYS cc_start: 0.7505 (mttt) cc_final: 0.6835 (mttm)
REVERT: B  211 TRP cc_start: 0.7142 (m100) cc_final: 0.5999 (m100)
REVERT: B  215 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8092 (tm-30)
REVERT: B  266 HIS cc_start: 0.8378 (t-170) cc_final: 0.7888 (t70)
REVERT: B  292 PHE cc_start: 0.7893 (m-10) cc_final: 0.7353 (m-10)
REVERT: B  339 TRP cc_start: 0.8757 (m100) cc_final: 0.8287 (m100)
REVERT: C   40 TYR cc_start: 0.8741 (t80) cc_final: 0.8506 (t80)
REVERT: R  185 ILE cc_start: 0.8693 (tp) cc_final: 0.8368 (mm)
REVERT: R  262 ARG cc_start: 0.7583 (mtp85) cc_final: 0.7052 (mtm180)
REVERT: R  301 LYS cc_start: 0.8627 (tttt) cc_final: 0.8302 (ttmm)
REVERT: P   21 TYR cc_start: 0.8092 (m-80) cc_final: 0.7522 (m-80)
  outliers start: 26
  outliers final: 13
  residues processed: 192
  average time/residue: 0.2012
  time to fit residues: 50.6661
Evaluate side-chains
  180 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 165
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 89 optimal weight:   10.0000
   chunk 12 optimal weight:    0.7980
   chunk 48 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 24 optimal weight:   10.0000
   chunk 77 optimal weight:    0.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 288 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.124096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.099566 restraints weight = 16827.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 4.00
r_work: 0.3411 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.2837

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= 0.170
  Angle     :  0.593   7.680  10050  Z= 0.295
  Chirality :  0.042   0.181   1183
  Planarity :  0.004   0.048   1262
  Dihedral  :  4.545  45.986   1022
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 16.25 %
    Favored  : 80.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.58 (0.27), residues: 931
  helix:  0.87 (0.27), residues: 396
  sheet: -2.41 (0.39), residues: 157
  loop : -2.55 (0.28), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP B 297 
 HIS   0.002   0.001   HIS B 142 
 PHE   0.015   0.001   PHE B 292 
 TYR   0.020   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
  197 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 169
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8636 (pp20)
REVERT: A   18 MET cc_start: 0.8819 (tpp) cc_final: 0.8612 (tpp)
REVERT: A   33 GLU cc_start: 0.9081 (pp20) cc_final: 0.8552 (pp20)
REVERT: A  191 PHE cc_start: 0.8481 (t80) cc_final: 0.8081 (t80)
REVERT: A  261 ASP cc_start: 0.8420 (t0) cc_final: 0.8069 (t0)
REVERT: A  276 GLU cc_start: 0.9396 (mp0) cc_final: 0.9044 (mp0)
REVERT: A  278 ILE cc_start: 0.8692 (mm) cc_final: 0.8300 (mt)
REVERT: A  315 ASP cc_start: 0.8021 (p0) cc_final: 0.7720 (p0)
REVERT: A  337 ASP cc_start: 0.8648 (m-30) cc_final: 0.7973 (m-30)
REVERT: B   45 MET cc_start: 0.8248 (mmt) cc_final: 0.7998 (mmt)
REVERT: B   59 TYR cc_start: 0.8403 (m-80) cc_final: 0.8072 (m-80)
REVERT: B  209 LYS cc_start: 0.7512 (mttt) cc_final: 0.6934 (mttm)
REVERT: B  211 TRP cc_start: 0.7050 (m100) cc_final: 0.5998 (m100)
REVERT: B  215 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8110 (tm-30)
REVERT: B  266 HIS cc_start: 0.8298 (t-170) cc_final: 0.7915 (t70)
REVERT: B  292 PHE cc_start: 0.7879 (m-10) cc_final: 0.7300 (m-10)
REVERT: B  339 TRP cc_start: 0.8758 (m100) cc_final: 0.8355 (m100)
REVERT: C   40 TYR cc_start: 0.8731 (t80) cc_final: 0.8526 (t80)
REVERT: R  215 TYR cc_start: 0.7135 (m-80) cc_final: 0.6448 (t80)
REVERT: R  262 ARG cc_start: 0.7666 (mtp85) cc_final: 0.7180 (mtm180)
REVERT: R  301 LYS cc_start: 0.8634 (tttt) cc_final: 0.8291 (ttmm)
REVERT: P   15 GLU cc_start: 0.8648 (pm20) cc_final: 0.8369 (pm20)
REVERT: P   21 TYR cc_start: 0.8136 (m-80) cc_final: 0.7597 (m-80)
  outliers start: 28
  outliers final: 19
  residues processed: 184
  average time/residue: 0.1982
  time to fit residues: 48.5719
Evaluate side-chains
  177 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 158
