Starting phenix.real_space_refine
on Wed Mar  4 02:09:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lr1_63312/03_2026/9lr1_63312.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lr1_63312/03_2026/9lr1_63312.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lr1_63312/03_2026/9lr1_63312.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lr1_63312/03_2026/9lr1_63312.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lr1_63312/03_2026/9lr1_63312.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lr1_63312/03_2026/9lr1_63312.map"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=  -0.000 sd=   0.002
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      77      5.16       5
     C    6293      2.51       5
     N    1683      2.21       5
     O    1860      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9913
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1748
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1748
          Classifications: {'peptide': 217}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2607
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "G"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "S"
      Number of atoms: 1777
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1777
          Classifications: {'peptide': 231}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 962
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 962
          Classifications: {'peptide': 129}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "R"
      Number of atoms: 2375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 297, 2375
          Classifications: {'peptide': 297}
          Link IDs: {'PTRANS': 11, 'TRANS': 285}
          Chain breaks: 1
  Time building chain proxies: 1.98, per 1000 atoms: 0.20
  Number of scatterers: 9913
  At special positions: 0
  Unit cell: (88.35, 118.11, 157.17, 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      77     16.00
     O    1860      8.00
     N    1683      7.00
     C    6293      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  33 " - pdb=" SG  CYS C 110 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 102 " - pdb=" SG  CYS R 181 " 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: 0.78
  Conformation dependent library (CDL) restraints added in 500.9 milliseconds
  

  2502 Ramachandran restraints generated.
    1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2362

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 16 sheets defined
      36.1% alpha, 22.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.662A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.380A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.680A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 4.293A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 4.046A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 3.698A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 3 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 6 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.677A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 208 through 212
      removed outlier: 3.749A  pdb=" N   VAL S 212 " --> pdb=" O   ALA S 209 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 90
    Processing helix  chain 'R' and resid 30 through 55
      removed outlier: 3.598A  pdb=" N   THR R  44 " --> pdb=" O   LEU R  40 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   VAL R  49 " --> pdb=" O   GLY R  45 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 64 through 77
    Processing helix  chain 'R' and resid 81 through 91
      removed outlier: 3.530A  pdb=" N   TRP R  85 " --> pdb=" O   THR R  81 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 97 through 132
      removed outlier: 4.151A  pdb=" N   PHE R 101 " --> pdb=" O   PHE R  97 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 145
    Processing helix  chain 'R' and resid 146 through 161
      removed outlier: 3.500A  pdb=" N   THR R 150 " --> pdb=" O   GLY R 146 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ALA R 161 " --> pdb=" O   ALA R 157 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 161 through 167
    Processing helix  chain 'R' and resid 193 through 232
      removed outlier: 5.027A  pdb=" N   VAL R 212 " --> pdb=" O   VAL R 208 " (cutoff:3.500A)
      Proline residue:  R 213  - end of helix
    Processing helix  chain 'R' and resid 236 through 260
      removed outlier: 3.502A  pdb=" N   PHE R 257 " --> pdb=" O   LEU R 253 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 261 through 273
      removed outlier: 3.605A  pdb=" N   VAL R 267 " --> pdb=" O   PRO R 263 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 274 through 276
      No H-bonds generated for 'chain 'R' and resid 274 through 276'
    Processing helix  chain 'R' and resid 282 through 299
      Proline residue:  R 292  - end of helix
    Processing helix  chain 'R' and resid 299 through 310
      removed outlier: 3.541A  pdb=" N   CYS R 303 " --> pdb=" O   TYR R 299 " (cutoff:3.500A)
      Proline residue:  R 306  - end of helix
    Processing helix  chain 'R' and resid 313 through 325
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 3.501A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.225A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.631A  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: 6.538A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.660A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.911A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.954A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.032A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.238A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.913A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.073A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.313A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.980A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.820A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 4.983A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.172A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.537A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.813A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.753A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 4.226A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129
    Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136
      removed outlier: 6.502A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 4.686A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 46 through 47
      removed outlier: 3.709A  pdb=" N   GLU C  46 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 67 through 72
      removed outlier: 3.656A  pdb=" N   ILE C  77 " --> pdb=" O   ASP C  72 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'R' and resid 168 through 171
      removed outlier: 3.541A  pdb=" N   THR R 169 " --> pdb=" O   TYR R 182 " (cutoff:3.500A)

    487 hydrogen bonds defined for protein.
    1335 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.53

