Starting phenix.real_space_refine
on Tue Mar  3 19:05:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wz4_32904/03_2026/7wz4_32904.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wz4_32904/03_2026/7wz4_32904.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wz4_32904/03_2026/7wz4_32904.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wz4_32904/03_2026/7wz4_32904.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wz4_32904/03_2026/7wz4_32904.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wz4_32904/03_2026/7wz4_32904.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.036
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      57      5.16       5
     C    5185      2.51       5
     N    1419      2.21       5
     O    1526      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8187
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 1692
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1692
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 9, 'TRANS': 223}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 94
          Unresolved non-hydrogen angles: 124
          Unresolved non-hydrogen dihedrals: 81
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'TYR:plan': 2, 'ASP:plan': 1, 'TRP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 60
    Chain: "A"
      Number of atoms: 1715
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1715
          Classifications: {'peptide': 216}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 2, 'TRANS': 213}
          Chain breaks: 2
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 17
    Chain: "B"
      Number of atoms: 2577
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2577
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "G"
      Number of atoms: 431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 431
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "S"
      Number of atoms: 1772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1772
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
  Time building chain proxies: 1.62, per 1000 atoms: 0.20
  Number of scatterers: 8187
  At special positions: 0
  Unit cell: (90.95, 119.85, 125.8, 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      57     16.00
     O    1526      8.00
     N    1419      7.00
     C    5185      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.04

  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: 0.87
  Conformation dependent library (CDL) restraints added in 295.5 milliseconds
  

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1994

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 13 sheets defined
      37.2% alpha, 24.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'R' and resid 34 through 59
      removed outlier: 3.512A  pdb=" N   TYR R  38 " --> pdb=" O   VAL R  34 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   SER R  39 " --> pdb=" O   SER R  35 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   GLY R  40 " --> pdb=" O   LEU R  36 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 60 through 63
    Processing helix  chain 'R' and resid 64 through 88
      removed outlier: 3.819A  pdb=" N   PHE R  69 " --> pdb=" O   THR R  65 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   MET R  85 " --> pdb=" O   CYS R  81 " (cutoff:3.500A)
      Proline residue:  R  86  - end of helix
    Processing helix  chain 'R' and resid 116 through 144
      removed outlier: 3.591A  pdb=" N   CYS R 132 " --> pdb=" O   LEU R 128 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 145 through 153
    Processing helix  chain 'R' and resid 154 through 175
      removed outlier: 3.743A  pdb=" N   TRP R 166 " --> pdb=" O   LEU R 162 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 191 through 227
      removed outlier: 4.173A  pdb=" N   LEU R 195 " --> pdb=" O   HIS R 191 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   LEU R 196 " --> pdb=" O   TYR R 192 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ALA R 197 " --> pdb=" O   PRO R 193 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ALA R 198 " --> pdb=" O   ALA R 194 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   VAL R 216 " --> pdb=" O   TYR R 212 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 283 through 308
      removed outlier: 3.652A  pdb=" N   LEU R 287 " --> pdb=" O   GLY R 283 " (cutoff:3.500A)
      Proline residue:  R 299  - end of helix
    Processing helix  chain 'R' and resid 317 through 337
      Proline residue:  R 333  - end of helix
    Processing helix  chain 'R' and resid 340 through 351
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.647A  pdb=" N   MET A  53 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.374A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.799A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 255
      removed outlier: 3.831A  pdb=" N   SER A 246 " --> pdb=" O   ARG A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 4.013A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 329 through 351
      removed outlier: 3.520A  pdb=" N   GLN A 333 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   LYS A 349 " --> pdb=" O   LYS A 345 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ASP A 350 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   CYS A 351 " --> pdb=" O   ASN A 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 25
      removed outlier: 3.583A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 9 through 24
    Processing helix  chain 'G' and resid 29 through 45
      removed outlier: 3.558A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'G' and resid 55 through 59
      removed outlier: 3.532A  pdb=" N   ASN G  59 " --> pdb=" O   ALA G  56 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 4.135A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.719A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.737A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.673A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.130A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.637A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.664A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.746A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.712A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.081A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.729A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.146A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.887A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.984A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.609A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.144A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.547A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192
      removed outlier: 3.650A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.649A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.845A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.945A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.653A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 4 through 7
    Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12
      removed outlier: 6.975A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12
      removed outlier: 4.380A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129
    Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136
      removed outlier: 3.823A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ILE S 177 " --> pdb=" O   TRP S 164 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   LEU S 166 " --> pdb=" O   LEU S 175 " (cutoff:3.500A)
      removed outlier: 5.508A  pdb=" N   LEU S 175 " --> pdb=" O   LEU S 166 " (cutoff:3.500A)

    412 hydrogen bonds defined for protein.
    1152 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.28