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
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   50 LEU
Chi-restraints excluded: chain C residue   51 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
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:    7.9990
   chunk 26 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 6 optimal weight:   10.0000
   chunk 7 optimal weight:    2.9990
   chunk 22 optimal weight:    8.9990
   chunk 24 optimal weight:    0.0000
   chunk 43 optimal weight:    0.5980
   chunk 36 optimal weight:    9.9990
   overall best weight:    1.0986

-------------------------------------------------------------------------------
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 100 ASN
R 288 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.121303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.096179 restraints weight = 16497.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 3.95
r_work: 0.3397 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.3013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7391  Z= 0.177
  Angle     :  0.590   8.808  10050  Z= 0.293
  Chirality :  0.043   0.292   1183
  Planarity :  0.004   0.046   1262
  Dihedral  :  4.454  41.736   1022
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 19.02 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.27), residues: 931
  helix:  1.00 (0.27), residues: 397
  sheet: -2.36 (0.38), residues: 162
  loop : -2.47 (0.28), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 297 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.013   0.001   PHE R 340 
 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
  191 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 166
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8678 (pp20)
REVERT: A   18 MET cc_start: 0.8806 (tpp) cc_final: 0.8561 (tpp)
REVERT: A   33 GLU cc_start: 0.9078 (pp20) cc_final: 0.8584 (pp20)
REVERT: A   35 LYS cc_start: 0.9058 (mppt) cc_final: 0.8654 (mptt)
REVERT: A  191 PHE cc_start: 0.8462 (t80) cc_final: 0.7964 (t80)
REVERT: A  195 HIS cc_start: 0.8538 (m-70) cc_final: 0.7772 (m-70)
REVERT: A  261 ASP cc_start: 0.8498 (t0) cc_final: 0.8124 (t0)
REVERT: A  276 GLU cc_start: 0.9400 (mp0) cc_final: 0.9020 (mp0)
REVERT: A  315 ASP cc_start: 0.8047 (p0) cc_final: 0.7741 (p0)
REVERT: A  337 ASP cc_start: 0.8752 (m-30) cc_final: 0.8037 (m-30)
REVERT: B   45 MET cc_start: 0.8342 (mmt) cc_final: 0.8037 (mmp)
REVERT: B   59 TYR cc_start: 0.8390 (m-80) cc_final: 0.8122 (m-80)
REVERT: B  215 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8149 (tm-30)
REVERT: B  266 HIS cc_start: 0.8354 (t-170) cc_final: 0.7963 (t70)
REVERT: B  292 PHE cc_start: 0.8038 (m-10) cc_final: 0.7454 (m-10)
REVERT: B  339 TRP cc_start: 0.8788 (m100) cc_final: 0.8411 (m100)
REVERT: C   40 TYR cc_start: 0.8745 (t80) cc_final: 0.8534 (t80)
REVERT: R  116 TRP cc_start: 0.7961 (t-100) cc_final: 0.7715 (t60)
REVERT: R  215 TYR cc_start: 0.7122 (m-80) cc_final: 0.6422 (t80)
REVERT: R  256 ASN cc_start: 0.8488 (t0) cc_final: 0.8277 (t0)
REVERT: R  262 ARG cc_start: 0.7757 (mtp85) cc_final: 0.7288 (mtm180)
REVERT: R  301 LYS cc_start: 0.8637 (tttt) cc_final: 0.8276 (ttmm)
REVERT: P   21 TYR cc_start: 0.8213 (m-80) cc_final: 0.7719 (m-80)
  outliers start: 25
  outliers final: 17
  residues processed: 181
  average time/residue: 0.1959
  time to fit residues: 47.3038
Evaluate side-chains
  173 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 156
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
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   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  225 LEU
Chi-restraints excluded: chain R residue  227 LEU
Chi-restraints excluded: chain R residue  259 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 70 optimal weight:    0.0470
   chunk 45 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   chunk 87 optimal weight:    4.9990
   chunk 56 optimal weight:    9.9990
   chunk 82 optimal weight:    0.8980
