Starting phenix.real_space_refine
on Sat Aug 23 01:40:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kfy_37208/08_2025/8kfy_37208.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kfy_37208/08_2025/8kfy_37208.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kfy_37208/08_2025/8kfy_37208.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kfy_37208/08_2025/8kfy_37208.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kfy_37208/08_2025/8kfy_37208.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kfy_37208/08_2025/8kfy_37208.cif"
  }
  resolution = 3.06
  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=   0.001 sd=   0.024
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      66      5.16       5
     C    5754      2.51       5
     N    1505      2.21       5
     O    1667      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8992
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1812
          Classifications: {'peptide': 225}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "C"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 429
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "R"
      Number of atoms: 2342
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2342
          Classifications: {'peptide': 288}
          Link IDs: {'PTRANS': 5, 'TRANS': 282}
    Chain: "S"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1783
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Unusual residues: {'OXF': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.89, per 1000 atoms: 0.21
  Number of scatterers: 8992
  At special positions: 0
  Unit cell: (94.64, 120.64, 128.96, 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      66     16.00
     O    1667      8.00
     N    1505      7.00
     C    5754      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 183 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " 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: 0.66
  Conformation dependent library (CDL) restraints added in 350.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2138

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 13 sheets defined
      39.2% alpha, 23.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 4.137A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 3.524A  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 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 4.145A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.790A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 3.702A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.600A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 8 through 24
      removed outlier: 3.621A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'R' and resid 31 through 62
    Processing helix  chain 'R' and resid 68 through 86
    Processing helix  chain 'R' and resid 87 through 97
    Processing helix  chain 'R' and resid 102 through 137
    Processing helix  chain 'R' and resid 137 through 145
      removed outlier: 3.831A  pdb=" N   LYS R 143 " --> pdb=" O   VAL R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 171
      Proline residue:  R 167  - end of helix
    Processing helix  chain 'R' and resid 191 through 205
      removed outlier: 3.799A  pdb=" N   LYS R 195 " --> pdb=" O   THR R 191 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ILE R 196 " --> pdb=" O   LEU R 192 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ASN R 199 " --> pdb=" O   LYS R 195 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 207 through 227
      removed outlier: 3.637A  pdb=" N   ILE R 213 " --> pdb=" O   ILE R 209 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 232 through 266
      Proline residue:  R 253  - end of helix
    Processing helix  chain 'R' and resid 271 through 290
    Processing helix  chain 'R' and resid 291 through 301
      Proline residue:  R 297  - end of helix
    Processing helix  chain 'R' and resid 304 through 317
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 3.887A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 208 through 212
      removed outlier: 4.003A  pdb=" N   VAL S 212 " --> pdb=" O   ALA S 209 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.266A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.601A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.541A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 7.182A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.813A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.093A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.194A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.527A  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 151
      removed outlier: 6.418A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.026A  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: 6.810A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.051A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.534A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.865A  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: 6.405A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 172 through 177
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 3.616A  pdb=" N   THR S 118 " --> pdb=" O   GLY S  10 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ALA S  49 " --> pdb=" O   TRP S  36 " (cutoff:3.500A)
      removed outlier: 5.922A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.255A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (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: 3.528A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   GLY S 213 " --> pdb=" O   LEU S 233 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)

    473 hydrogen bonds defined for protein.
    1353 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: 0.98

  Time building geometry restraints manager: 0.81 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: 2856
        1.34 -     1.46: 2115
        1.46 -     1.58: 4116
        1.58 -     1.69: 0
        1.69 -     1.81: 95
  Bond restraints: 9182
  Sorted by residual:
  bond pdb=" CA  TYR S 161 "
       pdb=" CB  TYR S 161 "
    ideal  model  delta    sigma   weight residual
    1.525  1.497  0.028 1.47e-02 4.63e+03 3.61e+00
  bond pdb=" C12 OXF R 601 "
       pdb=" O3  OXF R 601 "
    ideal  model  delta    sigma   weight residual
    1.363  1.391 -0.028 2.00e-02 2.50e+03 2.01e+00
  bond pdb=" SD  MET R 105 "
       pdb=" CE  MET R 105 "
    ideal  model  delta    sigma   weight residual
    1.791  1.758  0.033 2.50e-02 1.60e+03 1.72e+00
  bond pdb=" C   MET R 105 "
       pdb=" O   MET R 105 "
    ideal  model  delta    sigma   weight residual
    1.237  1.224  0.012 1.17e-02 7.31e+03 1.12e+00
  bond pdb=" CG  LEU R 278 "
       pdb=" CD2 LEU R 278 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.05e+00
  ... (remaining 9177 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 12284
        2.01 -     4.03: 126
        4.03 -     6.04: 12
        6.04 -     8.05: 2
        8.05 -    10.06: 1
  Bond angle restraints: 12425
  Sorted by residual:
  angle pdb=" CB  MET R 105 "
        pdb=" CG  MET R 105 "
        pdb=" SD  MET R 105 "
      ideal   model   delta    sigma   weight residual
     112.70  122.76  -10.06 3.00e+00 1.11e-01 1.13e+01
  angle pdb=" C   ARG S 179 "
        pdb=" N   MET S 180 "
        pdb=" CA  MET S 180 "
      ideal   model   delta    sigma   weight residual
     121.54  127.67   -6.13 1.91e+00 2.74e-01 1.03e+01
  angle pdb=" N   THR S 198 "
        pdb=" CA  THR S 198 "
        pdb=" C   THR S 198 "
      ideal   model   delta    sigma   weight residual
     113.43  109.56    3.87 1.26e+00 6.30e-01 9.45e+00
  angle pdb=" CG  ARG B  19 "
        pdb=" CD  ARG B  19 "
        pdb=" NE  ARG B  19 "
      ideal   model   delta    sigma   weight residual
     112.00  118.59   -6.59 2.20e+00 2.07e-01 8.98e+00
  angle pdb=" C   PHE R 290 "
        pdb=" N   THR R 291 "
        pdb=" CA  THR R 291 "
      ideal   model   delta    sigma   weight residual
     121.18  115.92    5.26 1.98e+00 2.55e-01 7.05e+00
  ... (remaining 12420 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.68: 4723
       17.68 -    35.37: 561
       35.37 -    53.05: 143
       53.05 -    70.73: 16
       70.73 -    88.42: 4
  Dihedral angle restraints: 5447
    sinusoidal: 2133
      harmonic: 3314
  Sorted by residual:
  dihedral pdb=" CA  PHE R 290 "
           pdb=" C   PHE R 290 "
           pdb=" N   THR R 291 "
           pdb=" CA  THR R 291 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.76   31.24     0      5.00e+00 4.00e-02 3.90e+01
  dihedral pdb=" CA  ARG S 179 "
           pdb=" C   ARG S 179 "
           pdb=" N   MET S 180 "
           pdb=" CA  MET S 180 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.42   22.58     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" CA  GLN S 130 "
           pdb=" C   GLN S 130 "
           pdb=" N   ALA S 131 "
           pdb=" CA  ALA S 131 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.21  -17.79     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 5444 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 969
       0.036 -    0.071: 318
       0.071 -    0.107: 102
       0.107 -    0.142: 20
       0.142 -    0.178: 5
  Chirality restraints: 1414
  Sorted by residual:
  chirality pdb=" CA  PHE R 290 "
            pdb=" N   PHE R 290 "
            pdb=" C   PHE R 290 "
            pdb=" CB  PHE R 290 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.88e-01
  chirality pdb=" CB  VAL R 109 "
            pdb=" CA  VAL R 109 "
            pdb=" CG1 VAL R 109 "
            pdb=" CG2 VAL R 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.51e-01
  chirality pdb=" CB  THR R 291 "
            pdb=" CA  THR R 291 "
            pdb=" OG1 THR R 291 "
            pdb=" CG2 THR R 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.50e-01
  ... (remaining 1411 not shown)