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2671
        1.34 -     1.46: 1981
        1.46 -     1.58: 3611
        1.58 -     1.70: 0
        1.70 -     1.82: 80
  Bond restraints: 8343
  Sorted by residual:
  bond pdb=" N   TRP R 179 "
       pdb=" CA  TRP R 179 "
    ideal  model  delta    sigma   weight residual
    1.455  1.481 -0.026 1.25e-02 6.40e+03 4.31e+00
  bond pdb=" CA  THR B 181 "
       pdb=" CB  THR B 181 "
    ideal  model  delta    sigma   weight residual
    1.527  1.562 -0.034 2.48e-02 1.63e+03 1.93e+00
  bond pdb=" C   TRP R 179 "
       pdb=" O   TRP R 179 "
    ideal  model  delta    sigma   weight residual
    1.234  1.244 -0.010 1.22e-02 6.72e+03 7.18e-01
  bond pdb=" CA  GLY B  41 "
       pdb=" C   GLY B  41 "
    ideal  model  delta    sigma   weight residual
    1.523  1.513  0.010 1.19e-02 7.06e+03 6.94e-01
  bond pdb=" CB  ASP G  26 "
       pdb=" CG  ASP G  26 "
    ideal  model  delta    sigma   weight residual
    1.516  1.536 -0.020 2.50e-02 1.60e+03 6.61e-01
  ... (remaining 8338 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 11125
        1.88 -     3.75: 166
        3.75 -     5.63: 16
        5.63 -     7.50: 2
        7.50 -     9.38: 1
  Bond angle restraints: 11310
  Sorted by residual:
  angle pdb=" N   THR R 337 "
        pdb=" CA  THR R 337 "
        pdb=" C   THR R 337 "
      ideal   model   delta    sigma   weight residual
     110.44  114.15   -3.71 1.20e+00 6.94e-01 9.57e+00
  angle pdb=" CA  TRP R 179 "
        pdb=" C   TRP R 179 "
        pdb=" O   TRP R 179 "
      ideal   model   delta    sigma   weight residual
     120.99  117.82    3.17 1.12e+00 7.97e-01 8.01e+00
  angle pdb=" CA  LEU R 152 "
        pdb=" CB  LEU R 152 "
        pdb=" CG  LEU R 152 "
      ideal   model   delta    sigma   weight residual
     116.30  125.68   -9.38 3.50e+00 8.16e-02 7.18e+00
  angle pdb=" N   ALA S  92 "
        pdb=" CA  ALA S  92 "
        pdb=" C   ALA S  92 "
      ideal   model   delta    sigma   weight residual
     107.88  111.57   -3.69 1.41e+00 5.03e-01 6.85e+00
  angle pdb=" C   GLY S 197 "
        pdb=" N   THR S 198 "
        pdb=" CA  THR S 198 "
      ideal   model   delta    sigma   weight residual
     123.05  126.89   -3.84 1.57e+00 4.06e-01 5.99e+00
  ... (remaining 11305 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 4544
       17.44 -    34.88: 331
       34.88 -    52.32: 62
       52.32 -    69.76: 8
       69.76 -    87.20: 6
  Dihedral angle restraints: 4951
    sinusoidal: 1858
      harmonic: 3093
  Sorted by residual:
  dihedral pdb=" CA  TRP B 332 "
           pdb=" C   TRP B 332 "
           pdb=" N   ASP B 333 "
           pdb=" CA  ASP B 333 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.53   21.47     0      5.00e+00 4.00e-02 1.84e+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  162.59   17.41     0      5.00e+00 4.00e-02 1.21e+01
  dihedral pdb=" CA  LEU R  83 "
           pdb=" C   LEU R  83 "
           pdb=" N   TRP R  84 "
           pdb=" CA  TRP R  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.36  -16.64     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 4948 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 822
       0.032 -    0.065: 323
       0.065 -    0.097: 98
       0.097 -    0.129: 57
       0.129 -    0.161: 5
  Chirality restraints: 1305
  Sorted by residual:
  chirality pdb=" CB  THR B 181 "
            pdb=" CA  THR B 181 "
            pdb=" OG1 THR B 181 "
            pdb=" CG2 THR B 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.50e-01
  chirality pdb=" CA  MET R  85 "
            pdb=" N   MET R  85 "
            pdb=" C   MET R  85 "
            pdb=" CB  MET R  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.34e-01
  chirality pdb=" CB  THR B  47 "
            pdb=" CA  THR B  47 "
            pdb=" OG1 THR B  47 "
            pdb=" CG2 THR B  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 5.97e-01
  ... (remaining 1302 not shown)