  Time building geometry restraints manager: 1.05 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3177
        1.34 -     1.46: 2425
        1.46 -     1.58: 4411
        1.58 -     1.70: 0
        1.70 -     1.82: 112
  Bond restraints: 10125
  Sorted by residual:
  bond pdb=" CA  GLU S 222 "
       pdb=" C   GLU S 222 "
    ideal  model  delta    sigma   weight residual
    1.521  1.502  0.019 1.23e-02 6.61e+03 2.50e+00
  bond pdb=" CA  ASP B 186 "
       pdb=" C   ASP B 186 "
    ideal  model  delta    sigma   weight residual
    1.523  1.506  0.017 1.32e-02 5.74e+03 1.63e+00
  bond pdb=" C   MET R 262 "
       pdb=" O   MET R 262 "
    ideal  model  delta    sigma   weight residual
    1.244  1.231  0.013 1.00e-02 1.00e+04 1.58e+00
  bond pdb=" C   MET R 262 "
       pdb=" N   PRO R 263 "
    ideal  model  delta    sigma   weight residual
    1.333  1.351 -0.017 1.44e-02 4.82e+03 1.46e+00
  bond pdb=" CA  HIS A 195 "
       pdb=" C   HIS A 195 "
    ideal  model  delta    sigma   weight residual
    1.523  1.508  0.015 1.28e-02 6.10e+03 1.30e+00
  ... (remaining 10120 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 13563
        2.00 -     3.99: 124
        3.99 -     5.99: 23
        5.99 -     7.98: 3
        7.98 -     9.98: 1
  Bond angle restraints: 13714
  Sorted by residual:
  angle pdb=" CB  MET R  36 "
        pdb=" CG  MET R  36 "
        pdb=" SD  MET R  36 "
      ideal   model   delta    sigma   weight residual
     112.70  122.68   -9.98 3.00e+00 1.11e-01 1.11e+01
  angle pdb=" N   SER B 245 "
        pdb=" CA  SER B 245 "
        pdb=" C   SER B 245 "
      ideal   model   delta    sigma   weight residual
     109.18  113.71   -4.53 1.42e+00 4.96e-01 1.02e+01
  angle pdb=" CA  MET R 262 "
        pdb=" C   MET R 262 "
        pdb=" N   PRO R 263 "
      ideal   model   delta    sigma   weight residual
     120.77  117.79    2.98 9.70e-01 1.06e+00 9.45e+00
  angle pdb=" N   THR R 176 "
        pdb=" CA  THR R 176 "
        pdb=" C   THR R 176 "
      ideal   model   delta    sigma   weight residual
     114.64  110.11    4.53 1.52e+00 4.33e-01 8.88e+00
  angle pdb=" C   CYS A   3 "
        pdb=" N   THR A   4 "
        pdb=" CA  THR A   4 "
      ideal   model   delta    sigma   weight residual
     121.54  127.07   -5.53 1.91e+00 2.74e-01 8.37e+00
  ... (remaining 13709 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.63: 5298
       17.63 -    35.26: 504
       35.26 -    52.89: 160
       52.89 -    70.52: 14
       70.52 -    88.15: 9
  Dihedral angle restraints: 5985
    sinusoidal: 2311
      harmonic: 3674
  Sorted by residual:
  dihedral pdb=" CB  CYS R 102 "
           pdb=" SG  CYS R 102 "
           pdb=" SG  CYS R 181 "
           pdb=" CB  CYS R 181 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  169.23  -76.23     1      1.00e+01 1.00e-02 7.31e+01
  dihedral pdb=" CB  CYS C  22 "
           pdb=" SG  CYS C  22 "
           pdb=" SG  CYS C  95 "
           pdb=" CB  CYS C  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   47.68   45.32     1      1.00e+01 1.00e-02 2.85e+01
  dihedral pdb=" CA  PHE S  32 "
           pdb=" C   PHE S  32 "
           pdb=" N   GLY S  33 "
           pdb=" CA  GLY S  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.49   18.51     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 5982 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 996
       0.030 -    0.061: 362
       0.061 -    0.091: 107
       0.091 -    0.122: 75
       0.122 -    0.152: 3
  Chirality restraints: 1543
  Sorted by residual:
  chirality pdb=" CA  THR A   4 "
            pdb=" N   THR A   4 "
            pdb=" C   THR A   4 "
            pdb=" CB  THR A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.37    0.15 2.00e-01 2.50e+01 5.79e-01
  chirality pdb=" CA  PHE R 291 "
            pdb=" N   PHE R 291 "
            pdb=" C   PHE R 291 "
            pdb=" CB  PHE R 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 3.97e-01
  chirality pdb=" CA  ILE S 204 "
            pdb=" N   ILE S 204 "
            pdb=" C   ILE S 204 "
            pdb=" CB  ILE S 204 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.92e-01
  ... (remaining 1540 not shown)

