Starting phenix.real_space_refine
on Fri Aug 22 17:34:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8unn_42410/08_2025/8unn_42410.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8unn_42410/08_2025/8unn_42410.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8unn_42410/08_2025/8unn_42410.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8unn_42410/08_2025/8unn_42410.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8unn_42410/08_2025/8unn_42410.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8unn_42410/08_2025/8unn_42410.cif"
  }
  resolution = 3.4
  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=   0.023
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: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      39      5.16       5
     C    4183      2.51       5
     N    1122      2.21       5
     O    1156      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6503
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1690
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 231, 1678
          Classifications: {'peptide': 231}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 65}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 245
          Unresolved non-hydrogen angles: 294
          Unresolved non-hydrogen dihedrals: 199
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ARG:plan': 10, 'ASN:plan1': 1, 'GLU:plan': 16, 'GLN:plan1': 3, 'ASP:plan': 9, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 162
      Conformer: "B"
        Number of residues, atoms: 231, 1678
          Classifications: {'peptide': 231}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 65}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 245
          Unresolved non-hydrogen angles: 294
          Unresolved non-hydrogen dihedrals: 199
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ARG:plan': 10, 'ASN:plan1': 1, 'GLU:plan': 16, 'GLN:plan1': 3, 'ASP:plan': 9, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 162
          bond proxies already assigned to first conformer: 1698
    Chain: "B"
      Number of atoms: 2384
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2384
          Classifications: {'peptide': 333}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 50}
          Link IDs: {'PTRANS': 5, 'TRANS': 327}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 176
          Unresolved non-hydrogen angles: 217
          Unresolved non-hydrogen dihedrals: 135
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ASP:plan': 14, 'GLN:plan1': 6, 'ARG:plan': 7, 'GLU:plan': 6, 'ASN:plan1': 3}
          Unresolved non-hydrogen planarities: 134
    Chain: "G"
      Number of atoms: 338
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 338
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 73
          Unresolved non-hydrogen angles: 86
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 39
    Chain: "R"
      Number of atoms: 2043
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2043
          Classifications: {'peptide': 284}
          Incomplete info: {'truncation_to_alanine': 72}
          Link IDs: {'PTRANS': 7, 'TRANS': 276}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 249
          Unresolved non-hydrogen angles: 307
          Unresolved non-hydrogen dihedrals: 202
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 9, 'ARG:plan': 7, 'ASP:plan': 5, 'ASN:plan1': 4, 'GLN:plan1': 4, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 133
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 16
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR A 360 " occ=0.51
      ... (22 atoms not shown)
      pdb=" OH BTYR A 360 " occ=0.49
  Time building chain proxies: 2.05, per 1000 atoms: 0.32
  Number of scatterers: 6503
  At special positions: 0
  Unit cell: (83.2992, 138.832, 98.9178, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      39     16.00
     P       3     15.00
     O    1156      8.00
     N    1122      7.00
     C    4183      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.63
  Conformation dependent library (CDL) restraints added in 435.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1708

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 8 sheets defined
      48.6% alpha, 16.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 40
      removed outlier: 3.877A  pdb=" N   LYS A  17 " --> pdb=" O   ARG A  13 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   GLU A  21 " --> pdb=" O   LYS A  17 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ALA A  22 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   THR A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 61
    Processing helix  chain 'A' and resid 224 through 228
      removed outlier: 3.786A  pdb=" N   GLN A 227 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ARG A 228 " --> pdb=" O   GLY A 225 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 224 through 228'
    Processing helix  chain 'A' and resid 235 through 239
      removed outlier: 3.574A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 302
      removed outlier: 3.884A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ALA A 298 " --> pdb=" O   GLN A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.071A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 317