  Planarity restraints: 1556
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.038 5.00e-02 4.00e+02   5.81e-02 5.40e+00
        pdb=" N   PRO B 236 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR S 223 "   -0.038 5.00e-02 4.00e+02   5.69e-02 5.18e+00
        pdb=" N   PRO S 224 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO S 224 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO S 224 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET R 105 "    0.010 2.00e-02 2.50e+03   2.00e-02 3.99e+00
        pdb=" C   MET R 105 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   MET R 105 "    0.013 2.00e-02 2.50e+03
        pdb=" N   CYS R 106 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1553 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 251
        2.70 -     3.25: 8859
        3.25 -     3.80: 14802
        3.80 -     4.35: 19109
        4.35 -     4.90: 32205
  Nonbonded interactions: 75226
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 170 "
            pdb=" OG1 THR B 173 "
     model   vdw
     2.155 3.040
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 163 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" OH  TYR A 290 "
            pdb=" O   SER A 293 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" OD1 ASP B 247 "
            pdb=" OG1 THR B 249 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" O   ASP B 163 "
            pdb=" OG1 THR B 164 "
     model   vdw
     2.269 3.040
  ... (remaining 75221 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:             1.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.630
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
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   0.034   9185  Z= 0.161
  Angle     :  0.537  10.063  12431  Z= 0.300
  Chirality :  0.041   0.178   1414
  Planarity :  0.004   0.058   1556
  Dihedral  : 15.791  88.418   3300
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 25.61 %
    Favored  : 74.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 aren not related in a simple way.
  whole:  1.35 (0.25), residues: 1125
  helix:  2.52 (0.26), residues: 398
  sheet:  0.62 (0.30), residues: 288
  loop : -0.42 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B  19 
 TYR   0.014   0.001   TYR B  85 
 PHE   0.021   0.001   PHE R  84 
 TRP   0.017   0.001   TRP S  47 
 HIS   0.003   0.001   HIS R 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 9182)
  covalent geometry    : angle       0.53719 (12425)
  SS BOND              : bond        0.00132 (    3)
  SS BOND              : angle       0.73425 (    6)
  hydrogen bonds       : bond        0.17613 (  473)
  hydrogen bonds       : angle       6.82847 ( 1353)

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

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 225
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.7448 (mpp) cc_final: 0.7088 (mmm)
REVERT: A  349 LYS cc_start: 0.7793 (mtmm) cc_final: 0.7577 (mtmm)
REVERT: B   19 ARG cc_start: 0.7405 (mtm-85) cc_final: 0.7122 (mtm-85)
REVERT: R   46 PHE cc_start: 0.8327 (t80) cc_final: 0.8053 (t80)
REVERT: R  202 MET cc_start: 0.7523 (mmm) cc_final: 0.7200 (mtp)
REVERT: S  154 LEU cc_start: 0.8196 (tp) cc_final: 0.7943 (tp)
  outliers start: 2
  outliers final: 1
  residues processed: 227
  average time/residue: 0.1040
  time to fit residues: 30.6644
Evaluate side-chains
  223 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 222
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  234 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    1.9990
   chunk 106 optimal weight:    0.0370
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
S 155 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.133659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.113551 restraints weight = 13792.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 2.22
r_work: 0.3314 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3154 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.0855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9185  Z= 0.143
  Angle     :  0.518   7.951  12431  Z= 0.286
  Chirality :  0.041   0.194   1414
  Planarity :  0.004   0.060   1556
  Dihedral  :  4.750  50.751   1252
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 21.46 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.53 (0.25), residues: 1125
  helix:  2.71 (0.25), residues: 403
  sheet:  0.61 (0.30), residues: 286
  loop : -0.31 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  19 
 TYR   0.016   0.001   TYR S 178 
 PHE   0.021   0.001   PHE R 214 
 TRP   0.017   0.002   TRP B 169 
 HIS   0.007   0.001   HIS S 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 9182)
  covalent geometry    : angle       0.51827 (12425)
  SS BOND              : bond        0.00197 (    3)
  SS BOND              : angle       0.72228 (    6)
  hydrogen bonds       : bond        0.04454 (  473)
  hydrogen bonds       : angle       5.02362 ( 1353)