  Planarity restraints: 1731
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE R 291 "   -0.030 5.00e-02 4.00e+02   4.56e-02 3.33e+00
        pdb=" N   PRO R 292 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO R 292 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO R 292 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R  82 "    0.027 5.00e-02 4.00e+02   4.10e-02 2.69e+00
        pdb=" N   PRO R  83 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO R  83 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO R  83 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.027 5.00e-02 4.00e+02   4.07e-02 2.64e+00
        pdb=" N   PRO B 236 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1728 not shown)

  Histogram of nonbonded interaction distances:
        1.97 -     2.55: 60
        2.55 -     3.14: 7387
        3.14 -     3.73: 15479
        3.73 -     4.31: 22221
        4.31 -     4.90: 37227
  Nonbonded interactions: 82374
  Sorted by model distance:
  nonbonded pdb=" NE  ARG B 197 "
            pdb=" NH1 ARG B 214 "
     model   vdw
     1.969 3.200
  nonbonded pdb=" OE2 GLU B   3 "
            pdb=" NH2 ARG G  13 "
     model   vdw
     1.981 3.120
  nonbonded pdb=" O   TYR C 105 "
            pdb=" NH1 ARG R 168 "
     model   vdw
     2.207 3.120
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 163 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   THR A   4 "
            pdb=" OG1 THR A   4 "
     model   vdw
     2.267 3.040
  ... (remaining 82369 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:             1.170
  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:             0.020
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.180
  Find NCS groups from input model:        0.050
  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:9.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10130  Z= 0.131
  Angle     :  0.530   9.980  13724  Z= 0.295
  Chirality :  0.040   0.152   1543
  Planarity :  0.004   0.046   1731
  Dihedral  : 15.360  88.148   3608
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.80 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  : 20.39 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.24), residues: 1251
  helix:  1.86 (0.26), residues: 415
  sheet:  1.13 (0.31), residues: 279
  loop : -0.37 (0.26), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R  55 
 TYR   0.022   0.001   TYR R 182 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.008   0.001   TRP B  63 
 HIS   0.003   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (10125)
  covalent geometry    : angle       0.52961 (13714)
  SS BOND              : bond        0.00303 (    5)
  SS BOND              : angle       0.93759 (   10)
  hydrogen bonds       : bond        0.16453 (  480)
  hydrogen bonds       : angle       6.28102 ( 1335)

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

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

  2502 Ramachandran restraints generated.
    1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2502 Ramachandran restraints generated.
    1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 151
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: A  195 HIS cc_start: 0.7994 (m-70) cc_final: 0.7512 (t-170)
  outliers start: 4
  outliers final: 1
  residues processed: 155
  average time/residue: 0.7479
  time to fit residues: 122.1543
Evaluate side-chains
  143 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  270 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 117 optimal weight:    0.7980
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A 188 HIS
A 304 GLN
B  75 GLN
S   3 GLN
C 113 ASN
R 175 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.176231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.118639 restraints weight = 9931.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 1.84
r_work: 0.3111 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 3.07 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.1021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  10130  Z= 0.213
  Angle     :  0.596   8.478  13724  Z= 0.317
  Chirality :  0.044   0.157   1543
  Planarity :  0.005   0.048   1731
  Dihedral  :  4.656  25.675   1382
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.28 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 16.87 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.14 (0.24), residues: 1251
  helix:  2.00 (0.26), residues: 416
  sheet:  0.78 (0.28), residues: 317
  loop : -0.23 (0.28), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG S 179 
 TYR   0.013   0.002   TYR S 103 
 PHE   0.018   0.002   PHE B 199 
 TRP   0.015   0.002   TRP B 169 
 HIS   0.005   0.002   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 (10125)
  covalent geometry    : angle       0.59579 (13714)
  SS BOND              : bond        0.00583 (    5)
  SS BOND              : angle       0.98775 (   10)
  hydrogen bonds       : bond        0.04613 (  480)
  hydrogen bonds       : angle       4.82595 ( 1335)