      removed outlier: 3.674A  pdb=" N   ARG A 317 " --> pdb=" O   GLU A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.678A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.536A  pdb=" N   PHE A 376 " --> pdb=" O   ILE A 372 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   TYR A 391 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 26
      removed outlier: 4.118A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   GLN B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   LEU B  14 " --> pdb=" O   GLU B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.583A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 11 through 24
      removed outlier: 3.709A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.519A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 33 through 61
      removed outlier: 3.540A  pdb=" N   ASN R  51 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 68 through 97
      removed outlier: 3.777A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 120
    Processing helix  chain 'R' and resid 121 through 137
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 164
      removed outlier: 3.987A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 166 through 171
    Processing helix  chain 'R' and resid 172 through 175
      removed outlier: 3.628A  pdb=" N   ARG R 175 " --> pdb=" O   HIS R 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 172 through 175'
    Processing helix  chain 'R' and resid 178 through 187
      removed outlier: 3.719A  pdb=" N   ALA R 186 " --> pdb=" O   ILE R 182 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   GLU R 187 " --> pdb=" O   ASN R 183 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 196 through 208
    Processing helix  chain 'R' and resid 208 through 238
    Processing helix  chain 'R' and resid 269 through 299
      removed outlier: 3.814A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.538A  pdb=" N   VAL R 292 " --> pdb=" O   PRO R 288 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE R 298 " --> pdb=" O   ILE R 294 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
      removed outlier: 3.769A  pdb=" N   TYR R 308 " --> pdb=" O   ARG R 304 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 318 through 321
    Processing helix  chain 'R' and resid 322 through 327
    Processing helix  chain 'R' and resid 329 through 341
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 3.586A  pdb=" N   PHE A 222 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.220A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.292A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.768A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.153A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 9.287A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.720A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.635A  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: 4.024A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.939A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.199A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.895A  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: 3.680A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.884A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.659A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.121A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.866A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.529A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)

    351 hydrogen bonds defined for protein.
    1026 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: 1.05

  Time building geometry restraints manager: 0.76 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1369
        1.33 -     1.45: 1613
        1.45 -     1.57: 3608
        1.57 -     1.69: 5
        1.69 -     1.81: 53
  Bond restraints: 6648
  Sorted by residual:
  bond pdb=" CA  GLN A 227 "
       pdb=" C   GLN A 227 "
    ideal  model  delta    sigma   weight residual
    1.522  1.442  0.081 1.43e-02 4.89e+03 3.20e+01
  bond pdb=" C5  GTP A 401 "
       pdb=" C6  GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.390  1.479 -0.089 2.00e-02 2.50e+03 1.97e+01
  bond pdb=" C4  GTP A 401 "
       pdb=" C5  GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.390  1.465 -0.075 2.00e-02 2.50e+03 1.42e+01
  bond pdb=" CA  THR A 325 "
       pdb=" C   THR A 325 "
    ideal  model  delta    sigma   weight residual
    1.522  1.476  0.046 1.22e-02 6.72e+03 1.41e+01
  bond pdb=" N   GLU A 230 "
       pdb=" CA  GLU A 230 "
    ideal  model  delta    sigma   weight residual
    1.459  1.416  0.043 1.21e-02 6.83e+03 1.24e+01
  ... (remaining 6643 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.40: 8988
        2.40 -     4.81: 102
        4.81 -     7.21: 21
        7.21 -     9.61: 0
        9.61 -    12.02: 3
  Bond angle restraints: 9114
  Sorted by residual:
  angle pdb=" N   GLN G  11 "
        pdb=" CA  GLN G  11 "
        pdb=" C   GLN G  11 "
      ideal   model   delta    sigma   weight residual
     111.28   99.26   12.02 1.09e+00 8.42e-01 1.22e+02
  angle pdb=" C   THR A 325 "
        pdb=" CA  THR A 325 "
        pdb=" CB  THR A 325 "
      ideal   model   delta    sigma   weight residual
     110.17  102.99    7.18 1.11e+00 8.12e-01 4.19e+01
  angle pdb=" N   ASP B   5 "
        pdb=" CA  ASP B   5 "
        pdb=" C   ASP B   5 "
      ideal   model   delta    sigma   weight residual
     111.28  105.50    5.78 1.09e+00 8.42e-01 2.82e+01
  angle pdb=" N   ALA B  11 "
        pdb=" CA  ALA B  11 "
        pdb=" C   ALA B  11 "