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

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 225
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.7255 (mpp) cc_final: 0.6999 (mmm)
REVERT: A  184 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8237 (tt)
REVERT: A  279 LYS cc_start: 0.8528 (mttt) cc_final: 0.8309 (mptt)
REVERT: A  298 GLU cc_start: 0.7129 (tp30) cc_final: 0.6680 (tp30)
REVERT: A  328 ASP cc_start: 0.7242 (OUTLIER) cc_final: 0.7011 (m-30)
REVERT: B   19 ARG cc_start: 0.7774 (mtm-85) cc_final: 0.7357 (mtm-85)
REVERT: B  134 ARG cc_start: 0.8298 (ttp80) cc_final: 0.7966 (ttp80)
REVERT: B  212 ASP cc_start: 0.7875 (t0) cc_final: 0.7550 (t0)
REVERT: B  263 THR cc_start: 0.8247 (p) cc_final: 0.7883 (m)
REVERT: B  335 PHE cc_start: 0.8467 (m-80) cc_final: 0.7986 (m-80)
REVERT: R   46 PHE cc_start: 0.8267 (t80) cc_final: 0.8030 (t80)
REVERT: R  124 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7878 (mm)
REVERT: R  202 MET cc_start: 0.7801 (mmm) cc_final: 0.7534 (mtp)
REVERT: R  257 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.8082 (p)
REVERT: S   34 MET cc_start: 0.8195 (mmm) cc_final: 0.7981 (mmm)
REVERT: S  154 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7753 (tp)
REVERT: S  160 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8381 (m)
  outliers start: 39
  outliers final: 22
  residues processed: 245
  average time/residue: 0.0893
  time to fit residues: 29.0764
Evaluate side-chains
  243 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 215
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain R residue   85 VAL
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  151 THR
Chi-restraints excluded: chain R residue  163 MET
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain R residue  195 LYS
Chi-restraints excluded: chain R residue  226 LYS
Chi-restraints excluded: chain R residue  257 VAL
Chi-restraints excluded: chain R residue  294 CYS
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  154 LEU
Chi-restraints excluded: chain S residue  160 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 3 optimal weight:    0.0970
   chunk 56 optimal weight:    4.9990
   chunk 109 optimal weight:    0.8980
   chunk 15 optimal weight:    0.4980
   chunk 55 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   chunk 89 optimal weight:    0.4980
   chunk 108 optimal weight:    6.9990
   chunk 82 optimal weight:    0.9990
   chunk 60 optimal weight:    6.9990
   chunk 98 optimal weight:    0.5980
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 142 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.133612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.113618 restraints weight = 13775.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 2.21
r_work: 0.3316 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3156 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.1188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9185  Z= 0.130
  Angle     :  0.489   7.498  12431  Z= 0.268
  Chirality :  0.040   0.193   1414
  Planarity :  0.004   0.055   1556
  Dihedral  :  4.668  52.036   1252
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 22.17 %
    Favored  : 73.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.57 (0.25), residues: 1125
  helix:  2.73 (0.25), residues: 404
  sheet:  0.62 (0.30), residues: 281
  loop : -0.25 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  32 
 TYR   0.028   0.002   TYR S 223 
 PHE   0.019   0.001   PHE R 214 
 TRP   0.017   0.002   TRP B 169 
 HIS   0.002   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9182)
  covalent geometry    : angle       0.48858 (12425)
  SS BOND              : bond        0.00152 (    3)
  SS BOND              : angle       0.53113 (    6)
  hydrogen bonds       : bond        0.03961 (  473)
  hydrogen bonds       : angle       4.76452 ( 1353)

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

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 223
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.7122 (mpp) cc_final: 0.6786 (mmm)
REVERT: A  184 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8301 (tt)
REVERT: A  279 LYS cc_start: 0.8520 (mttt) cc_final: 0.8301 (mptt)
REVERT: A  298 GLU cc_start: 0.7205 (tp30) cc_final: 0.6800 (tp30)
REVERT: A  317 LYS cc_start: 0.8270 (ptpp) cc_final: 0.7477 (ptpp)
REVERT: A  328 ASP cc_start: 0.7224 (OUTLIER) cc_final: 0.6997 (m-30)
REVERT: A  345 LYS cc_start: 0.8313 (ttpt) cc_final: 0.7807 (mptt)
REVERT: B   19 ARG cc_start: 0.7760 (mtm-85) cc_final: 0.7325 (mtm-85)
REVERT: B  134 ARG cc_start: 0.8300 (ttp80) cc_final: 0.7989 (ttp80)
REVERT: B  137 ARG cc_start: 0.8456 (tpp80) cc_final: 0.8211 (tpp80)
REVERT: B  197 ARG cc_start: 0.7407 (mpt-90) cc_final: 0.7001 (mpt-90)
REVERT: B  212 ASP cc_start: 0.7907 (t0) cc_final: 0.7559 (t0)
REVERT: B  335 PHE cc_start: 0.8437 (m-80) cc_final: 0.7965 (m-80)
REVERT: R   46 PHE cc_start: 0.8305 (t80) cc_final: 0.8059 (t80)
REVERT: R   72 VAL cc_start: 0.8075 (t) cc_final: 0.7713 (p)
REVERT: R  250 PHE cc_start: 0.7417 (m-10) cc_final: 0.7113 (m-10)
REVERT: R  257 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.8063 (p)
REVERT: S  148 ARG cc_start: 0.7584 (ttm110) cc_final: 0.7281 (ttm170)
REVERT: S  154 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7774 (tp)
  outliers start: 41
  outliers final: 26
  residues processed: 244
  average time/residue: 0.0895
  time to fit residues: 29.2759
Evaluate side-chains
  246 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 216
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain R residue   61 VAL
Chi-restraints excluded: chain R residue   85 VAL
Chi-restraints excluded: chain R residue  103 THR
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain R residue  226 LYS
Chi-restraints excluded: chain R residue  257 VAL
Chi-restraints excluded: chain R residue  294 CYS
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  154 LEU
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  223 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0980
   chunk 69 optimal weight:    0.5980
   chunk 55 optimal weight:    0.2980
   chunk 98 optimal weight:    0.9990
   chunk 102 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0070
   chunk 107 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.4000