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

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

  2502 Ramachandran restraints generated.
    1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2502 Ramachandran restraints generated.
    1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 152
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
REVERT: A  195 HIS cc_start: 0.8335 (m-70) cc_final: 0.7042 (t-90)
REVERT: A  273 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7840 (tt)
REVERT: G   42 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6958 (tp30)
REVERT: S  148 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7820 (ptt-90)
  outliers start: 35
  outliers final: 15
  residues processed: 172
  average time/residue: 0.7494
  time to fit residues: 135.9250
Evaluate side-chains
  160 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 142
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  148 ARG
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain R residue   73 VAL
Chi-restraints excluded: chain R residue  199 VAL
Chi-restraints excluded: chain R residue  240 LEU
Chi-restraints excluded: chain R residue  259 LEU
Chi-restraints excluded: chain R residue  262 MET
Chi-restraints excluded: chain R residue  316 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 58 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 109 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0980
   chunk 56 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 97 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
G  18 GLN
S   3 GLN
S  82 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.176861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.118397 restraints weight = 10006.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 1.96
r_work: 0.3091 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2968 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.1147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10130  Z= 0.124
  Angle     :  0.502   7.193  13724  Z= 0.268
  Chirality :  0.041   0.147   1543
  Planarity :  0.004   0.046   1731
  Dihedral  :  4.370  26.129   1382
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.04 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 18.44 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.24), residues: 1251
  helix:  2.21 (0.26), residues: 416
  sheet:  0.76 (0.30), residues: 289
  loop : -0.33 (0.27), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  46 
 TYR   0.010   0.001   TYR S 178 
 PHE   0.014   0.001   PHE B 199 
 TRP   0.017   0.001   TRP B 169 
 HIS   0.003   0.001   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (10125)
  covalent geometry    : angle       0.50214 (13714)
  SS BOND              : bond        0.00431 (    5)
  SS BOND              : angle       0.70545 (   10)
  hydrogen bonds       : bond        0.03687 (  480)
  hydrogen bonds       : angle       4.49798 ( 1335)

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

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

  2502 Ramachandran restraints generated.
    1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2502 Ramachandran restraints generated.
    1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 154
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
REVERT: A  195 HIS cc_start: 0.8344 (m-70) cc_final: 0.6968 (t-90)
REVERT: A  273 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7869 (tt)
REVERT: G   42 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7028 (tp30)
REVERT: R   63 SER cc_start: 0.6820 (OUTLIER) cc_final: 0.6601 (p)
REVERT: R  165 MET cc_start: 0.7752 (tpp) cc_final: 0.7344 (tpp)
REVERT: R  316 PHE cc_start: 0.4295 (OUTLIER) cc_final: 0.4080 (m-10)
REVERT: R  323 MET cc_start: 0.1297 (mtp) cc_final: 0.1010 (mtt)
  outliers start: 21
  outliers final: 12
  residues processed: 166
  average time/residue: 0.7302
  time to fit residues: 128.0390
Evaluate side-chains
  162 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 146
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain R residue   41 LEU
Chi-restraints excluded: chain R residue   63 SER
Chi-restraints excluded: chain R residue  109 ILE
Chi-restraints excluded: chain R residue  174 GLU
Chi-restraints excluded: chain R residue  199 VAL
Chi-restraints excluded: chain R residue  240 LEU
Chi-restraints excluded: chain R residue  298 SER
Chi-restraints excluded: chain R residue  316 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   chunk 54 optimal weight:   10.0000
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0030
   chunk 119 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 51 optimal weight:    6.9990
   chunk 60 optimal weight:    0.6980
   overall best weight:    0.8594

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
S   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.177876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.121526 restraints weight = 10052.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 1.77
r_work: 0.3151 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3035 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.1293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10130  Z= 0.123
  Angle     :  0.499   7.078  13724  Z= 0.264
  Chirality :  0.040   0.144   1543
  Planarity :  0.004   0.046   1731
  Dihedral  :  4.295  26.883   1382
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.88 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.96 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.21 (0.24), residues: 1251
  helix:  2.32 (0.26), residues: 416
  sheet:  0.77 (0.29), residues: 289
  loop : -0.36 (0.27), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  46 
 TYR   0.010   0.001   TYR R  88 
 PHE   0.014   0.001   PHE B 199 
 TRP   0.015   0.001   TRP B 169 
 HIS   0.003   0.001   HIS R 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (10125)
  covalent geometry    : angle       0.49901 (13714)
  SS BOND              : bond        0.00363 (    5)
  SS BOND              : angle       0.66027 (   10)
  hydrogen bonds       : bond        0.03501 (  480)
  hydrogen bonds       : angle       4.38157 ( 1335)