  Planarity restraints: 1431
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 338 "    0.010 2.00e-02 2.50e+03   1.01e-02 2.56e+00
        pdb=" CG  TRP R 338 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 338 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 338 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 338 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 338 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 338 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 338 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 338 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 338 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B  87 "   -0.006 2.00e-02 2.50e+03   1.24e-02 1.55e+00
        pdb=" C   THR B  87 "    0.022 2.00e-02 2.50e+03
        pdb=" O   THR B  87 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   ASN B  88 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA S  40 "    0.020 5.00e-02 4.00e+02   3.09e-02 1.53e+00
        pdb=" N   PRO S  41 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO S  41 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO S  41 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1428 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 78
        2.66 -     3.22: 7228
        3.22 -     3.78: 11695
        3.78 -     4.34: 16121
        4.34 -     4.90: 28264
  Nonbonded interactions: 63386
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.096 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.101 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" OD2 ASP B  83 "
            pdb=" OG1 THR B  86 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" NH2 ARG S 190 "
            pdb=" OD2 ASP S 211 "
     model   vdw
     2.282 3.120
  ... (remaining 63381 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:             2.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.070
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
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   0.039   8345  Z= 0.158
  Angle     :  0.591   9.377  11314  Z= 0.347
  Chirality :  0.042   0.161   1305
  Planarity :  0.003   0.031   1431
  Dihedral  : 12.942  87.201   2951
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.23 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.26), residues: 1051
  helix:  2.46 (0.28), residues: 349
  sheet:  0.58 (0.31), residues: 283
  loop : -0.68 (0.29), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 197 
 TYR   0.008   0.001   TYR B 105 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.027   0.001   TRP R 338 
 HIS   0.005   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 8343)
  covalent geometry    : angle       0.59047 (11310)
  SS BOND              : bond        0.00517 (    2)
  SS BOND              : angle       1.08363 (    4)
  hydrogen bonds       : bond        0.17687 (  407)
  hydrogen bonds       : angle       5.90766 ( 1152)

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 158
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
REVERT: R  155 ARG cc_start: 0.4093 (mmt180) cc_final: 0.3818 (mmt180)
REVERT: R  217 ARG cc_start: 0.6608 (ttm-80) cc_final: 0.6404 (ptm160)
REVERT: R  339 ARG cc_start: 0.8284 (mmm160) cc_final: 0.7705 (mmt-90)
REVERT: A   26 ASP cc_start: 0.7396 (m-30) cc_final: 0.7170 (m-30)
REVERT: A  308 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7592 (mt-10)
REVERT: B   19 ARG cc_start: 0.7362 (ttm170) cc_final: 0.7070 (ttm110)
REVERT: B  127 LYS cc_start: 0.8971 (mttm) cc_final: 0.8691 (mttt)
REVERT: B  134 ARG cc_start: 0.7719 (mtm110) cc_final: 0.7489 (mtp-110)
REVERT: G   58 GLU cc_start: 0.7835 (pm20) cc_final: 0.6927 (mm-30)
REVERT: S  211 ASP cc_start: 0.8392 (m-30) cc_final: 0.8109 (m-30)
  outliers start: 1
  outliers final: 2
  residues processed: 159
  average time/residue: 0.6022
  time to fit residues: 100.8072
Evaluate side-chains
  130 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 128
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   85 MET
Chi-restraints excluded: chain R residue  179 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.0070
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.0270
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.1980
   overall best weight:    0.3256

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

Flipped N/Q/H residues before XYZ refinement:
R  67 ASN
B  16 ASN
B  32 GLN
B 340 ASN
S 130 GLN
S 167 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.165296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.108971 restraints weight = 9395.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 2.90
r_work: 0.3178 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.1430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8345  Z= 0.095
  Angle     :  0.492   8.463  11314  Z= 0.256
  Chirality :  0.041   0.131   1305
  Planarity :  0.003   0.030   1431
  Dihedral  :  4.511  52.840   1160
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 10.50 %
    Favored  : 87.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.41 (0.27), residues: 1051
  helix:  2.84 (0.28), residues: 345
  sheet:  0.66 (0.30), residues: 290
  loop : -0.52 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 197 
 TYR   0.012   0.001   TYR S 178 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.014   0.001   TRP R 338 
 HIS   0.002   0.001   HIS R 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00195 ( 8343)
  covalent geometry    : angle       0.49139 (11310)
  SS BOND              : bond        0.00530 (    2)
  SS BOND              : angle       0.93255 (    4)
  hydrogen bonds       : bond        0.03572 (  407)
  hydrogen bonds       : angle       3.99444 ( 1152)

