Starting phenix.real_space_refine
on Fri Oct 10 13:54:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8unz_42422/10_2025/8unz_42422.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8unz_42422/10_2025/8unz_42422.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8unz_42422/10_2025/8unz_42422.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8unz_42422/10_2025/8unz_42422.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8unz_42422/10_2025/8unz_42422.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8unz_42422/10_2025/8unz_42422.cif"
  }
  resolution = 3.8
  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=   0.017
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      38      5.16       5
     C    4059      2.51       5
     N    1097      2.21       5
     O    1132      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6329
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1554
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 80}
          Link IDs: {'PTRANS': 6, 'TRANS': 217}
          Chain breaks: 4
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 321
          Unresolved non-hydrogen angles: 394
          Unresolved non-hydrogen dihedrals: 261
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'ASP:plan': 12, 'GLN:plan1': 5, 'ARG:plan': 14, 'ASN:plan1': 2, 'GLU:plan': 16, 'PHE:plan': 3, 'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 228
    Chain: "B"
      Number of atoms: 2376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2376
          Classifications: {'peptide': 335}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 57}
          Link IDs: {'PTRANS': 5, 'TRANS': 329}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 201
          Unresolved non-hydrogen angles: 248
          Unresolved non-hydrogen dihedrals: 154
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 14, 'GLN:plan1': 6, 'ARG:plan': 8, 'ASN:plan1': 4}
          Unresolved non-hydrogen planarities: 146
    Chain: "G"
      Number of atoms: 348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 348
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 83
          Unresolved non-hydrogen angles: 99
          Unresolved non-hydrogen dihedrals: 69
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 43
    Chain: "R"
      Number of atoms: 2004
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2004
          Classifications: {'peptide': 283}
          Incomplete info: {'truncation_to_alanine': 78}
          Link IDs: {'PTRANS': 7, 'TRANS': 275}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 281
          Unresolved non-hydrogen angles: 351
          Unresolved non-hydrogen dihedrals: 225
          Unresolved non-hydrogen chiralities: 23
          Planarities with less than four sites: {'GLU:plan': 12, 'TRP:plan': 1, 'PHE:plan': 2, 'ASN:plan1': 5, 'ARG:plan': 6, 'TYR:plan': 1, 'ASP:plan': 6, 'GLN:plan1': 6}
          Unresolved non-hydrogen planarities: 163
    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: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.65, per 1000 atoms: 0.26
  Number of scatterers: 6329
  At special positions: 0
  Unit cell: (85.0346, 136.229, 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      38     16.00
     P       3     15.00
     O    1132      8.00
     N    1097      7.00
     C    4059      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 184 " - pdb=" SG  CYS R 190 " 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: 0.60
  Conformation dependent library (CDL) restraints added in 436.1 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1704

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 9 sheets defined
      47.7% alpha, 15.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 40
      removed outlier: 3.614A  pdb=" N   ASN A  23 " --> pdb=" O   GLN A  19 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   THR A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 57
    Processing helix  chain 'A' and resid 234 through 239
      removed outlier: 3.832A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 254
      removed outlier: 4.509A  pdb=" N   ASN A 254 " --> pdb=" O   SER A 251 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 251 through 254'
    Processing helix  chain 'A' and resid 266 through 278
    Processing helix  chain 'A' and resid 279 through 283
      removed outlier: 3.583A  pdb=" N   ARG A 283 " --> pdb=" O   ARG A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 302
      removed outlier: 3.541A  pdb=" N   LYS A 300 " --> pdb=" O   LEU A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 331 through 354
      removed outlier: 3.671A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   ASP A 354 " --> pdb=" O   THR A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 391
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.715A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.527A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 8 through 22
      removed outlier: 3.774A  pdb=" N   LYS G  20 " --> pdb=" O   VAL G  16 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.562A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 31 through 61