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

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

  2502 Ramachandran restraints generated.
    1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2502 Ramachandran restraints generated.
    1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 154
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: A  195 HIS cc_start: 0.8266 (m-70) cc_final: 0.6943 (t70)
REVERT: A  273 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7851 (tt)
REVERT: G   42 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6949 (tp30)
REVERT: R  165 MET cc_start: 0.7686 (tpp) cc_final: 0.7317 (tpp)
REVERT: R  323 MET cc_start: 0.1242 (mtp) cc_final: 0.0950 (mtt)
  outliers start: 31
  outliers final: 14
  residues processed: 175
  average time/residue: 0.6982
  time to fit residues: 129.0777
Evaluate side-chains
  165 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 149
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain R residue  109 ILE
Chi-restraints excluded: chain R residue  113 MET
Chi-restraints excluded: chain R residue  169 THR
Chi-restraints excluded: chain R residue  174 GLU
Chi-restraints excluded: chain R residue  199 VAL
Chi-restraints excluded: chain R residue  226 GLN
Chi-restraints excluded: chain R residue  298 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 69 optimal weight:    2.9990
   chunk 87 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 112 optimal weight:    0.0870
   chunk 57 optimal weight:    0.6980
   chunk 41 optimal weight:    5.9990
   chunk 95 optimal weight:    3.9990
   chunk 90 optimal weight:    0.0770
   overall best weight:    0.5116

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
B  75 GLN
S   3 GLN
R 175 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.179267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.123214 restraints weight = 10043.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 1.79
r_work: 0.3168 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3051 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.1397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  10130  Z= 0.099
  Angle     :  0.484  10.386  13724  Z= 0.252
  Chirality :  0.040   0.140   1543
  Planarity :  0.004   0.046   1731
  Dihedral  :  4.131  26.972   1382
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.64 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 17.15 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.24), residues: 1251
  helix:  2.42 (0.26), residues: 416
  sheet:  0.71 (0.30), residues: 288
  loop : -0.32 (0.27), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 241 
 TYR   0.010   0.001   TYR C 109 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.016   0.001   TRP B 169 
 HIS   0.002   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 (10125)
  covalent geometry    : angle       0.48402 (13714)
  SS BOND              : bond        0.00307 (    5)
  SS BOND              : angle       0.63453 (   10)
  hydrogen bonds       : bond        0.03161 (  480)
  hydrogen bonds       : angle       4.23590 ( 1335)

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

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

  2502 Ramachandran restraints generated.
    1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2502 Ramachandran restraints generated.
    1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 150
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
REVERT: A  195 HIS cc_start: 0.8260 (m-70) cc_final: 0.6896 (t70)
REVERT: A  273 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7835 (tt)
REVERT: R  165 MET cc_start: 0.7662 (tpp) cc_final: 0.7321 (tpp)
REVERT: R  236 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.6153 (mpt-90)
REVERT: R  284 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.7160 (m-30)
REVERT: R  323 MET cc_start: 0.0952 (mtp) cc_final: 0.0654 (mtt)
  outliers start: 29
  outliers final: 12
  residues processed: 170
  average time/residue: 0.7203
  time to fit residues: 129.3514
Evaluate side-chains
  159 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 144
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain R residue   41 LEU
Chi-restraints excluded: chain R residue  169 THR
Chi-restraints excluded: chain R residue  174 GLU
Chi-restraints excluded: chain R residue  236 ARG
Chi-restraints excluded: chain R residue  240 LEU
Chi-restraints excluded: chain R residue  284 ASP
Chi-restraints excluded: chain R residue  298 SER
Chi-restraints excluded: chain R residue  302 SER
Chi-restraints excluded: chain R residue  316 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 83 optimal weight:    0.0370
   chunk 118 optimal weight:    0.0370
   chunk 60 optimal weight:    4.9990
   chunk 81 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 107 optimal weight:    6.9990
   chunk 12 optimal weight:    4.9990
   chunk 113 optimal weight:    0.9980
   chunk 98 optimal weight:    0.8980
   overall best weight:    0.5736

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

Flipped N/Q/H residues before XYZ refinement:
S   3 GLN
R 175 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.179358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.123164 restraints weight = 10051.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 1.79
r_work: 0.3172 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.1470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  10130  Z= 0.101
  Angle     :  0.482   8.791  13724  Z= 0.251
  Chirality :  0.040   0.139   1543
  Planarity :  0.004   0.046   1731
  Dihedral  :  4.077  26.868   1382
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.96 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 17.89 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.24), residues: 1251
  helix:  2.47 (0.26), residues: 416
  sheet:  0.69 (0.29), residues: 290
  loop : -0.30 (0.27), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 241 
 TYR   0.019   0.001   TYR R 182 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.015   0.001   TRP B 169 
 HIS   0.002   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 (10125)
  covalent geometry    : angle       0.48236 (13714)
  SS BOND              : bond        0.00342 (    5)
  SS BOND              : angle       0.60501 (   10)
  hydrogen bonds       : bond        0.03139 (  480)
  hydrogen bonds       : angle       4.19162 ( 1335)