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 136
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
REVERT: R  339 ARG cc_start: 0.8406 (mmm160) cc_final: 0.7848 (mmt-90)
REVERT: A   22 ASN cc_start: 0.7037 (m-40) cc_final: 0.6793 (m110)
REVERT: A   51 LYS cc_start: 0.7988 (ttmm) cc_final: 0.7537 (ttpp)
REVERT: A  309 ASP cc_start: 0.7830 (p0) cc_final: 0.7462 (p0)
REVERT: A  313 ARG cc_start: 0.7704 (ptp90) cc_final: 0.7460 (ptp90)
REVERT: B   19 ARG cc_start: 0.6811 (ttm170) cc_final: 0.6563 (ttm110)
REVERT: B  127 LYS cc_start: 0.8677 (mttm) cc_final: 0.8465 (mttt)
REVERT: B  134 ARG cc_start: 0.7890 (mtm110) cc_final: 0.7677 (mtp-110)
REVERT: B  175 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.6923 (mp10)
REVERT: B  217 MET cc_start: 0.8150 (ptt) cc_final: 0.7937 (ppp)
REVERT: G   58 GLU cc_start: 0.7686 (pm20) cc_final: 0.6893 (mm-30)
REVERT: S    3 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7605 (pt0)
  outliers start: 15
  outliers final: 5
  residues processed: 143
  average time/residue: 0.6417
  time to fit residues: 96.4975
Evaluate side-chains
  128 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 121
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  179 TRP
Chi-restraints excluded: chain R residue  337 THR
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue  109 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 74 optimal weight:    4.9990
   chunk 16 optimal weight:    7.9990
   chunk 29 optimal weight:    0.0050
   chunk 71 optimal weight:    0.1980
   chunk 0 optimal weight:   20.0000
   chunk 69 optimal weight:    0.6980
   chunk 92 optimal weight:    0.7980
   chunk 75 optimal weight:    2.9990
   chunk 104 optimal weight:    0.4980
   chunk 79 optimal weight:    1.9990
   chunk 36 optimal weight:   10.0000
   overall best weight:    0.4394

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
B  16 ASN
B  32 GLN
B 259 GLN
B 340 ASN
S 174 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.164952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.108539 restraints weight = 9330.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 2.95
r_work: 0.3169 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.1666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8345  Z= 0.092
  Angle     :  0.467   7.974  11314  Z= 0.244
  Chirality :  0.040   0.130   1305
  Planarity :  0.003   0.029   1431
  Dihedral  :  3.921  47.004   1157
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 12.23 %
    Favored  : 85.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.59 (0.27), residues: 1051
  helix:  3.06 (0.28), residues: 345
  sheet:  0.73 (0.30), residues: 289
  loop : -0.43 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 197 
 TYR   0.010   0.001   TYR S 178 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.010   0.001   TRP B  82 
 HIS   0.002   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00198 ( 8343)
  covalent geometry    : angle       0.46643 (11310)
  SS BOND              : bond        0.00526 (    2)
  SS BOND              : angle       0.98742 (    4)
  hydrogen bonds       : bond        0.03260 (  407)
  hydrogen bonds       : angle       3.77602 ( 1152)

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
REVERT: A   22 ASN cc_start: 0.7092 (m-40) cc_final: 0.6848 (m110)
REVERT: A   26 ASP cc_start: 0.7006 (m-30) cc_final: 0.6788 (m-30)
REVERT: A  251 ASP cc_start: 0.7466 (t0) cc_final: 0.7099 (t0)
REVERT: A  309 ASP cc_start: 0.7611 (p0) cc_final: 0.7261 (p0)
REVERT: A  313 ARG cc_start: 0.7680 (ptp90) cc_final: 0.7339 (ptp90)
REVERT: B  127 LYS cc_start: 0.8698 (mttm) cc_final: 0.8490 (mttt)
REVERT: G   58 GLU cc_start: 0.7649 (pm20) cc_final: 0.6844 (mm-30)
  outliers start: 21
  outliers final: 11
  residues processed: 139
  average time/residue: 0.6234
  time to fit residues: 91.2402
Evaluate side-chains
  132 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 121
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  179 TRP
Chi-restraints excluded: chain R residue  337 THR
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain G residue   20 LYS
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  185 SER
Chi-restraints excluded: chain S residue  226 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 50 optimal weight:    0.1980
   chunk 11 optimal weight:    7.9990
   chunk 14 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 83 optimal weight:    0.0010
   chunk 53 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 18 optimal weight:    7.9990
   chunk 87 optimal weight:    0.2980
   chunk 35 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9990
   overall best weight:    0.4186

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

Flipped N/Q/H residues before XYZ refinement:
B  16 ASN
B  32 GLN
B 340 ASN
S 174 GLN
S 182 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.165228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.108966 restraints weight = 9546.439|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 2.98
r_work: 0.3175 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8345  Z= 0.089
  Angle     :  0.470   7.864  11314  Z= 0.242
  Chirality :  0.040   0.130   1305
  Planarity :  0.003   0.029   1431
  Dihedral  :  3.855  45.798   1157
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 2.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 13.96 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.70 (0.27), residues: 1051
  helix:  3.12 (0.28), residues: 346
  sheet:  0.80 (0.30), residues: 290
  loop : -0.37 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 197 
 TYR   0.010   0.001   TYR S 178 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.010   0.001   TRP B  82 
 HIS   0.002   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00192 ( 8343)
  covalent geometry    : angle       0.46940 (11310)
  SS BOND              : bond        0.00517 (    2)
  SS BOND              : angle       0.91045 (    4)
  hydrogen bonds       : bond        0.03073 (  407)
  hydrogen bonds       : angle       3.66721 ( 1152)