      removed outlier: 3.695A  pdb=" N   ILE R  38 " --> pdb=" O   VAL R  34 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   VAL R  54 " --> pdb=" O   GLY R  50 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 97
      removed outlier: 3.701A  pdb=" N   TYR R  70 " --> pdb=" O   THR R  66 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.515A  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 137
      removed outlier: 4.158A  pdb=" N   ILE R 121 " --> pdb=" O   VAL R 117 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   GLU R 122 " --> pdb=" O   THR R 118 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   THR R 123 " --> pdb=" O   ALA R 119 " (cutoff:3.500A)
      removed outlier: 4.987A  pdb=" N   LEU R 124 " --> pdb=" O   SER R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 164
      removed outlier: 3.930A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 166 through 171
      removed outlier: 3.894A  pdb=" N   MET R 171 " --> pdb=" O   LEU R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
      removed outlier: 3.541A  pdb=" N   ALA R 200 " --> pdb=" O   ASN R 196 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ILE R 201 " --> pdb=" O   GLN R 197 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 209 through 237
      removed outlier: 3.833A  pdb=" N   VAL R 213 " --> pdb=" O   TYR R 209 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   ILE R 214 " --> pdb=" O   VAL R 210 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   MET R 215 " --> pdb=" O   PRO R 211 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 287
      removed outlier: 4.768A  pdb=" N   THR R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 288 through 299
      removed outlier: 4.842A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
      removed outlier: 3.693A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 317 through 326
      removed outlier: 3.828A  pdb=" N   PHE R 321 " --> pdb=" O   VAL R 317 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ASN R 322 " --> pdb=" O   ASN R 318 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 339
      removed outlier: 3.584A  pdb=" N   ALA R 335 " --> pdb=" O   ASP R 331 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 213
      removed outlier: 6.795A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.304A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.323A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 9.056A  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: 6.964A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.854A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.207A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   SER B  72 " --> pdb=" O   ILE B  80 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 115
      removed outlier: 3.690A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.711A  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: 7.006A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 7.172A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.885A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.429A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.628A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.862A  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: 3.632A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 250 through 252
      removed outlier: 3.627A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.002A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LEU B 285 " --> pdb=" O   TRP B 297 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   TYR B 289 " --> pdb=" O   ASN B 293 " (cutoff:3.500A)
      removed outlier: 5.061A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)

    325 hydrogen bonds defined for protein.
    954 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.95

  Time building geometry restraints manager: 0.79 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2039
        1.34 -     1.46: 1305
        1.46 -     1.58: 3065
        1.58 -     1.70: 5
        1.70 -     1.82: 50
  Bond restraints: 6464
  Sorted by residual:
  bond pdb=" N   VAL R  39 "
       pdb=" CA  VAL R  39 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.035 1.21e-02 6.83e+03 8.18e+00
  bond pdb=" N   THR R  66 "
       pdb=" CA  THR R  66 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.16e-02 7.43e+03 7.96e+00
  bond pdb=" N   VAL R  48 "
       pdb=" CA  VAL R  48 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.034 1.21e-02 6.83e+03 7.86e+00
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.451 -0.054 2.00e-02 2.50e+03 7.22e+00
  bond pdb=" N   ASN A 254 "
       pdb=" CA  ASN A 254 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.036 1.33e-02 5.65e+03 7.15e+00
  ... (remaining 6459 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 8527
        2.06 -     4.11: 295
        4.11 -     6.17: 33
        6.17 -     8.22: 7
        8.22 -    10.28: 6
  Bond angle restraints: 8868
  Sorted by residual:
  angle pdb=" N   SER G   8 "
        pdb=" CA  SER G   8 "
        pdb=" C   SER G   8 "
      ideal   model   delta    sigma   weight residual