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS
B 268 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.133572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.113604 restraints weight = 13826.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 2.20
r_work: 0.3321 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9185  Z= 0.116
  Angle     :  0.479   7.039  12431  Z= 0.263
  Chirality :  0.040   0.192   1414
  Planarity :  0.004   0.055   1556
  Dihedral  :  4.578  53.271   1252
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 22.27 %
    Favored  : 73.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.58 (0.25), residues: 1125
  helix:  2.73 (0.25), residues: 407
  sheet:  0.60 (0.30), residues: 282
  loop : -0.24 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  32 
 TYR   0.020   0.001   TYR S 223 
 PHE   0.018   0.001   PHE R 214 
 TRP   0.021   0.001   TRP B 169 
 HIS   0.002   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 9182)
  covalent geometry    : angle       0.47890 (12425)
  SS BOND              : bond        0.00180 (    3)
  SS BOND              : angle       0.46930 (    6)
  hydrogen bonds       : bond        0.03630 (  473)
  hydrogen bonds       : angle       4.60825 ( 1353)

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

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 228
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.7124 (mpp) cc_final: 0.6787 (mmm)
REVERT: A  279 LYS cc_start: 0.8481 (mttt) cc_final: 0.8255 (mptt)
REVERT: A  298 GLU cc_start: 0.7197 (tp30) cc_final: 0.6821 (tp30)
REVERT: A  345 LYS cc_start: 0.8319 (ttpt) cc_final: 0.7816 (mptt)
REVERT: B   19 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.7378 (mtm-85)
REVERT: B  134 ARG cc_start: 0.8248 (ttp80) cc_final: 0.7959 (ttp80)
REVERT: B  178 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8373 (p)
REVERT: B  197 ARG cc_start: 0.7412 (mpt-90) cc_final: 0.6998 (mpt-90)
REVERT: B  212 ASP cc_start: 0.7904 (t0) cc_final: 0.7568 (t0)
REVERT: B  263 THR cc_start: 0.8206 (p) cc_final: 0.7818 (m)
REVERT: B  335 PHE cc_start: 0.8377 (m-80) cc_final: 0.7965 (m-80)
REVERT: R   46 PHE cc_start: 0.8349 (t80) cc_final: 0.8100 (t80)
REVERT: R   72 VAL cc_start: 0.8075 (t) cc_final: 0.7766 (p)
REVERT: R  208 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7784 (mp)
REVERT: R  250 PHE cc_start: 0.7360 (m-10) cc_final: 0.7096 (m-10)
REVERT: R  257 VAL cc_start: 0.8357 (OUTLIER) cc_final: 0.8072 (p)
REVERT: R  278 LEU cc_start: 0.8085 (mm) cc_final: 0.7799 (mt)
REVERT: S  148 ARG cc_start: 0.7605 (ttm110) cc_final: 0.7304 (ttm170)
REVERT: S  154 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7762 (tp)
REVERT: S  185 SER cc_start: 0.8475 (m) cc_final: 0.8212 (p)
  outliers start: 41
  outliers final: 28
  residues processed: 245
  average time/residue: 0.0950
  time to fit residues: 31.4535
Evaluate side-chains
  255 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 223
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain R residue   61 VAL
Chi-restraints excluded: chain R residue   85 VAL
Chi-restraints excluded: chain R residue  108 VAL
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  226 LYS
Chi-restraints excluded: chain R residue  257 VAL
Chi-restraints excluded: chain R residue  294 CYS
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  154 LEU
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  223 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 84 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9990
   chunk 97 optimal weight:    0.8980
   chunk 106 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 98 optimal weight:    0.8980
   chunk 108 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0870
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
B 119 ASN
B 142 HIS
S  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.131965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.111952 restraints weight = 13829.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 2.19
r_work: 0.3302 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.1554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9185  Z= 0.161
  Angle     :  0.501   6.983  12431  Z= 0.274
  Chirality :  0.041   0.194   1414
  Planarity :  0.004   0.057   1556
  Dihedral  :  4.642  52.856   1252
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 20.65 %
    Favored  : 74.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.53 (0.25), residues: 1125
  helix:  2.68 (0.25), residues: 405
  sheet:  0.50 (0.30), residues: 282
  loop : -0.20 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  32 
 TYR   0.019   0.002   TYR S 223 
 PHE   0.022   0.001   PHE R 214 
 TRP   0.017   0.002   TRP S  47 
 HIS   0.003   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 9182)
  covalent geometry    : angle       0.50080 (12425)
  SS BOND              : bond        0.00148 (    3)
  SS BOND              : angle       0.46981 (    6)
  hydrogen bonds       : bond        0.03804 (  473)
  hydrogen bonds       : angle       4.60454 ( 1353)