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.7112 (m-40) cc_final: 0.6865 (m110)
REVERT: A   26 ASP cc_start: 0.6997 (m-30) cc_final: 0.6766 (m-30)
REVERT: A  251 ASP cc_start: 0.7422 (t0) cc_final: 0.7095 (t0)
REVERT: A  309 ASP cc_start: 0.7492 (p0) cc_final: 0.7111 (p0)
REVERT: A  313 ARG cc_start: 0.7699 (ptp90) cc_final: 0.7305 (ptp90)
REVERT: A  348 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6313 (mp)
REVERT: B  127 LYS cc_start: 0.8682 (mttm) cc_final: 0.8214 (mttt)
REVERT: B  134 ARG cc_start: 0.7956 (mtp-110) cc_final: 0.7663 (mtm110)
REVERT: G   58 GLU cc_start: 0.7605 (pm20) cc_final: 0.6821 (mm-30)
REVERT: S    3 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7573 (pt0)
  outliers start: 23
  outliers final: 13
  residues processed: 141
  average time/residue: 0.6302
  time to fit residues: 93.5199
Evaluate side-chains
  134 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  179 TRP
Chi-restraints excluded: chain R residue  337 THR
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  185 SER
Chi-restraints excluded: chain S residue  226 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 22 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 1 optimal weight:   10.0000
   chunk 74 optimal weight:    4.9990
   chunk 62 optimal weight:    0.0980
   chunk 69 optimal weight:    0.0370
   chunk 37 optimal weight:    0.9980
   chunk 97 optimal weight:    0.0370
   chunk 80 optimal weight:    0.6980
   overall best weight:    0.3736

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

Flipped N/Q/H residues before XYZ refinement:
B  16 ASN
B  32 GLN
B 340 ASN
S 174 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.163514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.111902 restraints weight = 9607.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 2.60
r_work: 0.3125 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.2007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8345  Z= 0.085
  Angle     :  0.450   7.121  11314  Z= 0.235
  Chirality :  0.040   0.205   1305
  Planarity :  0.003   0.031   1431
  Dihedral  :  3.742  44.350   1157
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 15.34 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.79 (0.27), residues: 1051
  helix:  3.17 (0.28), residues: 346
  sheet:  0.81 (0.30), residues: 295
  loop : -0.27 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 197 
 TYR   0.010   0.001   TYR S 178 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.010   0.001   TRP B  82 
 HIS   0.002   0.000   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00182 ( 8343)
  covalent geometry    : angle       0.44958 (11310)
  SS BOND              : bond        0.00484 (    2)
  SS BOND              : angle       0.85373 (    4)
  hydrogen bonds       : bond        0.02915 (  407)
  hydrogen bonds       : angle       3.57416 ( 1152)

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 126
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.7516 (m-40) cc_final: 0.7265 (m110)
REVERT: A  251 ASP cc_start: 0.7713 (t0) cc_final: 0.7418 (t0)
REVERT: A  309 ASP cc_start: 0.7487 (p0) cc_final: 0.7090 (p0)
REVERT: A  313 ARG cc_start: 0.7751 (ptp90) cc_final: 0.7332 (ptp90)
REVERT: B  127 LYS cc_start: 0.8752 (mttm) cc_final: 0.8281 (mttt)
REVERT: G   21 MET cc_start: 0.6570 (ttt) cc_final: 0.6149 (mmt)
REVERT: G   58 GLU cc_start: 0.7714 (pm20) cc_final: 0.6909 (mm-30)
  outliers start: 19
  outliers final: 13
  residues processed: 138
  average time/residue: 0.6471
  time to fit residues: 93.9598
Evaluate side-chains
  130 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  179 TRP
Chi-restraints excluded: chain R residue  301 VAL
Chi-restraints excluded: chain R residue  337 THR
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  185 SER
Chi-restraints excluded: chain S residue  226 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 102 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 4 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9980
   chunk 79 optimal weight:    0.8980
   chunk 64 optimal weight:    4.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
B  16 ASN
S 174 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.157726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.107299 restraints weight = 9619.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3143 rms_B_bonded: 2.47
r_work: 0.2995 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2851 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   8345  Z= 0.189
  Angle     :  0.564   8.692  11314  Z= 0.295
  Chirality :  0.043   0.154   1305
  Planarity :  0.003   0.035   1431
  Dihedral  :  4.282  45.389   1157
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 15.46 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.47 (0.26), residues: 1051
  helix:  3.01 (0.28), residues: 346
  sheet:  0.60 (0.30), residues: 291
  loop : -0.52 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 197 
 TYR   0.013   0.002   TYR B 105 
 PHE   0.017   0.002   PHE A 196 
 TRP   0.015   0.001   TRP S  47 
 HIS   0.007   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 ( 8343)
  covalent geometry    : angle       0.56325 (11310)
  SS BOND              : bond        0.00842 (    2)
  SS BOND              : angle       1.48082 (    4)
  hydrogen bonds       : bond        0.04122 (  407)
  hydrogen bonds       : angle       3.88319 ( 1152)