     111.28  105.00    6.28 1.09e+00 8.42e-01 3.32e+01
  angle pdb=" N   MET R  40 "
        pdb=" CA  MET R  40 "
        pdb=" C   MET R  40 "
      ideal   model   delta    sigma   weight residual
     111.28  105.47    5.81 1.09e+00 8.42e-01 2.85e+01
  angle pdb=" N   GLN A  19 "
        pdb=" CA  GLN A  19 "
        pdb=" C   GLN A  19 "
      ideal   model   delta    sigma   weight residual
     111.71  105.92    5.79 1.15e+00 7.56e-01 2.54e+01
  angle pdb=" N   ASN A 371 "
        pdb=" CA  ASN A 371 "
        pdb=" C   ASN A 371 "
      ideal   model   delta    sigma   weight residual
     113.72  107.41    6.31 1.30e+00 5.92e-01 2.36e+01
  angle pdb=" N   ARG G  13 "
        pdb=" CA  ARG G  13 "
        pdb=" C   ARG G  13 "
      ideal   model   delta    sigma   weight residual
     111.28  106.44    4.84 1.09e+00 8.42e-01 1.97e+01
  ... (remaining 8863 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.04: 3641
       34.04 -    68.08: 64
       68.08 -   102.11: 3
      102.11 -   136.15: 1
      136.15 -   170.19: 2
  Dihedral angle restraints: 3711
    sinusoidal: 1094
      harmonic: 2617
  Sorted by residual:
  dihedral pdb=" CB  CYS R 106 "
           pdb=" SG  CYS R 106 "
           pdb=" SG  CYS R 191 "
           pdb=" CB  CYS R 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -157.05   71.05     1      1.00e+01 1.00e-02 6.48e+01
  dihedral pdb=" CB  CYS R 184 "
           pdb=" SG  CYS R 184 "
           pdb=" SG  CYS R 190 "
           pdb=" CB  CYS R 190 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.49  -60.49     1      1.00e+01 1.00e-02 4.87e+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  -85.22 -170.19     1      2.00e+01 2.50e-03 4.76e+01
  ... (remaining 3708 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 860
       0.060 -    0.120: 166
       0.120 -    0.180: 44
       0.180 -    0.241: 6
       0.241 -    0.301: 5
  Chirality restraints: 1081
  Sorted by residual:
  chirality pdb=" CA  GLN B  17 "
            pdb=" N   GLN B  17 "
            pdb=" C   GLN B  17 "
            pdb=" CB  GLN B  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.81   -0.30 2.00e-01 2.50e+01 2.26e+00
  chirality pdb=" CA  ILE G   9 "
            pdb=" N   ILE G   9 "
            pdb=" C   ILE G   9 "
            pdb=" CB  ILE G   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.27 2.00e-01 2.50e+01 1.83e+00
  chirality pdb=" CA  LEU B   4 "
            pdb=" N   LEU B   4 "
            pdb=" C   LEU B   4 "
            pdb=" CB  LEU B   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.71e+00
  ... (remaining 1078 not shown)

  Planarity restraints: 1111
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU R  62 "    0.011 2.00e-02 2.50e+03   2.17e-02 4.70e+00
        pdb=" C   GLU R  62 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   GLU R  62 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ARG R  63 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A  14 "   -0.010 2.00e-02 2.50e+03   1.98e-02 3.92e+00
        pdb=" C   ASN A  14 "    0.034 2.00e-02 2.50e+03
        pdb=" O   ASN A  14 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   GLU A  15 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY R  35 "   -0.010 2.00e-02 2.50e+03   1.97e-02 3.89e+00
        pdb=" C   GLY R  35 "    0.034 2.00e-02 2.50e+03
        pdb=" O   GLY R  35 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   MET R  36 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1108 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1164
        2.77 -     3.30: 6045
        3.30 -     3.84: 9866
        3.84 -     4.37: 10324
        4.37 -     4.90: 18661
  Nonbonded interactions: 46060
  Sorted by model distance:
  nonbonded pdb=" OG  SER R 111 "
            pdb=" O   SER R 165 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" OG1 THR A  55 "
            pdb=" O1A GTP A 401 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" OG  SER A  54 "
            pdb=" O1A GTP A 401 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" ND2 ASN B 230 "
            pdb=" OD1 ASP B 246 "
     model   vdw
     2.373 3.120
  nonbonded pdb=" OD1 ASP A 223 "
            pdb=" N   VAL A 224 "
     model   vdw
     2.396 3.120
  ... (remaining 46055 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             2.290
  Set stop_for_unknowns flag:              0.010
  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:          0.130
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.250
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.270
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
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   0.054   6466  Z= 0.339
  Angle     :  0.811  10.276   8872  Z= 0.542
  Chirality :  0.056   0.301   1081
  Planarity :  0.003   0.036   1111
  Dihedral  : 13.666 170.188   2001
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  1.00 (0.29), residues: 878
  helix:  2.35 (0.28), residues: 377
  sheet: -0.17 (0.44), residues: 145
  loop : -0.85 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 380 
 TYR   0.018   0.001   TYR R 185 
 PHE   0.013   0.001   PHE B 151 