   chunk 42 optimal weight:    8.9990
   chunk 60 optimal weight:    0.6980
   chunk 14 optimal weight:    9.9990
   chunk 47 optimal weight:    9.9990
   overall best weight:    1.9282

-------------------------------------------------------------------------------
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 220 GLN
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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.119484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.093929 restraints weight = 16663.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 3.95
r_work: 0.3350 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.3247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7391  Z= 0.234
  Angle     :  0.625  12.214  10050  Z= 0.314
  Chirality :  0.044   0.399   1183
  Planarity :  0.004   0.046   1262
  Dihedral  :  4.475  37.224   1022
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.68 %
    Favored  : 77.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.27), residues: 931
  helix:  1.02 (0.27), residues: 397
  sheet: -2.18 (0.40), residues: 159
  loop : -2.45 (0.28), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 297 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.013   0.001   PHE B 292 
 TYR   0.008   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
  188 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 164
  time to evaluate  : 0.731 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.8835 (tpp) cc_final: 0.8619 (tpp)
REVERT: A   33 GLU cc_start: 0.9078 (pp20) cc_final: 0.8583 (pp20)
REVERT: A   35 LYS cc_start: 0.9105 (mppt) cc_final: 0.8698 (mptt)
REVERT: A  191 PHE cc_start: 0.8436 (t80) cc_final: 0.7993 (t80)
REVERT: A  195 HIS cc_start: 0.8584 (m-70) cc_final: 0.7818 (m-70)
REVERT: A  261 ASP cc_start: 0.8509 (t0) cc_final: 0.8116 (t0)
REVERT: A  276 GLU cc_start: 0.9407 (mp0) cc_final: 0.9010 (mp0)
REVERT: A  315 ASP cc_start: 0.8050 (p0) cc_final: 0.7692 (p0)
REVERT: A  337 ASP cc_start: 0.8820 (m-30) cc_final: 0.8100 (m-30)
REVERT: B   45 MET cc_start: 0.8412 (mmt) cc_final: 0.8059 (mmp)
REVERT: B   59 TYR cc_start: 0.8511 (m-80) cc_final: 0.8305 (m-80)
REVERT: B   78 LYS cc_start: 0.8226 (mmmt) cc_final: 0.7797 (mmmt)
REVERT: B  215 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8143 (tm-30)
REVERT: B  266 HIS cc_start: 0.8323 (t-170) cc_final: 0.7909 (t70)
REVERT: B  325 MET cc_start: 0.7179 (tpp) cc_final: 0.6919 (tpp)
REVERT: B  339 TRP cc_start: 0.8832 (m100) cc_final: 0.8425 (m100)
REVERT: C   40 TYR cc_start: 0.8775 (t80) cc_final: 0.8525 (t80)
REVERT: R  188 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6570 (pp20)
REVERT: R  256 ASN cc_start: 0.8485 (t0) cc_final: 0.8208 (t0)
REVERT: R  262 ARG cc_start: 0.7917 (mtp85) cc_final: 0.7390 (mtm180)
REVERT: R  301 LYS cc_start: 0.8653 (tttt) cc_final: 0.8382 (ttmm)
REVERT: P   21 TYR cc_start: 0.8206 (m-10) cc_final: 0.7687 (m-80)
  outliers start: 24
  outliers final: 16
  residues processed: 179
  average time/residue: 0.2043
  time to fit residues: 48.3725
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  : 0.859 
-------------------------------------------------------------------------------
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  164 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  190 LEU
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  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:    0.9990
   chunk 38 optimal weight:    8.9990
   chunk 49 optimal weight:    0.9990
   chunk 32 optimal weight:    8.9990
   chunk 23 optimal weight:    0.4980
   chunk 58 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 77 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3872 r_free = 0.3872 target = 0.120377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.095027 restraints weight = 16370.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 3.90
r_work: 0.3377 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.3350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7391  Z= 0.177