      ideal   model   delta    sigma   weight residual
     111.28  117.01   -5.73 1.09e+00 8.42e-01 2.76e+01
  angle pdb=" N   GLN B   9 "
        pdb=" CA  GLN B   9 "
        pdb=" C   GLN B   9 "
      ideal   model   delta    sigma   weight residual
     111.28  106.25    5.03 1.09e+00 8.42e-01 2.13e+01
  ... (remaining 9109 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.22: 3758
       33.22 -    66.43: 52
       66.43 -    99.65: 2
       99.65 -   132.87: 2
      132.87 -   166.08: 3
  Dihedral angle restraints: 3817
    sinusoidal: 1185
      harmonic: 2632
  Sorted by residual:
  dihedral pdb=" C5' GTP A 401 "
           pdb=" O5' GTP A 401 "
           pdb=" PA  GTP A 401 "
           pdb=" O3A GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -124.65 -166.08     1      2.00e+01 2.50e-03 4.73e+01
  dihedral pdb=" C8  GTP A 401 "
           pdb=" C1' GTP A 401 "
           pdb=" N9  GTP A 401 "
           pdb=" O4' GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -59.70  164.30     1      2.00e+01 2.50e-03 4.71e+01
  dihedral pdb=" O3B GTP A 401 "
           pdb=" O3A GTP A 401 "
           pdb=" PB  GTP A 401 "
           pdb=" PA  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     291.08  142.41  148.67     1      2.00e+01 2.50e-03 4.45e+01
  ... (remaining 3814 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 681
       0.030 -    0.060: 252
       0.060 -    0.090: 100
       0.090 -    0.120: 50
       0.120 -    0.150: 11
  Chirality restraints: 1094
  Sorted by residual:
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.55   -0.15 2.00e-01 2.50e+01 5.66e-01
  chirality pdb=" CA  GLN G  11 "
            pdb=" N   GLN G  11 "
            pdb=" C   GLN G  11 "
            pdb=" CB  GLN G  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.54e-01
  chirality pdb=" CB  VAL A 224 "
            pdb=" CA  VAL A 224 "
            pdb=" CG1 VAL A 224 "
            pdb=" CG2 VAL A 224 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.51e-01
  ... (remaining 1091 not shown)

  Planarity restraints: 1145
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "    0.053 5.00e-02 4.00e+02   8.06e-02 1.04e+01
        pdb=" N   PRO G  49 "   -0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 226 "    0.015 2.00e-02 2.50e+03   3.07e-02 9.45e+00
        pdb=" C   GLY A 226 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   GLY A 226 "    0.020 2.00e-02 2.50e+03
        pdb=" N   GLN A 227 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 222 "   -0.012 2.00e-02 2.50e+03   1.22e-02 2.61e+00
        pdb=" CG  PHE A 222 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 222 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 222 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 222 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 222 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 222 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1142 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1049
        2.76 -     3.29: 5980
        3.29 -     3.83: 10224
        3.83 -     4.36: 11087
        4.36 -     4.90: 20550
  Nonbonded interactions: 48890
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" OD1 ASP A 295 "
            pdb=" N   LEU A 296 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" OG1 THR B  86 "
            pdb=" OD1 ASN B  88 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" OE1 GLN A  19 "
            pdb=" ND2 ASN B  88 "
     model   vdw
     2.342 3.120
  ... (remaining 48885 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=0.49 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:             2.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.290
  Find NCS groups from input model:        0.030
  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:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
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      :  0.005   0.089   6649  Z= 0.279
  Angle     :  0.672  12.017   9116  Z= 0.415
  Chirality :  0.042   0.150   1094
  Planarity :  0.004   0.081   1145
  Dihedral  : 13.918 166.085   2106
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.86 (0.28), residues: 888
  helix:  2.27 (0.27), residues: 368
  sheet: -0.06 (0.40), residues: 172
  loop : -0.96 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 389 
 TYR   0.019   0.001   TYR B  59 
 PHE   0.026   0.001   PHE A 222 
 TRP   0.012   0.001   TRP R 313 
 HIS   0.006   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 ( 6648)
  covalent geometry    : angle       0.67167 ( 9114)
  SS BOND              : bond        0.00174 (    1)
  SS BOND              : angle       0.98764 (    2)
  hydrogen bonds       : bond        0.19734 (  351)
  hydrogen bonds       : angle       6.50624 ( 1026)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.263 
Fit side-chains
REVERT: R  272 LEU cc_start: 0.8446 (tp) cc_final: 0.8236 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.0668
  time to fit residues: 8.8329
Evaluate side-chains
  71 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    0.2980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    6.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 236 GLN
A 294 GLN
R 178 HIS
R 179 GLN
R 296 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.129870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.104285 restraints weight = 41022.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 4.45