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

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

  2502 Ramachandran restraints generated.
    1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2502 Ramachandran restraints generated.
    1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 152
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
REVERT: A  195 HIS cc_start: 0.8239 (m-70) cc_final: 0.6891 (t70)
REVERT: B  219 ARG cc_start: 0.8440 (mtm-85) cc_final: 0.7885 (mtp85)
REVERT: R  165 MET cc_start: 0.7730 (tpp) cc_final: 0.7484 (tpp)
REVERT: R  236 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.6188 (mpt-90)
REVERT: R  241 ARG cc_start: 0.7483 (ttp-110) cc_final: 0.7169 (ttm110)
REVERT: R  323 MET cc_start: 0.0820 (mtp) cc_final: 0.0514 (mtt)
  outliers start: 24
  outliers final: 13
  residues processed: 169
  average time/residue: 0.7148
  time to fit residues: 127.6697
Evaluate side-chains
  160 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 146
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain R residue   37 LEU
Chi-restraints excluded: chain R residue   41 LEU
Chi-restraints excluded: chain R residue   63 SER
Chi-restraints excluded: chain R residue  169 THR
Chi-restraints excluded: chain R residue  174 GLU
Chi-restraints excluded: chain R residue  236 ARG
Chi-restraints excluded: chain R residue  302 SER
Chi-restraints excluded: chain R residue  316 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 84 optimal weight:    9.9990
   chunk 25 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 86 optimal weight:    8.9990
   chunk 3 optimal weight:    3.9990
   chunk 83 optimal weight:    0.0040
   chunk 26 optimal weight:    0.1980
   chunk 73 optimal weight:    4.9990
   overall best weight:    0.7394

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
S   3 GLN
R 175 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.178444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.122035 restraints weight = 10039.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 1.78
r_work: 0.3167 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3050 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.1516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10130  Z= 0.111
  Angle     :  0.497   9.158  13724  Z= 0.257
  Chirality :  0.040   0.141   1543
  Planarity :  0.004   0.046   1731
  Dihedral  :  4.151  27.061   1382
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.80 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 18.35 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.24), residues: 1251
  helix:  2.45 (0.26), residues: 416
  sheet:  0.64 (0.29), residues: 296
  loop : -0.26 (0.28), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 241 
 TYR   0.020   0.001   TYR R 182 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.014   0.001   TRP B 169 
 HIS   0.002   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (10125)
  covalent geometry    : angle       0.49703 (13714)
  SS BOND              : bond        0.00381 (    5)
  SS BOND              : angle       0.63983 (   10)
  hydrogen bonds       : bond        0.03230 (  480)
  hydrogen bonds       : angle       4.21766 ( 1335)

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

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

  2502 Ramachandran restraints generated.
    1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2502 Ramachandran restraints generated.
    1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 151
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
REVERT: A  195 HIS cc_start: 0.8239 (m-70) cc_final: 0.6926 (t70)
REVERT: A  273 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7819 (tt)
REVERT: B  219 ARG cc_start: 0.8446 (mtm-85) cc_final: 0.7894 (mtp85)
REVERT: R  165 MET cc_start: 0.7671 (tpp) cc_final: 0.7440 (tpp)
REVERT: R  236 ARG cc_start: 0.6826 (OUTLIER) cc_final: 0.6186 (mpt-90)
REVERT: R  241 ARG cc_start: 0.7411 (ttp-110) cc_final: 0.7133 (ttm110)
REVERT: R  323 MET cc_start: 0.0985 (mtp) cc_final: 0.0668 (mtt)
  outliers start: 25
  outliers final: 15
  residues processed: 166
  average time/residue: 0.7297
  time to fit residues: 128.0612
Evaluate side-chains
  164 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 147
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain R residue   37 LEU
Chi-restraints excluded: chain R residue   41 LEU
Chi-restraints excluded: chain R residue   63 SER
Chi-restraints excluded: chain R residue  109 ILE
Chi-restraints excluded: chain R residue  169 THR
Chi-restraints excluded: chain R residue  174 GLU
Chi-restraints excluded: chain R residue  199 VAL
Chi-restraints excluded: chain R residue  236 ARG
Chi-restraints excluded: chain R residue  298 SER
Chi-restraints excluded: chain R residue  316 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 112 optimal weight:    0.7980
   chunk 109 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 101 optimal weight:    0.7980
   chunk 117 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0030
   chunk 82 optimal weight:    8.9990
   chunk 35 optimal weight:    4.9990
   chunk 119 optimal weight:    4.9990
   chunk 40 optimal weight:    0.0070
   overall best weight:    0.4608