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 125
  time to evaluate  : 0.282 
Fit side-chains
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
REVERT: A   22 ASN cc_start: 0.7545 (m-40) cc_final: 0.7221 (m110)
REVERT: A   26 ASP cc_start: 0.7362 (m-30) cc_final: 0.7058 (m-30)
REVERT: A  251 ASP cc_start: 0.7719 (t0) cc_final: 0.7442 (t0)
REVERT: A  309 ASP cc_start: 0.7588 (p0) cc_final: 0.7176 (p0)
REVERT: A  313 ARG cc_start: 0.7749 (ptp90) cc_final: 0.7447 (ptp-170)
REVERT: B   46 ARG cc_start: 0.7694 (mtm-85) cc_final: 0.6955 (mtp85)
REVERT: B  127 LYS cc_start: 0.8995 (mttm) cc_final: 0.8550 (mttt)
REVERT: B  219 ARG cc_start: 0.7803 (mmt180) cc_final: 0.7514 (mpt90)
REVERT: B  291 ASP cc_start: 0.7691 (m-30) cc_final: 0.7482 (m-30)
REVERT: G   21 MET cc_start: 0.6764 (ttt) cc_final: 0.6289 (mmt)
REVERT: G   58 GLU cc_start: 0.7769 (pm20) cc_final: 0.6941 (mm-30)
REVERT: S  211 ASP cc_start: 0.8255 (m-30) cc_final: 0.8005 (m-30)
  outliers start: 28
  outliers final: 17
  residues processed: 141
  average time/residue: 0.6622
  time to fit residues: 98.1067
Evaluate side-chains
  137 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  179 TRP
Chi-restraints excluded: chain R residue  301 VAL
Chi-restraints excluded: chain R residue  337 THR
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  185 SER
Chi-restraints excluded: chain S residue  226 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 47 optimal weight:    0.6980
   chunk 86 optimal weight:    0.0870
   chunk 96 optimal weight:    5.9990
   chunk 89 optimal weight:    0.6980
   chunk 70 optimal weight:    0.8980
   chunk 90 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
B  16 ASN
S 174 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.159688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.108809 restraints weight = 9718.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 2.51
r_work: 0.3101 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
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      :  0.002   0.031   8345  Z= 0.101
  Angle     :  0.474   6.806  11314  Z= 0.249
  Chirality :  0.040   0.134   1305
  Planarity :  0.003   0.035   1431
  Dihedral  :  3.990  44.352   1157
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.65 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.27), residues: 1051
  helix:  3.15 (0.28), residues: 345
  sheet:  0.64 (0.30), residues: 292
  loop : -0.47 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 197 
 TYR   0.010   0.001   TYR S 178 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 8343)
  covalent geometry    : angle       0.47368 (11310)
  SS BOND              : bond        0.00584 (    2)
  SS BOND              : angle       0.97251 (    4)
  hydrogen bonds       : bond        0.03209 (  407)
  hydrogen bonds       : angle       3.66035 ( 1152)

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 0.326 
Fit side-chains
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: R  344 ARG cc_start: 0.6272 (OUTLIER) cc_final: 0.5958 (mtt180)
REVERT: A   22 ASN cc_start: 0.7526 (m-40) cc_final: 0.7213 (m110)
REVERT: A   26 ASP cc_start: 0.7448 (m-30) cc_final: 0.7156 (m-30)
REVERT: A   51 LYS cc_start: 0.8050 (ttmm) cc_final: 0.7530 (ttpp)
REVERT: A  271 LYS cc_start: 0.7540 (ttmt) cc_final: 0.7093 (tttt)
REVERT: A  309 ASP cc_start: 0.7459 (p0) cc_final: 0.7059 (p0)
REVERT: B   46 ARG cc_start: 0.7605 (mtm-85) cc_final: 0.6859 (mtp85)
REVERT: B  127 LYS cc_start: 0.8899 (mttm) cc_final: 0.8414 (mttt)
REVERT: B  234 PHE cc_start: 0.9274 (OUTLIER) cc_final: 0.8987 (m-80)
REVERT: G   21 MET cc_start: 0.6724 (ttt) cc_final: 0.6296 (mmt)
REVERT: G   58 GLU cc_start: 0.7802 (pm20) cc_final: 0.6985 (mm-30)
REVERT: S    3 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7681 (pt0)
REVERT: S  211 ASP cc_start: 0.8298 (m-30) cc_final: 0.8089 (m-30)
  outliers start: 21
  outliers final: 14
  residues processed: 141
  average time/residue: 0.6836
  time to fit residues: 101.1748
Evaluate side-chains
  139 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  221 VAL
Chi-restraints excluded: chain R residue  301 VAL
Chi-restraints excluded: chain R residue  337 THR
Chi-restraints excluded: chain R residue  344 ARG
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  185 SER
Chi-restraints excluded: chain S residue  226 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 102 optimal weight:    5.9990
   chunk 55 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 87 optimal weight:    0.2980
   chunk 64 optimal weight:    4.9990
   chunk 74 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
B  16 ASN
S 174 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.159395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.108953 restraints weight = 9588.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 2.47
r_work: 0.3062 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
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      :  0.003   0.031   8345  Z= 0.133
  Angle     :  0.513   8.825  11314  Z= 0.267
  Chirality :  0.041   0.132   1305
  Planarity :  0.003   0.036   1431
  Dihedral  :  3.878  29.640   1155
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 17.88 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.49 (0.26), residues: 1051
  helix:  3.11 (0.28), residues: 345
  sheet:  0.54 (0.30), residues: 291
  loop : -0.52 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 197 
 TYR   0.013   0.001   TYR A 302 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.013   0.001   TRP S  47 
 HIS   0.005   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 8343)
  covalent geometry    : angle       0.51292 (11310)
  SS BOND              : bond        0.00701 (    2)
  SS BOND              : angle       1.20594 (    4)
  hydrogen bonds       : bond        0.03542 (  407)
  hydrogen bonds       : angle       3.74360 ( 1152)