r_work: 0.3074 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3060
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3060
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.1167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6649  Z= 0.129
  Angle     :  0.497   5.959   9116  Z= 0.270
  Chirality :  0.041   0.149   1094
  Planarity :  0.003   0.060   1145
  Dihedral  :  9.975 160.436    985
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  7.52 %
    Favored  : 91.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.11 (0.28), residues: 888
  helix:  2.37 (0.26), residues: 390
  sheet: -0.02 (0.40), residues: 172
  loop : -0.86 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 389 
 TYR   0.010   0.001   TYR A 358 
 PHE   0.033   0.001   PHE A 222 
 TRP   0.007   0.001   TRP B  99 
 HIS   0.010   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 6648)
  covalent geometry    : angle       0.49633 ( 9114)
  SS BOND              : bond        0.00782 (    1)
  SS BOND              : angle       1.56577 (    2)
  hydrogen bonds       : bond        0.04836 (  351)
  hydrogen bonds       : angle       4.59638 ( 1026)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 78
  time to evaluate  : 0.276 
Fit side-chains
  outliers start: 7
  outliers final: 6
  residues processed: 82
  average time/residue: 0.0622
  time to fit residues: 7.5433
Evaluate side-chains
  76 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 14 optimal weight:    9.9990
   chunk 69 optimal weight:    0.5980
   chunk 66 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 71 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0970
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
A 264 ASN
A 294 GLN
B 183 HIS
B 259 GLN
R 178 HIS
R 296 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.130930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.104250 restraints weight = 35688.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 4.23
r_work: 0.3095 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3097
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3097
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.1422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   6649  Z= 0.106
  Angle     :  0.456   6.250   9116  Z= 0.246
  Chirality :  0.040   0.149   1094
  Planarity :  0.003   0.055   1145
  Dihedral  :  9.388 164.694    985
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 11.36 %
    Favored  : 87.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.27 (0.29), residues: 888
  helix:  2.51 (0.27), residues: 391
  sheet:  0.07 (0.40), residues: 171
  loop : -0.81 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 389 
 TYR   0.010   0.001   TYR A 358 
 PHE   0.027   0.001   PHE A 222 
 TRP   0.007   0.001   TRP A 277 
 HIS   0.013   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 6648)
  covalent geometry    : angle       0.45540 ( 9114)
  SS BOND              : bond        0.00217 (    1)
  SS BOND              : angle       1.25175 (    2)
  hydrogen bonds       : bond        0.04172 (  351)
  hydrogen bonds       : angle       4.29769 ( 1026)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.263 
Fit side-chains
  outliers start: 6
  outliers final: 6
  residues processed: 79
  average time/residue: 0.0690
  time to fit residues: 7.8483
Evaluate side-chains
  76 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  295 VAL
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 83 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 60 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   chunk 81 optimal weight:    4.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
A 294 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 178 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.130310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.103542 restraints weight = 35146.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 4.17
r_work: 0.3089 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3080
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3080
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.1634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6649  Z= 0.110
  Angle     :  0.450   6.613   9116  Z= 0.242
  Chirality :  0.040   0.146   1094
  Planarity :  0.003   0.051   1145
  Dihedral  :  9.104 170.791    985
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 13.29 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (0.29), residues: 888
  helix:  2.40 (0.27), residues: 403
  sheet:  0.02 (0.40), residues: 172
  loop : -0.83 (0.32), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 389 
 TYR   0.011   0.001   TYR A 358 
 PHE   0.019   0.001   PHE A 222 
 TRP   0.006   0.001   TRP A 277 
 HIS   0.010   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 6648)
  covalent geometry    : angle       0.45019 ( 9114)
  SS BOND              : bond        0.00408 (    1)
  SS BOND              : angle       1.01439 (    2)
  hydrogen bonds       : bond        0.03997 (  351)
  hydrogen bonds       : angle       4.08813 ( 1026)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A  294 GLN cc_start: 0.8986 (tp-100) cc_final: 0.8725 (tp40)
REVERT: B  209 LYS cc_start: 0.9248 (mttm) cc_final: 0.9018 (mttm)
REVERT: R  192 ASP cc_start: 0.8103 (m-30) cc_final: 0.7867 (m-30)
  outliers start: 11
  outliers final: 10
  residues processed: 84
  average time/residue: 0.0632
  time to fit residues: 7.7635