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

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 225
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.7217 (mpp) cc_final: 0.6886 (mmm)
REVERT: A  279 LYS cc_start: 0.8485 (mttt) cc_final: 0.8259 (mptt)
REVERT: A  298 GLU cc_start: 0.7200 (tp30) cc_final: 0.6835 (tp30)
REVERT: A  345 LYS cc_start: 0.8333 (ttpt) cc_final: 0.7862 (mptt)
REVERT: B   19 ARG cc_start: 0.7800 (mtm-85) cc_final: 0.7335 (mtm-85)
REVERT: B  134 ARG cc_start: 0.8259 (ttp80) cc_final: 0.7946 (ttp80)
REVERT: B  137 ARG cc_start: 0.8470 (tpp80) cc_final: 0.7649 (tpp80)
REVERT: B  150 ARG cc_start: 0.8055 (mmt-90) cc_final: 0.7736 (mpt180)
REVERT: B  178 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8403 (p)
REVERT: B  197 ARG cc_start: 0.7467 (mpt-90) cc_final: 0.7004 (mpt-90)
REVERT: B  212 ASP cc_start: 0.8002 (t0) cc_final: 0.7624 (t0)
REVERT: B  263 THR cc_start: 0.8284 (p) cc_final: 0.7876 (m)
REVERT: B  283 ARG cc_start: 0.8347 (tpt-90) cc_final: 0.8034 (tpt170)
REVERT: B  301 LYS cc_start: 0.8405 (mtpt) cc_final: 0.8145 (mtpp)
REVERT: B  335 PHE cc_start: 0.8411 (m-80) cc_final: 0.7972 (m-80)
REVERT: R   46 PHE cc_start: 0.8396 (t80) cc_final: 0.8143 (t80)
REVERT: R   72 VAL cc_start: 0.8125 (t) cc_final: 0.7755 (p)
REVERT: R  257 VAL cc_start: 0.8351 (OUTLIER) cc_final: 0.8066 (p)
REVERT: R  278 LEU cc_start: 0.8170 (mm) cc_final: 0.7876 (mt)
REVERT: S  148 ARG cc_start: 0.7601 (ttm110) cc_final: 0.7287 (ttm170)
REVERT: S  154 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7786 (tp)
REVERT: S  160 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8389 (m)
REVERT: S  185 SER cc_start: 0.8481 (m) cc_final: 0.8215 (p)
REVERT: S  227 PHE cc_start: 0.8752 (m-80) cc_final: 0.8278 (m-80)
  outliers start: 51
  outliers final: 33
  residues processed: 248
  average time/residue: 0.0997
  time to fit residues: 32.6930
Evaluate side-chains
  253 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 216
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain R residue   61 VAL
Chi-restraints excluded: chain R residue   85 VAL
Chi-restraints excluded: chain R residue  108 VAL
Chi-restraints excluded: chain R residue  143 LYS
Chi-restraints excluded: chain R residue  151 THR
Chi-restraints excluded: chain R residue  163 MET
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain R residue  191 THR
Chi-restraints excluded: chain R residue  195 LYS
Chi-restraints excluded: chain R residue  226 LYS
Chi-restraints excluded: chain R residue  257 VAL
Chi-restraints excluded: chain R residue  294 CYS
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  154 LEU
Chi-restraints excluded: chain S residue  160 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 77 optimal weight:    0.6980
   chunk 60 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0060
   chunk 63 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS
B 268 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.131550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.111680 restraints weight = 13847.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 2.17
r_work: 0.3306 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9185  Z= 0.152
  Angle     :  0.498   6.523  12431  Z= 0.273
  Chirality :  0.041   0.201   1414
  Planarity :  0.004   0.054   1556
  Dihedral  :  4.646  53.186   1252
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 21.86 %
    Favored  : 73.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.50 (0.25), residues: 1125
  helix:  2.69 (0.25), residues: 405
  sheet:  0.45 (0.30), residues: 281
  loop : -0.23 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 314 
 TYR   0.023   0.002   TYR S 223 
 PHE   0.021   0.001   PHE R 214 
 TRP   0.018   0.002   TRP B 169 
 HIS   0.002   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 9182)
  covalent geometry    : angle       0.49798 (12425)
  SS BOND              : bond        0.00173 (    3)
  SS BOND              : angle       0.45614 (    6)
  hydrogen bonds       : bond        0.03706 (  473)
  hydrogen bonds       : angle       4.60078 ( 1353)

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

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 232
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.7237 (mpp) cc_final: 0.6907 (mmm)
REVERT: A  262 THR cc_start: 0.8294 (m) cc_final: 0.8060 (m)
REVERT: A  279 LYS cc_start: 0.8475 (mttt) cc_final: 0.8245 (mptt)
REVERT: A  298 GLU cc_start: 0.7224 (tp30) cc_final: 0.6815 (tp30)
REVERT: A  317 LYS cc_start: 0.8298 (ptpp) cc_final: 0.7924 (ptpt)
REVERT: A  345 LYS cc_start: 0.8331 (ttpt) cc_final: 0.7857 (mptt)
REVERT: B   19 ARG cc_start: 0.7806 (mtm-85) cc_final: 0.7325 (mtm-85)
REVERT: B  134 ARG cc_start: 0.8251 (ttp80) cc_final: 0.7959 (ttp80)
REVERT: B  137 ARG cc_start: 0.8454 (tpp80) cc_final: 0.7708 (tpp80)
REVERT: B  150 ARG cc_start: 0.8047 (mmt-90) cc_final: 0.7731 (mpt180)
REVERT: B  197 ARG cc_start: 0.7439 (mpt-90) cc_final: 0.6970 (mpt-90)
REVERT: B  212 ASP cc_start: 0.8002 (t0) cc_final: 0.7617 (t0)
REVERT: B  263 THR cc_start: 0.8250 (p) cc_final: 0.7966 (m)
REVERT: B  283 ARG cc_start: 0.8354 (tpt-90) cc_final: 0.8030 (tpt170)
REVERT: B  301 LYS cc_start: 0.8412 (mtpt) cc_final: 0.8151 (mtpp)
REVERT: B  335 PHE cc_start: 0.8381 (m-80) cc_final: 0.7959 (m-80)
REVERT: R   46 PHE cc_start: 0.8390 (t80) cc_final: 0.8144 (t80)
REVERT: R   72 VAL cc_start: 0.8122 (t) cc_final: 0.7753 (p)
REVERT: R  117 PHE cc_start: 0.8189 (t80) cc_final: 0.7864 (t80)
REVERT: R  257 VAL cc_start: 0.8349 (OUTLIER) cc_final: 0.8070 (p)
REVERT: R  278 LEU cc_start: 0.8175 (mm) cc_final: 0.7768 (mt)
REVERT: S  148 ARG cc_start: 0.7633 (ttm110) cc_final: 0.7320 (ttm170)
REVERT: S  185 SER cc_start: 0.8498 (m) cc_final: 0.8229 (p)
  outliers start: 46
  outliers final: 38
  residues processed: 251
  average time/residue: 0.0962
  time to fit residues: 31.9355
Evaluate side-chains
  269 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 230
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain R residue   61 VAL
Chi-restraints excluded: chain R residue   85 VAL
Chi-restraints excluded: chain R residue  103 THR
Chi-restraints excluded: chain R residue  108 VAL
Chi-restraints excluded: chain R residue  143 LYS
Chi-restraints excluded: chain R residue  151 THR
Chi-restraints excluded: chain R residue  163 MET
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain R residue  191 THR
Chi-restraints excluded: chain R residue  195 LYS
Chi-restraints excluded: chain R residue  226 LYS
Chi-restraints excluded: chain R residue  257 VAL
Chi-restraints excluded: chain R residue  294 CYS
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  223 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 60 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 69 optimal weight:    0.6980
   chunk 73 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS
B 268 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.130945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.110929 restraints weight = 13867.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 2.20
r_work: 0.3297 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3138 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.1743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   9185  Z= 0.170
  Angle     :  0.507   6.799  12431  Z= 0.278
  Chirality :  0.041   0.204   1414
  Planarity :  0.004   0.056   1556
  Dihedral  :  4.681  52.922   1252
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 22.67 %
    Favored  : 72.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.25), residues: 1125
  helix:  2.67 (0.25), residues: 405
  sheet:  0.38 (0.30), residues: 282
  loop : -0.25 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  32 
 TYR   0.022   0.002   TYR S 223 
 PHE   0.022   0.001   PHE R 214 
 TRP   0.018   0.002   TRP S  47 
 HIS   0.003   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 9182)
  covalent geometry    : angle       0.50667 (12425)
  SS BOND              : bond        0.00173 (    3)
  SS BOND              : angle       0.49377 (    6)
  hydrogen bonds       : bond        0.03779 (  473)
  hydrogen bonds       : angle       4.62595 ( 1353)