  Angle     :  0.625  14.064  10050  Z= 0.308
  Chirality :  0.044   0.412   1183
  Planarity :  0.004   0.046   1262
  Dihedral  :  4.155  27.123   1022
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 21.40 %
    Favored  : 75.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.27), residues: 931
  helix:  1.02 (0.27), residues: 397
  sheet: -2.10 (0.41), residues: 154
  loop : -2.33 (0.28), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP R 116 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.016   0.001   PHE B 222 
 TYR   0.012   0.001   TYR B 124 
 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
  190 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 169
  time to evaluate  : 0.853 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.9143 (tm-30) cc_final: 0.8657 (pp20)
REVERT: A   18 MET cc_start: 0.8806 (tpp) cc_final: 0.8562 (tpp)
REVERT: A   33 GLU cc_start: 0.9066 (pp20) cc_final: 0.8239 (pp20)
REVERT: A   35 LYS cc_start: 0.9080 (mppt) cc_final: 0.8730 (mptt)
REVERT: A  191 PHE cc_start: 0.8411 (t80) cc_final: 0.7974 (t80)
REVERT: A  195 HIS cc_start: 0.8582 (m-70) cc_final: 0.7603 (m-70)
REVERT: A  261 ASP cc_start: 0.8529 (t0) cc_final: 0.8177 (t0)
REVERT: A  275 GLU cc_start: 0.8968 (tp30) cc_final: 0.8680 (mm-30)
REVERT: A  276 GLU cc_start: 0.9395 (mp0) cc_final: 0.9020 (mp0)
REVERT: A  315 ASP cc_start: 0.8032 (p0) cc_final: 0.7654 (p0)
REVERT: A  337 ASP cc_start: 0.8764 (m-30) cc_final: 0.8034 (m-30)
REVERT: B   45 MET cc_start: 0.8407 (mmt) cc_final: 0.8082 (mmt)
REVERT: B   78 LYS cc_start: 0.8183 (mmmt) cc_final: 0.7739 (mmmt)
REVERT: B  124 TYR cc_start: 0.8435 (m-80) cc_final: 0.8228 (m-80)
REVERT: B  215 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8234 (tm-30)
REVERT: B  266 HIS cc_start: 0.8338 (t-170) cc_final: 0.7896 (t70)
REVERT: B  292 PHE cc_start: 0.8162 (m-10) cc_final: 0.7764 (m-80)
REVERT: B  325 MET cc_start: 0.7109 (tpp) cc_final: 0.6888 (tpp)
REVERT: B  339 TRP cc_start: 0.8801 (m100) cc_final: 0.8437 (m100)
REVERT: C   40 TYR cc_start: 0.8757 (t80) cc_final: 0.8527 (t80)
REVERT: C   46 LYS cc_start: 0.7899 (ptpp) cc_final: 0.7521 (tptt)
REVERT: R  135 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8460 (mm-40)
REVERT: R  188 GLU cc_start: 0.6845 (pp20) cc_final: 0.6565 (pp20)
REVERT: R  215 TYR cc_start: 0.7165 (m-80) cc_final: 0.6429 (t80)
REVERT: R  256 ASN cc_start: 0.8476 (t0) cc_final: 0.8241 (t0)
REVERT: R  262 ARG cc_start: 0.7846 (mtp85) cc_final: 0.7315 (mtm180)
REVERT: R  301 LYS cc_start: 0.8615 (tttt) cc_final: 0.8339 (ttmm)
REVERT: P   21 TYR cc_start: 0.8249 (m-10) cc_final: 0.7714 (m-80)
  outliers start: 21
  outliers final: 17
  residues processed: 181
  average time/residue: 0.2024
  time to fit residues: 48.2386
Evaluate side-chains
  176 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 158
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
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  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  259 GLN
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  135 GLN
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  263 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 22 optimal weight:    8.9990
   chunk 26 optimal weight:    0.0980
   chunk 6 optimal weight:    6.9990
   chunk 69 optimal weight:    0.6980
   chunk 54 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 59 optimal weight:    6.9990
   chunk 64 optimal weight:    0.8980
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.119657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.094225 restraints weight = 16447.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 3.91
r_work: 0.3366 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.3462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7391  Z= 0.195
  Angle     :  0.639  14.548  10050  Z= 0.316
  Chirality :  0.045   0.431   1183
  Planarity :  0.004   0.046   1262
  Dihedral  :  4.033  20.999   1022