Evaluate side-chains
  80 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  106 CYS
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  295 VAL
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 26 optimal weight:    0.0870
   chunk 55 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0470
   chunk 76 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 88 optimal weight:    4.9990
   overall best weight:    0.8258

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
R 178 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.130226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.103974 restraints weight = 37598.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 4.52
r_work: 0.3074 rms_B_bonded: 4.86 restraints_weight: 0.5000
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3074
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3074
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.1713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   6649  Z= 0.108
  Angle     :  0.446   6.656   9116  Z= 0.241
  Chirality :  0.040   0.145   1094
  Planarity :  0.003   0.054   1145
  Dihedral  :  9.056 176.329    985
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 12.94 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.23 (0.29), residues: 888
  helix:  2.48 (0.27), residues: 398
  sheet: -0.07 (0.40), residues: 172
  loop : -0.84 (0.32), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 389 
 TYR   0.008   0.001   TYR B 289 
 PHE   0.015   0.001   PHE A 222 
 TRP   0.006   0.001   TRP A 277 
 HIS   0.010   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 6648)
  covalent geometry    : angle       0.44594 ( 9114)
  SS BOND              : bond        0.00372 (    1)
  SS BOND              : angle       0.95719 (    2)
  hydrogen bonds       : bond        0.03888 (  351)
  hydrogen bonds       : angle       4.01056 ( 1026)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A  294 GLN cc_start: 0.9044 (tp-100) cc_final: 0.8770 (tp40)
REVERT: B  209 LYS cc_start: 0.9239 (mttm) cc_final: 0.9014 (mttm)
REVERT: R  192 ASP cc_start: 0.7935 (m-30) cc_final: 0.7673 (m-30)
  outliers start: 14
  outliers final: 12
  residues processed: 83
  average time/residue: 0.0652
  time to fit residues: 7.8737
Evaluate side-chains
  81 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  106 CYS
Chi-restraints excluded: chain R residue  157 VAL
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  295 VAL
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 36 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 75 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 178 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.129668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.104177 restraints weight = 24372.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 3.45
r_work: 0.3113 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3117
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3117 r_free = 0.3117    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3117 r_free = 0.3117    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3117
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.1834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   6649  Z= 0.111
  Angle     :  0.446   6.479   9116  Z= 0.240
  Chirality :  0.040   0.146   1094
  Planarity :  0.003   0.054   1145
  Dihedral  :  9.011 177.147    985
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 13.81 %
    Favored  : 83.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (0.29), residues: 888
  helix:  2.49 (0.27), residues: 398
  sheet: -0.14 (0.40), residues: 172
  loop : -0.80 (0.33), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 389 
 TYR   0.011   0.001   TYR A 358 
 PHE   0.013   0.001   PHE A 222 
 TRP   0.005   0.001   TRP B  99 
 HIS   0.009   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 6648)
  covalent geometry    : angle       0.44567 ( 9114)
  SS BOND              : bond        0.00351 (    1)
  SS BOND              : angle       0.94012 (    2)
  hydrogen bonds       : bond        0.03946 (  351)
  hydrogen bonds       : angle       3.97952 ( 1026)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 68
  time to evaluate  : 0.256 
Fit side-chains
REVERT: A  294 GLN cc_start: 0.8993 (tp-100) cc_final: 0.8755 (tp40)
REVERT: R  192 ASP cc_start: 0.7984 (m-30) cc_final: 0.7781 (m-30)
  outliers start: 14
  outliers final: 10
  residues processed: 80
  average time/residue: 0.0617
  time to fit residues: 7.3989
Evaluate side-chains
  77 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  106 CYS
Chi-restraints excluded: chain R residue  157 VAL
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  295 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 15 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 77 optimal weight:    0.0270
   chunk 20 optimal weight:    0.9990
   chunk 76 optimal weight:    5.9990
   overall best weight:    0.9042

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 178 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.129658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.103081 restraints weight = 36747.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 4.42
r_work: 0.3075 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3077
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3077 r_free = 0.3077    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3077 r_free = 0.3077    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3077