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
S   3 GLN
R 175 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.180053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.124168 restraints weight = 10021.036|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 1.81
r_work: 0.3186 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.1586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  10130  Z= 0.094
  Angle     :  0.477  10.154  13724  Z= 0.246
  Chirality :  0.039   0.136   1543
  Planarity :  0.003   0.047   1731
  Dihedral  :  3.998  27.008   1382
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.40 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 18.81 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.37 (0.24), residues: 1251
  helix:  2.54 (0.26), residues: 416
  sheet:  0.77 (0.30), residues: 278
  loop : -0.26 (0.27), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  46 
 TYR   0.020   0.001   TYR R 182 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.016   0.001   TRP B 169 
 HIS   0.002   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 (10125)
  covalent geometry    : angle       0.47694 (13714)
  SS BOND              : bond        0.00284 (    5)
  SS BOND              : angle       0.60901 (   10)
  hydrogen bonds       : bond        0.02987 (  480)
  hydrogen bonds       : angle       4.11501 ( 1335)

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

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

  2502 Ramachandran restraints generated.
    1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2502 Ramachandran restraints generated.
    1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 152
  time to evaluate  : 0.363 
Fit side-chains
REVERT: A  195 HIS cc_start: 0.8193 (m-70) cc_final: 0.6842 (t70)
REVERT: B  219 ARG cc_start: 0.8434 (mtm-85) cc_final: 0.7873 (mtp85)
REVERT: R  165 MET cc_start: 0.7647 (tpp) cc_final: 0.7270 (tpp)
REVERT: R  241 ARG cc_start: 0.7412 (ttp-110) cc_final: 0.7119 (ttm110)
REVERT: R  323 MET cc_start: 0.1115 (mtp) cc_final: 0.0827 (mtt)
  outliers start: 20
  outliers final: 14
  residues processed: 166
  average time/residue: 0.6991
  time to fit residues: 122.8673
Evaluate side-chains
  161 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 147
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain R residue   37 LEU
Chi-restraints excluded: chain R residue   63 SER
Chi-restraints excluded: chain R residue   80 VAL
Chi-restraints excluded: chain R residue  109 ILE
Chi-restraints excluded: chain R residue  169 THR
Chi-restraints excluded: chain R residue  174 GLU
Chi-restraints excluded: chain R residue  240 LEU
Chi-restraints excluded: chain R residue  298 SER
Chi-restraints excluded: chain R residue  316 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 121 optimal weight:    0.6980
   chunk 95 optimal weight:    0.2980
   chunk 97 optimal weight:    5.9990
   chunk 46 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 88 optimal weight:    9.9990
   chunk 68 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 30 optimal weight:    0.1980
   chunk 34 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
S   3 GLN
R 175 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.178484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.121570 restraints weight = 10031.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 1.89
r_work: 0.3157 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.1618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10130  Z= 0.118
  Angle     :  0.510  10.747  13724  Z= 0.261
  Chirality :  0.040   0.141   1543
  Planarity :  0.004   0.046   1731
  Dihedral  :  4.162  27.043   1382
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.64 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 18.91 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.34 (0.24), residues: 1251
  helix:  2.47 (0.26), residues: 417
  sheet:  0.70 (0.29), residues: 286
  loop : -0.22 (0.27), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  46 
 TYR   0.021   0.001   TYR R 182 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.014   0.001   TRP B 169 
 HIS   0.003   0.001   HIS R 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (10125)
  covalent geometry    : angle       0.50947 (13714)
  SS BOND              : bond        0.00369 (    5)
  SS BOND              : angle       0.73940 (   10)
  hydrogen bonds       : bond        0.03259 (  480)
  hydrogen bonds       : angle       4.21493 ( 1335)