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 0.326 
Fit side-chains
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: R  344 ARG cc_start: 0.6266 (OUTLIER) cc_final: 0.5942 (mtt180)
REVERT: A   22 ASN cc_start: 0.7584 (m-40) cc_final: 0.7256 (m110)
REVERT: A   26 ASP cc_start: 0.7416 (m-30) cc_final: 0.7105 (m-30)
REVERT: A   51 LYS cc_start: 0.8066 (ttmm) cc_final: 0.7553 (ttpp)
REVERT: A  309 ASP cc_start: 0.7453 (p0) cc_final: 0.7071 (p0)
REVERT: B   46 ARG cc_start: 0.7641 (mtm-85) cc_final: 0.7044 (mtp85)
REVERT: B  127 LYS cc_start: 0.8943 (mttm) cc_final: 0.8463 (mttt)
REVERT: B  234 PHE cc_start: 0.9287 (OUTLIER) cc_final: 0.9020 (m-80)
REVERT: G   58 GLU cc_start: 0.7791 (pm20) cc_final: 0.6979 (mm-30)
REVERT: S    3 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7716 (pt0)
REVERT: S  211 ASP cc_start: 0.8251 (m-30) cc_final: 0.8020 (m-30)
  outliers start: 25
  outliers final: 17
  residues processed: 140
  average time/residue: 0.6391
  time to fit residues: 94.2550
Evaluate side-chains
  143 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  221 VAL
Chi-restraints excluded: chain R residue  301 VAL
Chi-restraints excluded: chain R residue  337 THR
Chi-restraints excluded: chain R residue  344 ARG
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  185 SER
Chi-restraints excluded: chain S residue  214 VAL
Chi-restraints excluded: chain S residue  226 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 84 optimal weight:    0.0980
   chunk 92 optimal weight:    0.0070
   chunk 20 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 44 optimal weight:    7.9990
   chunk 54 optimal weight:    0.6980
   chunk 64 optimal weight:    3.9990
   chunk 60 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.4798

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
B  16 ASN
B 340 ASN
S 174 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.162332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.112089 restraints weight = 9660.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 2.49
r_work: 0.3108 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8345  Z= 0.094
  Angle     :  0.472   7.117  11314  Z= 0.248
  Chirality :  0.040   0.131   1305
  Planarity :  0.003   0.035   1431
  Dihedral  :  3.682  32.130   1155
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 18.34 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.60 (0.27), residues: 1051
  helix:  3.12 (0.28), residues: 345
  sheet:  0.63 (0.30), residues: 292
  loop : -0.41 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 197 
 TYR   0.012   0.001   TYR A 302 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 ( 8343)
  covalent geometry    : angle       0.47204 (11310)
  SS BOND              : bond        0.00546 (    2)
  SS BOND              : angle       0.86212 (    4)
  hydrogen bonds       : bond        0.03042 (  407)
  hydrogen bonds       : angle       3.62279 ( 1152)