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.1859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   6649  Z= 0.112
  Angle     :  0.445   6.523   9116  Z= 0.240
  Chirality :  0.040   0.145   1094
  Planarity :  0.003   0.055   1145
  Dihedral  :  8.850 171.647    985
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 13.99 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.23 (0.29), residues: 888
  helix:  2.49 (0.27), residues: 398
  sheet: -0.17 (0.40), residues: 172
  loop : -0.78 (0.32), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 389 
 TYR   0.010   0.001   TYR A 358 
 PHE   0.009   0.001   PHE B 199 
 TRP   0.009   0.001   TRP B  99 
 HIS   0.012   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 6648)
  covalent geometry    : angle       0.44514 ( 9114)
  SS BOND              : bond        0.00339 (    1)
  SS BOND              : angle       0.93229 (    2)
  hydrogen bonds       : bond        0.03934 (  351)
  hydrogen bonds       : angle       3.97609 ( 1026)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A  294 GLN cc_start: 0.9014 (tp-100) cc_final: 0.8787 (tp40)
REVERT: B   45 MET cc_start: 0.8626 (mmt) cc_final: 0.8007 (mmt)
REVERT: R  192 ASP cc_start: 0.7917 (m-30) cc_final: 0.7677 (m-30)
  outliers start: 14
  outliers final: 11
  residues processed: 81
  average time/residue: 0.0606
  time to fit residues: 7.2586
Evaluate side-chains
  79 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  106 CYS
Chi-restraints excluded: chain R residue  157 VAL
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  295 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 57 optimal weight:    0.5980
   chunk 20 optimal weight:    0.0030
   chunk 12 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 85 optimal weight:    0.0870
   chunk 21 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.4768

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 178 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.131463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.104584 restraints weight = 32979.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 4.26
r_work: 0.3086 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3074
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3074
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.2053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6649  Z= 0.088
  Angle     :  0.426   6.403   9116  Z= 0.229
  Chirality :  0.039   0.141   1094
  Planarity :  0.003   0.052   1145
  Dihedral  :  8.540 162.861    985
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 14.86 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.36 (0.29), residues: 888
  helix:  2.56 (0.27), residues: 399
  sheet: -0.06 (0.41), residues: 171
  loop : -0.72 (0.33), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 389 
 TYR   0.007   0.001   TYR B 289 
 PHE   0.009   0.001   PHE B 199 
 TRP   0.010   0.001   TRP B  99 
 HIS   0.010   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00182 ( 6648)
  covalent geometry    : angle       0.42552 ( 9114)
  SS BOND              : bond        0.00393 (    1)
  SS BOND              : angle       0.83428 (    2)
  hydrogen bonds       : bond        0.03224 (  351)
  hydrogen bonds       : angle       3.84624 ( 1026)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  294 GLN cc_start: 0.8965 (tp-100) cc_final: 0.8747 (tp40)
REVERT: B   45 MET cc_start: 0.8492 (mmt) cc_final: 0.7954 (mmt)
REVERT: R  174 TYR cc_start: 0.8235 (p90) cc_final: 0.7991 (p90)
REVERT: R  192 ASP cc_start: 0.7786 (m-30) cc_final: 0.7581 (m-30)
  outliers start: 10
  outliers final: 8
  residues processed: 86
  average time/residue: 0.0621
  time to fit residues: 7.8947
Evaluate side-chains
  80 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  106 CYS
Chi-restraints excluded: chain R residue  230 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 86 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0970
   chunk 9 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0370
   overall best weight:    0.5656

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 178 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.132301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.106337 restraints weight = 39431.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 4.51
r_work: 0.3080 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3071
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3071 r_free = 0.3071    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3071 r_free = 0.3071    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3071
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.2093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6649  Z= 0.094
  Angle     :  0.436   6.324   9116  Z= 0.234
  Chirality :  0.040   0.142   1094
  Planarity :  0.003   0.053   1145
  Dihedral  :  8.391 161.181    985
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 15.73 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.29), residues: 888
  helix:  2.57 (0.27), residues: 399
  sheet: -0.11 (0.40), residues: 174
  loop : -0.69 (0.33), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 389 
 TYR   0.011   0.001   TYR A 358 
 PHE   0.009   0.001   PHE B 199 
 TRP   0.016   0.001   TRP B  99 
 HIS   0.021   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 ( 6648)