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.66 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 22.46 %
    Favored  : 74.50 %
  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: -1.17 (0.28), residues: 931
  helix:  1.04 (0.27), residues: 396
  sheet: -1.94 (0.41), residues: 159
  loop : -2.26 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP R 116 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.008   0.001   PHE R 340 
 TYR   0.016   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
  179 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 156
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8696 (pp20)
REVERT: A   18 MET cc_start: 0.8789 (tpp) cc_final: 0.8554 (tpp)
REVERT: A   33 GLU cc_start: 0.9043 (pp20) cc_final: 0.8557 (pp20)
REVERT: A   35 LYS cc_start: 0.9068 (mppt) cc_final: 0.8654 (mptt)
REVERT: A  191 PHE cc_start: 0.8424 (t80) cc_final: 0.7942 (t80)
REVERT: A  195 HIS cc_start: 0.8577 (m-70) cc_final: 0.7913 (m-70)
REVERT: A  205 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.8173 (mtm-85)
REVERT: A  261 ASP cc_start: 0.8544 (t0) cc_final: 0.8141 (t0)
REVERT: A  275 GLU cc_start: 0.8969 (tp30) cc_final: 0.8675 (mm-30)
REVERT: A  276 GLU cc_start: 0.9393 (mp0) cc_final: 0.9013 (mp0)
REVERT: A  315 ASP cc_start: 0.8077 (p0) cc_final: 0.7688 (p0)
REVERT: A  337 ASP cc_start: 0.8792 (m-30) cc_final: 0.8058 (m-30)
REVERT: B   45 MET cc_start: 0.8442 (mmt) cc_final: 0.8108 (mmt)
REVERT: B  124 TYR cc_start: 0.8453 (m-80) cc_final: 0.8187 (m-80)
REVERT: B  215 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8430 (tt0)
REVERT: B  266 HIS cc_start: 0.8353 (t-170) cc_final: 0.7912 (t70)
REVERT: B  292 PHE cc_start: 0.8199 (m-10) cc_final: 0.7833 (m-80)
REVERT: B  339 TRP cc_start: 0.8812 (m100) cc_final: 0.8467 (m100)
REVERT: C   36 ASP cc_start: 0.8973 (m-30) cc_final: 0.8248 (t0)
REVERT: C   40 TYR cc_start: 0.8751 (t80) cc_final: 0.8535 (t80)
REVERT: R  135 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8490 (mm-40)
REVERT: R  262 ARG cc_start: 0.7902 (mtp85) cc_final: 0.7366 (mtm180)
REVERT: R  301 LYS cc_start: 0.8555 (tttt) cc_final: 0.8321 (ttmm)
REVERT: P   21 TYR cc_start: 0.8247 (m-10) cc_final: 0.7737 (m-80)
  outliers start: 23
  outliers final: 19
  residues processed: 172
  average time/residue: 0.2157
  time to fit residues: 49.0217
Evaluate side-chains
  173 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 153
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
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  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  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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 22 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 45 optimal weight:    8.9990
   chunk 79 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0870
   overall best weight:    0.9962

-------------------------------------------------------------------------------
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 155 HIS
** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 288 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.121125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.095671 restraints weight = 16590.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 3.96
r_work: 0.3369 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.3498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7391  Z= 0.189
  Angle     :  0.640  14.964  10050  Z= 0.317
  Chirality :  0.044   0.429   1183
  Planarity :  0.004   0.046   1262
  Dihedral  :  3.955  17.205   1022
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 22.06 %
    Favored  : 74.50 %
  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: -1.08 (0.28), residues: 931
  helix:  1.08 (0.27), residues: 395
  sheet: -1.88 (0.41), residues: 159
  loop : -2.16 (0.29), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP R 116 
 HIS   0.009   0.001   HIS B  91 
 PHE   0.009   0.001   PHE B 222 