 TRP   0.009   0.001   TRP R 109 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 ( 6464)
  covalent geometry    : angle       0.81076 ( 8868)
  SS BOND              : bond        0.00201 (    2)
  SS BOND              : angle       0.72408 (    4)
  hydrogen bonds       : bond        0.20887 (  325)
  hydrogen bonds       : angle       6.52636 (  954)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.250 
Fit side-chains
REVERT: B  143 THR cc_start: 0.8413 (p) cc_final: 0.8154 (t)
REVERT: B  233 CYS cc_start: 0.9348 (t) cc_final: 0.9011 (t)
REVERT: G   38 MET cc_start: 0.7924 (ptp) cc_final: 0.7678 (ptp)
REVERT: G   48 ASP cc_start: 0.8558 (t70) cc_final: 0.8130 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.0644
  time to fit residues: 8.4790
Evaluate side-chains
  67 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0270
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.3242

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 312 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.123856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.099109 restraints weight = 13114.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.101497 restraints weight = 7754.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.103150 restraints weight = 5450.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.104323 restraints weight = 4269.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.104821 restraints weight = 3596.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.1234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6466  Z= 0.147
  Angle     :  0.514   6.977   8872  Z= 0.278
  Chirality :  0.041   0.159   1081
  Planarity :  0.003   0.039   1111
  Dihedral  :  9.862 178.946    969
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 10.99 %
    Favored  : 87.71 %
  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:  0.98 (0.29), residues: 878
  helix:  2.20 (0.26), residues: 386
  sheet: -0.21 (0.42), residues: 153
  loop : -0.75 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 373 
 TYR   0.031   0.001   TYR R 185 
 PHE   0.016   0.001   PHE B 151 
 TRP   0.013   0.001   TRP R 109 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 6464)
  covalent geometry    : angle       0.51391 ( 8868)
  SS BOND              : bond        0.00232 (    2)
  SS BOND              : angle       0.82429 (    4)
  hydrogen bonds       : bond        0.04866 (  325)
  hydrogen bonds       : angle       4.22951 (  954)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.155 
Fit side-chains
REVERT: B  143 THR cc_start: 0.8286 (p) cc_final: 0.8030 (t)
REVERT: B  233 CYS cc_start: 0.8996 (t) cc_final: 0.8761 (t)
REVERT: G   38 MET cc_start: 0.8067 (ptp) cc_final: 0.7826 (ptp)
  outliers start: 7
  outliers final: 6
  residues processed: 83
  average time/residue: 0.0539
  time to fit residues: 6.6959
Evaluate side-chains
  78 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain R residue  201 ILE
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  275 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 29 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 50 optimal weight:    0.5980
   chunk 84 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 15 optimal weight:    9.9990
   chunk 19 optimal weight:    0.5980
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
R 178 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.125068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.100135 restraints weight = 12933.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.102540 restraints weight = 7674.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.104271 restraints weight = 5400.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.105359 restraints weight = 4219.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.105869 restraints weight = 3581.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.1452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6466  Z= 0.104
  Angle     :  0.462   6.065   8872  Z= 0.246
  Chirality :  0.039   0.150   1081
  Planarity :  0.003   0.037   1111
  Dihedral  :  9.412 179.369    969
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 13.04 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.16 (0.29), residues: 878
  helix:  2.36 (0.27), residues: 391
  sheet: -0.19 (0.43), residues: 154
  loop : -0.69 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 347 
 TYR   0.026   0.001   TYR R 185 
 PHE   0.009   0.001   PHE B 199 
 TRP   0.009   0.001   TRP R 109 
 HIS   0.005   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 6464)
  covalent geometry    : angle       0.46214 ( 8868)
  SS BOND              : bond        0.00195 (    2)
  SS BOND              : angle       0.58965 (    4)
  hydrogen bonds       : bond        0.03857 (  325)
  hydrogen bonds       : angle       3.79224 (  954)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.228 
Fit side-chains
REVERT: B  143 THR cc_start: 0.8436 (p) cc_final: 0.8207 (t)
REVERT: B  233 CYS cc_start: 0.8996 (t) cc_final: 0.8780 (t)
REVERT: G   38 MET cc_start: 0.8090 (ptp) cc_final: 0.7860 (ptp)
  outliers start: 8