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

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 234
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.7284 (mpp) cc_final: 0.7069 (mmt)
REVERT: A  279 LYS cc_start: 0.8510 (mttt) cc_final: 0.8276 (mptt)
REVERT: A  298 GLU cc_start: 0.7274 (tp30) cc_final: 0.6843 (tp30)
REVERT: A  317 LYS cc_start: 0.8349 (ptpp) cc_final: 0.7940 (ptpt)
REVERT: B   19 ARG cc_start: 0.7826 (mtm-85) cc_final: 0.7331 (mtm-85)
REVERT: B  137 ARG cc_start: 0.8446 (tpp80) cc_final: 0.7821 (tpp80)
REVERT: B  197 ARG cc_start: 0.7422 (mpt-90) cc_final: 0.6940 (mpt-90)
REVERT: B  263 THR cc_start: 0.8259 (p) cc_final: 0.7920 (m)
REVERT: B  301 LYS cc_start: 0.8427 (mtpt) cc_final: 0.8158 (mtpp)
REVERT: B  335 PHE cc_start: 0.8409 (m-80) cc_final: 0.7979 (m-80)
REVERT: R  257 VAL cc_start: 0.8338 (OUTLIER) cc_final: 0.8050 (p)
REVERT: R  278 LEU cc_start: 0.8229 (mm) cc_final: 0.7802 (mt)
REVERT: S  148 ARG cc_start: 0.7566 (ttm110) cc_final: 0.7269 (ttm170)
REVERT: S  185 SER cc_start: 0.8493 (m) cc_final: 0.8209 (p)
  outliers start: 44
  outliers final: 37
  residues processed: 248
  average time/residue: 0.1103
  time to fit residues: 36.1569
Evaluate side-chains
  269 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 231
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain R residue   61 VAL
Chi-restraints excluded: chain R residue   85 VAL
Chi-restraints excluded: chain R residue  108 VAL
Chi-restraints excluded: chain R residue  143 LYS
Chi-restraints excluded: chain R residue  151 THR
Chi-restraints excluded: chain R residue  163 MET
Chi-restraints excluded: chain R residue  191 THR
Chi-restraints excluded: chain R residue  195 LYS
Chi-restraints excluded: chain R residue  226 LYS
Chi-restraints excluded: chain R residue  257 VAL
Chi-restraints excluded: chain R residue  294 CYS
Chi-restraints excluded: chain R residue  308 LYS
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  154 LEU
Chi-restraints excluded: chain S residue  223 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 92 optimal weight:    0.4980
   chunk 90 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0670
   chunk 1 optimal weight:    2.9990
   chunk 81 optimal weight:    0.6980
   chunk 5 optimal weight:    0.4980
   chunk 74 optimal weight:    0.9980
   chunk 69 optimal weight:    0.5980
   chunk 96 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.4718

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.132367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.112417 restraints weight = 13789.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 2.18
r_work: 0.3312 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3154 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9185  Z= 0.124
  Angle     :  0.491   6.885  12431  Z= 0.269
  Chirality :  0.040   0.203   1414
  Planarity :  0.004   0.055   1556
  Dihedral  :  4.632  53.865   1252
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 23.18 %
    Favored  : 72.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.25), residues: 1125
  helix:  2.73 (0.25), residues: 405
  sheet:  0.37 (0.30), residues: 282
  loop : -0.21 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 134 
 TYR   0.020   0.001   TYR S 223 
 PHE   0.021   0.001   PHE R 117 
 TRP   0.017   0.001   TRP B 169 
 HIS   0.002   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 9182)
  covalent geometry    : angle       0.49057 (12425)
  SS BOND              : bond        0.00184 (    3)
  SS BOND              : angle       0.45295 (    6)
  hydrogen bonds       : bond        0.03569 (  473)
  hydrogen bonds       : angle       4.56721 ( 1353)