 TYR   0.007   0.001   TYR B 124 
 ARG   0.008   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
  184 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 158
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.9143 (tm-30) cc_final: 0.8686 (pp20)
REVERT: A   18 MET cc_start: 0.8795 (tpp) cc_final: 0.8566 (tpp)
REVERT: A   33 GLU cc_start: 0.9069 (pp20) cc_final: 0.8255 (pp20)
REVERT: A   35 LYS cc_start: 0.9075 (mppt) cc_final: 0.8731 (mptt)
REVERT: A  191 PHE cc_start: 0.8419 (t80) cc_final: 0.7947 (t80)
REVERT: A  195 HIS cc_start: 0.8595 (m-70) cc_final: 0.7639 (m-70)
REVERT: A  205 ARG cc_start: 0.8408 (mtm-85) cc_final: 0.8178 (mtm-85)
REVERT: A  231 ASP cc_start: 0.8949 (OUTLIER) cc_final: 0.8641 (m-30)
REVERT: A  261 ASP cc_start: 0.8527 (t0) cc_final: 0.8129 (t0)
REVERT: A  275 GLU cc_start: 0.8978 (tp30) cc_final: 0.8684 (mm-30)
REVERT: A  276 GLU cc_start: 0.9388 (mp0) cc_final: 0.9008 (mp0)
REVERT: A  315 ASP cc_start: 0.8071 (p0) cc_final: 0.7685 (p0)
REVERT: A  337 ASP cc_start: 0.8792 (m-30) cc_final: 0.8051 (m-30)
REVERT: B   78 LYS cc_start: 0.8076 (mmmt) cc_final: 0.7643 (mmmt)
REVERT: B  124 TYR cc_start: 0.8456 (m-80) cc_final: 0.8125 (m-80)
REVERT: B  215 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8473 (tt0)
REVERT: B  266 HIS cc_start: 0.8365 (t-170) cc_final: 0.7899 (t70)
REVERT: B  292 PHE cc_start: 0.8199 (m-10) cc_final: 0.7821 (m-80)
REVERT: B  339 TRP cc_start: 0.8847 (m100) cc_final: 0.8490 (m100)
REVERT: C   36 ASP cc_start: 0.8999 (m-30) cc_final: 0.8283 (t0)
REVERT: C   40 TYR cc_start: 0.8758 (t80) cc_final: 0.8541 (t80)
REVERT: R  188 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6699 (pp20)
REVERT: R  215 TYR cc_start: 0.7153 (m-80) cc_final: 0.6444 (t80)
REVERT: R  262 ARG cc_start: 0.7897 (mtp85) cc_final: 0.7403 (mtm180)
REVERT: R  301 LYS cc_start: 0.8542 (tttt) cc_final: 0.8313 (ttmm)
REVERT: P   21 TYR cc_start: 0.8228 (m-10) cc_final: 0.7716 (m-80)
  outliers start: 26
  outliers final: 20
  residues processed: 176
  average time/residue: 0.2148
  time to fit residues: 49.7842
Evaluate side-chains
  172 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 150
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  231 ASP
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  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  259 GLN
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   81 MET
Chi-restraints excluded: chain R residue   94 VAL
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  204 THR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 90 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 39 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 26 optimal weight:    7.9990
   chunk 43 optimal weight:    6.9990
   chunk 86 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0570
   overall best weight:    1.1702

-------------------------------------------------------------------------------
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 155 HIS
** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 288 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.120946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.095556 restraints weight = 16650.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 3.96
r_work: 0.3376 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.3565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7391  Z= 0.198
  Angle     :  0.642  15.111  10050  Z= 0.320
  Chirality :  0.045   0.438   1183
  Planarity :  0.004   0.047   1262
  Dihedral  :  3.949  17.880   1022
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.66 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 22.72 %
    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: -1.03 (0.28), residues: 931
  helix:  1.11 (0.27), residues: 395
  sheet: -1.86 (0.41), residues: 159
  loop : -2.12 (0.29), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP R 116 
 HIS   0.008   0.001   HIS B  91 
 PHE   0.024   0.001   PHE B 222 