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

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

  2502 Ramachandran restraints generated.
    1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2502 Ramachandran restraints generated.
    1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 151
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
REVERT: A  195 HIS cc_start: 0.8240 (m-70) cc_final: 0.6914 (t70)
REVERT: B  219 ARG cc_start: 0.8432 (mtm-85) cc_final: 0.7876 (mtp85)
REVERT: R  165 MET cc_start: 0.7708 (tpp) cc_final: 0.7435 (tpp)
REVERT: R  241 ARG cc_start: 0.7404 (ttp-110) cc_final: 0.7127 (ttm110)
REVERT: R  323 MET cc_start: 0.1145 (mtp) cc_final: 0.0863 (mtt)
  outliers start: 19
  outliers final: 14
  residues processed: 162
  average time/residue: 0.6972
  time to fit residues: 119.7488
Evaluate side-chains
  160 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 146
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain R residue   41 LEU
Chi-restraints excluded: chain R residue   80 VAL
Chi-restraints excluded: chain R residue  169 THR
Chi-restraints excluded: chain R residue  174 GLU
Chi-restraints excluded: chain R residue  199 VAL
Chi-restraints excluded: chain R residue  240 LEU
Chi-restraints excluded: chain R residue  298 SER
Chi-restraints excluded: chain R residue  316 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 117 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9990
   chunk 119 optimal weight:    0.9980
   chunk 92 optimal weight:    0.8980
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
S   3 GLN
R 137 ASN
R 175 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.176910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.120088 restraints weight = 9949.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 1.79
r_work: 0.3137 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3019 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.1655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10130  Z= 0.147
  Angle     :  0.539  10.971  13724  Z= 0.279
  Chirality :  0.041   0.145   1543
  Planarity :  0.004   0.046   1731
  Dihedral  :  4.394  26.976   1382
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.88 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 19.28 %
    Favored  : 79.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.24), residues: 1251
  helix:  2.37 (0.26), residues: 417
  sheet:  0.71 (0.28), residues: 312
  loop : -0.26 (0.28), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 314 
 TYR   0.022   0.002   TYR R 182 
 PHE   0.014   0.001   PHE B 199 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (10125)
  covalent geometry    : angle       0.53850 (13714)
  SS BOND              : bond        0.00428 (    5)
  SS BOND              : angle       1.03047 (   10)
  hydrogen bonds       : bond        0.03550 (  480)
  hydrogen bonds       : angle       4.35369 ( 1335)

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

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

  2502 Ramachandran restraints generated.
    1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2502 Ramachandran restraints generated.
    1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 147
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A  195 HIS cc_start: 0.8254 (m-70) cc_final: 0.6938 (t70)
REVERT: B  219 ARG cc_start: 0.8435 (mtm-85) cc_final: 0.7877 (mtp85)
REVERT: C   82 MET cc_start: 0.7852 (mtp) cc_final: 0.6499 (mmp)
REVERT: R  165 MET cc_start: 0.7610 (tpp) cc_final: 0.7303 (tpp)
REVERT: R  241 ARG cc_start: 0.7419 (ttp-110) cc_final: 0.7155 (ttm110)
REVERT: R  323 MET cc_start: 0.1176 (mtp) cc_final: 0.0899 (mtt)
  outliers start: 17
  outliers final: 12
  residues processed: 156
  average time/residue: 0.7294
  time to fit residues: 120.1677
Evaluate side-chains
  157 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 145
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain R residue   80 VAL
Chi-restraints excluded: chain R residue  174 GLU
Chi-restraints excluded: chain R residue  199 VAL
Chi-restraints excluded: chain R residue  240 LEU
Chi-restraints excluded: chain R residue  298 SER
Chi-restraints excluded: chain R residue  316 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 39 optimal weight:    0.6980
   chunk 85 optimal weight:    8.9990
   chunk 51 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 116 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   chunk 27 optimal weight:    0.4980
   chunk 35 optimal weight:    0.2980
   chunk 48 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 73 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
S   3 GLN
R 175 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.178377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.122049 restraints weight = 10137.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 1.78
r_work: 0.3167 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3048 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.1745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  10130  Z= 0.107
  Angle     :  0.505  10.909  13724  Z= 0.260
  Chirality :  0.040   0.140   1543
  Planarity :  0.004   0.046   1731
  Dihedral  :  4.254  27.124   1382
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 19.93 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.31 (0.24), residues: 1251
  helix:  2.47 (0.26), residues: 416
  sheet:  0.67 (0.29), residues: 286
  loop : -0.25 (0.27), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 205 
 TYR   0.023   0.001   TYR R 182 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.015   0.001   TRP B 169 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 (10125)
  covalent geometry    : angle       0.50496 (13714)
  SS BOND              : bond        0.00317 (    5)
  SS BOND              : angle       0.83858 (   10)
  hydrogen bonds       : bond        0.03165 (  480)
  hydrogen bonds       : angle       4.22911 ( 1335)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5393.77 seconds
wall clock time: 92 minutes 11.35 seconds (5531.35 seconds total)