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

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 234
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A   53 MET cc_start: 0.7292 (mpp) cc_final: 0.6940 (mmt)
REVERT: A  262 THR cc_start: 0.8277 (m) cc_final: 0.8037 (m)
REVERT: A  279 LYS cc_start: 0.8461 (mttt) cc_final: 0.8216 (mptt)
REVERT: A  298 GLU cc_start: 0.7232 (tp30) cc_final: 0.6805 (tp30)
REVERT: A  317 LYS cc_start: 0.8345 (ptpp) cc_final: 0.7978 (ptpt)
REVERT: A  345 LYS cc_start: 0.8330 (ttpt) cc_final: 0.7836 (mptt)
REVERT: B   19 ARG cc_start: 0.7855 (mtm-85) cc_final: 0.7390 (mtm-85)
REVERT: B  134 ARG cc_start: 0.8257 (ttp80) cc_final: 0.7927 (ttp80)
REVERT: B  137 ARG cc_start: 0.8440 (tpp80) cc_final: 0.7869 (tpp80)
REVERT: B  150 ARG cc_start: 0.8023 (mmt-90) cc_final: 0.7719 (mpt180)
REVERT: B  197 ARG cc_start: 0.7399 (mpt-90) cc_final: 0.6942 (mpt-90)
REVERT: B  263 THR cc_start: 0.8258 (p) cc_final: 0.7920 (m)
REVERT: B  301 LYS cc_start: 0.8409 (mtpt) cc_final: 0.8115 (mtpp)
REVERT: B  335 PHE cc_start: 0.8362 (m-80) cc_final: 0.7968 (m-80)
REVERT: R   46 PHE cc_start: 0.8389 (t80) cc_final: 0.8114 (t80)
REVERT: R   72 VAL cc_start: 0.8120 (t) cc_final: 0.7805 (p)
REVERT: R  257 VAL cc_start: 0.8365 (OUTLIER) cc_final: 0.8084 (p)
REVERT: R  278 LEU cc_start: 0.8160 (mm) cc_final: 0.7726 (mt)
REVERT: S   29 PHE cc_start: 0.8478 (t80) cc_final: 0.7778 (t80)
REVERT: S  148 ARG cc_start: 0.7559 (ttm110) cc_final: 0.7267 (ttm170)
REVERT: S  179 ARG cc_start: 0.8209 (mtm-85) cc_final: 0.7960 (mtt90)
REVERT: S  182 ASN cc_start: 0.8573 (m110) cc_final: 0.8359 (m-40)
REVERT: S  185 SER cc_start: 0.8505 (m) cc_final: 0.8213 (p)
  outliers start: 43
  outliers final: 33
  residues processed: 252
  average time/residue: 0.1189
  time to fit residues: 39.5371
Evaluate side-chains
  265 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 231
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain R residue   61 VAL
Chi-restraints excluded: chain R residue   85 VAL
Chi-restraints excluded: chain R residue  103 THR
Chi-restraints excluded: chain R residue  108 VAL
Chi-restraints excluded: chain R residue  143 LYS
Chi-restraints excluded: chain R residue  191 THR
Chi-restraints excluded: chain R residue  257 VAL
Chi-restraints excluded: chain R residue  294 CYS
Chi-restraints excluded: chain R residue  308 LYS
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  154 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0970
   chunk 46 optimal weight:    0.6980
   chunk 69 optimal weight:    0.5980
   chunk 78 optimal weight:    0.4980
   chunk 15 optimal weight:    0.0170
   chunk 83 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.3816

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

Flipped N/Q/H residues before XYZ refinement:
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.132957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.112981 restraints weight = 13668.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 2.18
r_work: 0.3322 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.1934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9185  Z= 0.115
  Angle     :  0.492   8.643  12431  Z= 0.269
  Chirality :  0.040   0.205   1414
  Planarity :  0.004   0.055   1556
  Dihedral  :  4.609  55.085   1252
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 23.99 %
    Favored  : 72.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.50 (0.25), residues: 1125
  helix:  2.73 (0.25), residues: 405
  sheet:  0.40 (0.30), residues: 281
  loop : -0.22 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 134 
 TYR   0.023   0.001   TYR S 223 
 PHE   0.018   0.001   PHE R 117 
 TRP   0.016   0.001   TRP B 169 
 HIS   0.002   0.001   HIS R 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 9182)
  covalent geometry    : angle       0.49206 (12425)
  SS BOND              : bond        0.00175 (    3)
  SS BOND              : angle       0.42524 (    6)
  hydrogen bonds       : bond        0.03514 (  473)
  hydrogen bonds       : angle       4.54861 ( 1353)

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

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 239
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A   53 MET cc_start: 0.7282 (mpp) cc_final: 0.6922 (mmt)
REVERT: A  262 THR cc_start: 0.8288 (m) cc_final: 0.8057 (m)
REVERT: A  298 GLU cc_start: 0.7257 (tp30) cc_final: 0.6860 (tp30)
REVERT: A  317 LYS cc_start: 0.8336 (ptpp) cc_final: 0.7980 (ptpt)
REVERT: A  345 LYS cc_start: 0.8342 (ttpt) cc_final: 0.7831 (mptt)
REVERT: B   19 ARG cc_start: 0.7856 (mtm-85) cc_final: 0.7421 (mtm-85)
REVERT: B  134 ARG cc_start: 0.8253 (ttp80) cc_final: 0.7965 (ttp80)
REVERT: B  137 ARG cc_start: 0.8433 (tpp80) cc_final: 0.7890 (tpp80)
REVERT: B  150 ARG cc_start: 0.8022 (mmt-90) cc_final: 0.7725 (mpt180)
REVERT: B  197 ARG cc_start: 0.7388 (mpt-90) cc_final: 0.6923 (mpt-90)
REVERT: B  263 THR cc_start: 0.8249 (p) cc_final: 0.7963 (m)
REVERT: B  301 LYS cc_start: 0.8409 (mtpt) cc_final: 0.8110 (mtpp)
REVERT: B  325 MET cc_start: 0.7762 (ttp) cc_final: 0.6934 (ttm)
REVERT: B  335 PHE cc_start: 0.8360 (m-80) cc_final: 0.7948 (m-80)
REVERT: B  340 ASN cc_start: 0.7633 (t0) cc_final: 0.7313 (t0)
REVERT: R   46 PHE cc_start: 0.8414 (t80) cc_final: 0.8114 (t80)
REVERT: R   57 ILE cc_start: 0.8149 (mt) cc_final: 0.7853 (mm)
REVERT: R   72 VAL cc_start: 0.8086 (t) cc_final: 0.7795 (p)
REVERT: R  257 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8061 (p)
REVERT: R  278 LEU cc_start: 0.8158 (mm) cc_final: 0.7708 (mt)
REVERT: S   29 PHE cc_start: 0.8477 (t80) cc_final: 0.7764 (t80)
REVERT: S   34 MET cc_start: 0.8157 (mmm) cc_final: 0.7944 (mmm)
REVERT: S  148 ARG cc_start: 0.7650 (ttm110) cc_final: 0.7361 (ttm170)
REVERT: S  182 ASN cc_start: 0.8567 (m110) cc_final: 0.8356 (m-40)
REVERT: S  185 SER cc_start: 0.8521 (m) cc_final: 0.8220 (p)
REVERT: S  227 PHE cc_start: 0.8813 (m-80) cc_final: 0.8333 (m-80)
  outliers start: 37
  outliers final: 33
  residues processed: 254
  average time/residue: 0.1182
  time to fit residues: 39.5601
Evaluate side-chains
  269 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 235
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain R residue   61 VAL
Chi-restraints excluded: chain R residue   85 VAL
Chi-restraints excluded: chain R residue  108 VAL
Chi-restraints excluded: chain R residue  143 LYS
Chi-restraints excluded: chain R residue  191 THR
Chi-restraints excluded: chain R residue  195 LYS
Chi-restraints excluded: chain R residue  257 VAL
Chi-restraints excluded: chain R residue  294 CYS
Chi-restraints excluded: chain R residue  308 LYS
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  154 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 105 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 107 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 96 optimal weight:    4.9990
   chunk 12 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 102 optimal weight:    0.9980
   chunk 17 optimal weight:    0.4980
   chunk 49 optimal weight:    0.4980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.130992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.110879 restraints weight = 13759.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 2.21
r_work: 0.3296 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.1971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9185  Z= 0.168
  Angle     :  0.537  10.599  12431  Z= 0.294
  Chirality :  0.041   0.212   1414
  Planarity :  0.004   0.055   1556
  Dihedral  :  4.672  54.599   1252
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 24.29 %
    Favored  : 71.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.38 (0.25), residues: 1125
  helix:  2.61 (0.25), residues: 405
  sheet:  0.30 (0.30), residues: 283
  loop : -0.24 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  49 
 TYR   0.023   0.002   TYR S 223 
 PHE   0.045   0.002   PHE R 117 
 TRP   0.017   0.002   TRP S  47 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 9182)
  covalent geometry    : angle       0.53734 (12425)
  SS BOND              : bond        0.00203 (    3)
  SS BOND              : angle       0.48533 (    6)
  hydrogen bonds       : bond        0.03879 (  473)
  hydrogen bonds       : angle       4.64527 ( 1353)