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 0.263 
Fit side-chains
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.7513 (m-40) cc_final: 0.7213 (m110)
REVERT: A   26 ASP cc_start: 0.7352 (m-30) cc_final: 0.6990 (m-30)
REVERT: A   51 LYS cc_start: 0.8073 (ttmm) cc_final: 0.7568 (ttpp)
REVERT: A  271 LYS cc_start: 0.7361 (ttpt) cc_final: 0.7073 (tptt)
REVERT: A  309 ASP cc_start: 0.7278 (p0) cc_final: 0.6896 (p0)
REVERT: B   27 ASP cc_start: 0.7739 (t0) cc_final: 0.7293 (p0)
REVERT: B  127 LYS cc_start: 0.8845 (mttm) cc_final: 0.8592 (mttt)
REVERT: B  234 PHE cc_start: 0.9265 (OUTLIER) cc_final: 0.8969 (m-80)
REVERT: G   58 GLU cc_start: 0.7791 (pm20) cc_final: 0.6981 (mm-30)
REVERT: S    3 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7667 (pt0)
REVERT: S  211 ASP cc_start: 0.8268 (m-30) cc_final: 0.8056 (m-30)
  outliers start: 21
  outliers final: 14
  residues processed: 143
  average time/residue: 0.6538
  time to fit residues: 98.3774
Evaluate side-chains
  141 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  221 VAL
Chi-restraints excluded: chain R residue  301 VAL
Chi-restraints excluded: chain R residue  337 THR
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  185 SER
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 87 optimal weight:    0.4980
   chunk 93 optimal weight:    0.9980
   chunk 81 optimal weight:    0.4980
   chunk 44 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 4 optimal weight:    7.9990
   chunk 15 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
B  16 ASN
B 340 ASN
S 174 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.160861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.110557 restraints weight = 9551.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 2.47
r_work: 0.3073 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2927 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.2116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8345  Z= 0.112
  Angle     :  0.505   9.209  11314  Z= 0.262
  Chirality :  0.041   0.145   1305
  Planarity :  0.003   0.036   1431
  Dihedral  :  3.748  31.986   1155
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 18.92 %
    Favored  : 79.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.57 (0.27), residues: 1051
  helix:  3.11 (0.28), residues: 345
  sheet:  0.57 (0.30), residues: 297
  loop : -0.41 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 134 
 TYR   0.016   0.001   TYR A 302 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 8343)
  covalent geometry    : angle       0.50455 (11310)
  SS BOND              : bond        0.00631 (    2)
  SS BOND              : angle       1.02065 (    4)
  hydrogen bonds       : bond        0.03257 (  407)
  hydrogen bonds       : angle       3.65956 ( 1152)

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.7478 (m-40) cc_final: 0.7214 (m110)
REVERT: A   26 ASP cc_start: 0.7267 (m-30) cc_final: 0.6935 (m-30)
REVERT: A   51 LYS cc_start: 0.8025 (ttmm) cc_final: 0.7524 (ttpp)
REVERT: A  309 ASP cc_start: 0.7289 (p0) cc_final: 0.6902 (p0)
REVERT: B   27 ASP cc_start: 0.7807 (t0) cc_final: 0.7272 (p0)
REVERT: B   46 ARG cc_start: 0.7689 (mtm-85) cc_final: 0.7038 (mtp85)
REVERT: B  127 LYS cc_start: 0.8863 (mttm) cc_final: 0.8367 (mttt)
REVERT: B  234 PHE cc_start: 0.9278 (OUTLIER) cc_final: 0.8993 (m-80)
REVERT: G   58 GLU cc_start: 0.7770 (pm20) cc_final: 0.6961 (mm-30)
REVERT: S  211 ASP cc_start: 0.8211 (m-30) cc_final: 0.7991 (m-30)
  outliers start: 17
  outliers final: 14
  residues processed: 138
  average time/residue: 0.6716
  time to fit residues: 97.3086
Evaluate side-chains
  140 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 125
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  221 VAL
Chi-restraints excluded: chain R residue  301 VAL
Chi-restraints excluded: chain R residue  337 THR
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  185 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 104 optimal weight:    0.0170
   chunk 98 optimal weight:    0.5980
   chunk 86 optimal weight:    0.0570
   chunk 65 optimal weight:    3.9990
   chunk 80 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 82 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   overall best weight:    0.3936

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

Flipped N/Q/H residues before XYZ refinement:
B  16 ASN
B 340 ASN
S 174 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.162784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.111415 restraints weight = 9597.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 2.58
r_work: 0.3111 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2970 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.2269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8345  Z= 0.088
  Angle     :  0.468   7.166  11314  Z= 0.246
  Chirality :  0.040   0.144   1305
  Planarity :  0.003   0.035   1431
  Dihedral  :  3.579  35.544   1155
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 19.15 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.70 (0.27), residues: 1051
  helix:  3.13 (0.28), residues: 347
  sheet:  0.69 (0.30), residues: 290
  loop : -0.29 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 197 
 TYR   0.016   0.001   TYR A 302 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00193 ( 8343)
  covalent geometry    : angle       0.46805 (11310)
  SS BOND              : bond        0.00510 (    2)
  SS BOND              : angle       0.79943 (    4)
  hydrogen bonds       : bond        0.02873 (  407)
  hydrogen bonds       : angle       3.54408 ( 1152)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 3350.28 seconds
wall clock time: 57 minutes 39.31 seconds (3459.31 seconds total)