  covalent geometry    : angle       0.43599 ( 9114)
  SS BOND              : bond        0.00311 (    1)
  SS BOND              : angle       0.82486 (    2)
  hydrogen bonds       : bond        0.03310 (  351)
  hydrogen bonds       : angle       3.84217 ( 1026)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A  294 GLN cc_start: 0.8985 (tp-100) cc_final: 0.8763 (tp40)
REVERT: B   45 MET cc_start: 0.8542 (mmt) cc_final: 0.7978 (mmt)
REVERT: B  209 LYS cc_start: 0.9246 (mttm) cc_final: 0.9037 (mttm)
REVERT: R  174 TYR cc_start: 0.8213 (p90) cc_final: 0.7976 (p90)
REVERT: R  192 ASP cc_start: 0.7753 (m-30) cc_final: 0.7527 (m-30)
  outliers start: 9
  outliers final: 8
  residues processed: 80
  average time/residue: 0.0653
  time to fit residues: 7.5924
Evaluate side-chains
  79 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  106 CYS
Chi-restraints excluded: chain R residue  230 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 71 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   chunk 20 optimal weight:    6.9990
   chunk 21 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 14 optimal weight:    7.9990
   chunk 80 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0670
   overall best weight:    0.6720

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

Flipped N/Q/H residues before XYZ refinement:
R 178 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.130730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.104632 restraints weight = 31007.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 3.95
r_work: 0.3092 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3082
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3082 r_free = 0.3082    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3082 r_free = 0.3082    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3082
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.2138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6649  Z= 0.098
  Angle     :  0.438   6.143   9116  Z= 0.234
  Chirality :  0.040   0.141   1094
  Planarity :  0.003   0.052   1145
  Dihedral  :  8.220 162.464    985
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 15.91 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.29), residues: 888
  helix:  2.59 (0.27), residues: 399
  sheet: -0.15 (0.40), residues: 174
  loop : -0.68 (0.33), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 389 
 TYR   0.010   0.001   TYR A 358 
 PHE   0.027   0.001   PHE A 222 
 TRP   0.014   0.001   TRP B  99 
 HIS   0.019   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 6648)
  covalent geometry    : angle       0.43810 ( 9114)
  SS BOND              : bond        0.00298 (    1)
  SS BOND              : angle       0.86617 (    2)
  hydrogen bonds       : bond        0.03434 (  351)
  hydrogen bonds       : angle       3.81499 ( 1026)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.310 
Fit side-chains
REVERT: A  294 GLN cc_start: 0.8965 (tp-100) cc_final: 0.8745 (tp40)
REVERT: B   45 MET cc_start: 0.8507 (mmt) cc_final: 0.7980 (mmt)
REVERT: B  209 LYS cc_start: 0.9246 (mttm) cc_final: 0.9025 (mttm)
REVERT: R  174 TYR cc_start: 0.8230 (p90) cc_final: 0.7982 (p90)
REVERT: R  192 ASP cc_start: 0.7740 (m-30) cc_final: 0.7523 (m-30)
  outliers start: 8
  outliers final: 8
  residues processed: 79
  average time/residue: 0.0705
  time to fit residues: 8.1360
Evaluate side-chains
  78 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  106 CYS
Chi-restraints excluded: chain R residue  230 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 88 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0970
   chunk 74 optimal weight:    0.0970
   chunk 76 optimal weight:    5.9990
   chunk 71 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 41 optimal weight:    0.1980
   chunk 22 optimal weight:    0.2980
   overall best weight:    0.2976

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

Flipped N/Q/H residues before XYZ refinement:
R 178 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.133829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.107755 restraints weight = 30718.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 3.85
r_work: 0.3141 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3161
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3161
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.2283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6649  Z= 0.083
  Angle     :  0.429   5.935   9116  Z= 0.230
  Chirality :  0.039   0.139   1094
  Planarity :  0.003   0.051   1145
  Dihedral  :  7.942 163.483    985
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 15.73 %
    Favored  : 82.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.29), residues: 888
  helix:  2.64 (0.27), residues: 401
  sheet: -0.01 (0.40), residues: 177
  loop : -0.67 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 389 
 TYR   0.007   0.001   TYR A 253 
 PHE   0.027   0.001   PHE A 222 
 TRP   0.009   0.001   TRP B  99 
 HIS   0.018   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00165 ( 6648)
  covalent geometry    : angle       0.42925 ( 9114)
  SS BOND              : bond        0.00346 (    1)
  SS BOND              : angle       0.74322 (    2)
  hydrogen bonds       : bond        0.02877 (  351)
  hydrogen bonds       : angle       3.73081 ( 1026)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1777.42 seconds
wall clock time: 31 minutes 10.44 seconds (1870.44 seconds total)