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

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 230
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A   53 MET cc_start: 0.7243 (mpp) cc_final: 0.6992 (mmt)
REVERT: A  298 GLU cc_start: 0.7296 (tp30) cc_final: 0.6893 (tp30)
REVERT: B   19 ARG cc_start: 0.7904 (mtm-85) cc_final: 0.7451 (mtm-85)
REVERT: B   85 TYR cc_start: 0.8470 (m-10) cc_final: 0.7488 (m-80)
REVERT: B  134 ARG cc_start: 0.8271 (ttp80) cc_final: 0.7951 (ttp80)
REVERT: B  137 ARG cc_start: 0.8448 (tpp80) cc_final: 0.7895 (tpp80)
REVERT: B  197 ARG cc_start: 0.7445 (mpt-90) cc_final: 0.6949 (mpt-90)
REVERT: B  263 THR cc_start: 0.8294 (p) cc_final: 0.7972 (m)
REVERT: B  335 PHE cc_start: 0.8360 (m-80) cc_final: 0.7933 (m-80)
REVERT: R   46 PHE cc_start: 0.8418 (t80) cc_final: 0.8122 (t80)
REVERT: R   72 VAL cc_start: 0.8091 (t) cc_final: 0.7729 (p)
REVERT: R  105 MET cc_start: 0.5985 (ptt) cc_final: 0.5672 (ptt)
REVERT: R  257 VAL cc_start: 0.8283 (OUTLIER) cc_final: 0.8005 (p)
REVERT: R  278 LEU cc_start: 0.8210 (mm) cc_final: 0.7761 (mt)
REVERT: S   29 PHE cc_start: 0.8478 (t80) cc_final: 0.7816 (t80)
REVERT: S  148 ARG cc_start: 0.7693 (ttm110) cc_final: 0.7407 (ttm170)
REVERT: S  185 SER cc_start: 0.8567 (m) cc_final: 0.8265 (p)
REVERT: S  221 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7794 (mt)
  outliers start: 40
  outliers final: 33
  residues processed: 246
  average time/residue: 0.1212
  time to fit residues: 39.2133
Evaluate side-chains
  261 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 226
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain R residue   85 VAL
Chi-restraints excluded: chain R residue  103 THR
Chi-restraints excluded: chain R residue  108 VAL
Chi-restraints excluded: chain R residue  143 LYS
Chi-restraints excluded: chain R residue  191 THR
Chi-restraints excluded: chain R residue  195 LYS
Chi-restraints excluded: chain R residue  257 VAL
Chi-restraints excluded: chain R residue  283 HIS
Chi-restraints excluded: chain R residue  294 CYS
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  154 LEU
Chi-restraints excluded: chain S residue  221 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 82 optimal weight:    0.0070
   chunk 108 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 103 optimal weight:    0.8980
   chunk 80 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.9402

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.129434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.109624 restraints weight = 13598.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 2.14
r_work: 0.3290 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   9185  Z= 0.202
  Angle     :  0.553   7.901  12431  Z= 0.304
  Chirality :  0.043   0.230   1414
  Planarity :  0.004   0.056   1556
  Dihedral  :  4.757  53.325   1252
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 24.60 %
    Favored  : 71.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.25 (0.25), residues: 1125
  helix:  2.48 (0.25), residues: 405
  sheet:  0.25 (0.30), residues: 283
  loop : -0.31 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  49 
 TYR   0.029   0.002   TYR B  85 
 PHE   0.045   0.002   PHE R 117 
 TRP   0.022   0.002   TRP S  47 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 9182)
  covalent geometry    : angle       0.55329 (12425)
  SS BOND              : bond        0.00154 (    3)
  SS BOND              : angle       0.51481 (    6)
  hydrogen bonds       : bond        0.04105 (  473)
  hydrogen bonds       : angle       4.74067 ( 1353)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2391.90 seconds
wall clock time: 41 minutes 48.22 seconds (2508.22 seconds total)