 TYR   0.020   0.001   TYR R 110 
 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: 22
    poor density    : 153
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8706 (pp20)
REVERT: A   18 MET cc_start: 0.8791 (tpp) cc_final: 0.8559 (tpp)
REVERT: A   33 GLU cc_start: 0.9024 (pp20) cc_final: 0.8244 (pp20)
REVERT: A   35 LYS cc_start: 0.9077 (mppt) cc_final: 0.8730 (mptt)
REVERT: A  191 PHE cc_start: 0.8430 (t80) cc_final: 0.7929 (t80)
REVERT: A  195 HIS cc_start: 0.8592 (m-70) cc_final: 0.7645 (m-70)
REVERT: A  205 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.8176 (mtm-85)
REVERT: A  231 ASP cc_start: 0.8951 (OUTLIER) cc_final: 0.8640 (m-30)
REVERT: A  261 ASP cc_start: 0.8530 (t0) cc_final: 0.8134 (t0)
REVERT: A  275 GLU cc_start: 0.8987 (tp30) cc_final: 0.8690 (mm-30)
REVERT: A  276 GLU cc_start: 0.9386 (mp0) cc_final: 0.9010 (mp0)
REVERT: A  315 ASP cc_start: 0.8067 (p0) cc_final: 0.7683 (p0)
REVERT: A  337 ASP cc_start: 0.8805 (m-30) cc_final: 0.8077 (m-30)
REVERT: B   59 TYR cc_start: 0.8179 (m-80) cc_final: 0.7735 (m-80)
REVERT: B   78 LYS cc_start: 0.8103 (mmmt) cc_final: 0.7629 (mmmt)
REVERT: B  124 TYR cc_start: 0.8474 (m-80) cc_final: 0.8143 (m-80)
REVERT: B  215 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8471 (tt0)
REVERT: B  266 HIS cc_start: 0.8392 (t-170) cc_final: 0.7919 (t70)
REVERT: B  292 PHE cc_start: 0.8227 (m-10) cc_final: 0.7901 (m-80)
REVERT: B  339 TRP cc_start: 0.8806 (m100) cc_final: 0.8459 (m100)
REVERT: C   36 ASP cc_start: 0.9021 (m-30) cc_final: 0.8314 (t0)
REVERT: C   40 TYR cc_start: 0.8765 (t80) cc_final: 0.8542 (t80)
REVERT: R  188 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6673 (pp20)
REVERT: R  262 ARG cc_start: 0.7893 (mtp85) cc_final: 0.7396 (mtm180)
REVERT: R  301 LYS cc_start: 0.8556 (tttt) cc_final: 0.8331 (ttmm)
REVERT: P   21 TYR cc_start: 0.8248 (m-10) cc_final: 0.7732 (m-80)
  outliers start: 22
  outliers final: 19
  residues processed: 169
  average time/residue: 0.2086
  time to fit residues: 46.3717
Evaluate side-chains
  173 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 152
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  231 ASP
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  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  259 GLN
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   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  204 THR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 26 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9990
   chunk 9 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   chunk 8 optimal weight:    4.9990
   chunk 41 optimal weight:    8.9990
   chunk 1 optimal weight:    5.9990
   chunk 81 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    2.1186

-------------------------------------------------------------------------------
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 249 HIS
** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.118646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.092932 restraints weight = 16588.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 3.92
r_work: 0.3316 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.3751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7391  Z= 0.258
  Angle     :  0.697  16.746  10050  Z= 0.341
  Chirality :  0.046   0.430   1183
  Planarity :  0.004   0.046   1262
  Dihedral  :  4.087  18.866   1022
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 22.32 %
    Favored  : 74.24 %
  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: -1.10 (0.28), residues: 931
  helix:  1.04 (0.27), residues: 395
  sheet: -1.98 (0.40), residues: 161
  loop : -2.09 (0.30), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP R 116 
 HIS   0.007   0.001   HIS B  91 
 PHE   0.014   0.001   PHE B 222 
 TYR   0.020   0.001   TYR R 110 
 ARG   0.009   0.001   ARG A  21 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3779.86 seconds
wall clock time: 68 minutes 14.60 seconds (4094.60 seconds total)