  outliers final: 6
  residues processed: 83
  average time/residue: 0.0515
  time to fit residues: 6.2970
Evaluate side-chains
  76 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  201 ILE
Chi-restraints excluded: chain R residue  204 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 71 optimal weight:    7.9990
   chunk 7 optimal weight:    6.9990
   chunk 42 optimal weight:    3.9990
   chunk 5 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 75 optimal weight:   10.0000
   overall best weight:    2.5988

-------------------------------------------------------------------------------
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 = 0.3578 r_free = 0.3578 target = 0.119549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.094732 restraints weight = 13472.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.096974 restraints weight = 8099.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.098467 restraints weight = 5756.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.099551 restraints weight = 4602.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.100342 restraints weight = 3909.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.1848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   6466  Z= 0.242
  Angle     :  0.580   6.529   8872  Z= 0.315
  Chirality :  0.043   0.146   1081
  Planarity :  0.004   0.044   1111
  Dihedral  :  9.481 179.872    969
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 15.27 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.77 (0.29), residues: 878
  helix:  2.17 (0.27), residues: 386
  sheet: -0.61 (0.43), residues: 155
  loop : -0.90 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 347 
 TYR   0.017   0.002   TYR R 185 
 PHE   0.019   0.002   PHE B 151 
 TRP   0.015   0.002   TRP R 109 
 HIS   0.023   0.002   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00558 ( 6464)
  covalent geometry    : angle       0.58010 ( 8868)
  SS BOND              : bond        0.00259 (    2)
  SS BOND              : angle       0.75342 (    4)
  hydrogen bonds       : bond        0.05315 (  325)
  hydrogen bonds       : angle       4.20473 (  954)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.199 
Fit side-chains
REVERT: B   86 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8566 (m)
REVERT: B  143 THR cc_start: 0.8595 (p) cc_final: 0.8389 (t)
REVERT: B  340 ASN cc_start: 0.7869 (t0) cc_final: 0.7601 (t0)
REVERT: G   38 MET cc_start: 0.8227 (ptp) cc_final: 0.7863 (ptp)
  outliers start: 11
  outliers final: 8
  residues processed: 77
  average time/residue: 0.0532
  time to fit residues: 5.9736
Evaluate side-chains
  76 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   93 HIS
Chi-restraints excluded: chain R residue  201 ILE
Chi-restraints excluded: chain R residue  275 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 85 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 13 optimal weight:   20.0000
   chunk 9 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 72 optimal weight:    5.9990
   chunk 82 optimal weight:    0.9990
   chunk 67 optimal weight:    4.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
R 312 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.122084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.096972 restraints weight = 13353.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.099303 restraints weight = 7976.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.100878 restraints weight = 5658.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.102078 restraints weight = 4493.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.102655 restraints weight = 3787.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6466  Z= 0.126
  Angle     :  0.478   6.516   8872  Z= 0.257
  Chirality :  0.040   0.151   1081
  Planarity :  0.003   0.043   1111
  Dihedral  :  9.089 179.942    969
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 2.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 16.39 %
    Favored  : 81.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.29), residues: 878
  helix:  2.30 (0.27), residues: 386
  sheet: -0.56 (0.43), residues: 154
  loop : -0.80 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 175 
 TYR   0.017   0.001   TYR R 185 
 PHE   0.025   0.001   PHE R 289 
 TRP   0.012   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6464)
  covalent geometry    : angle       0.47816 ( 8868)
  SS BOND              : bond        0.00185 (    2)
  SS BOND              : angle       0.61965 (    4)
  hydrogen bonds       : bond        0.04033 (  325)
  hydrogen bonds       : angle       3.81120 (  954)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.308 
Fit side-chains
REVERT: G   38 MET cc_start: 0.8227 (ptp) cc_final: 0.7905 (ptp)
  outliers start: 11
  outliers final: 5
  residues processed: 81
  average time/residue: 0.0472
  time to fit residues: 5.8765
Evaluate side-chains
  72 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  201 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0040
   chunk 56 optimal weight:    4.9990
   chunk 14 optimal weight:    6.9990
   chunk 71 optimal weight:    4.9990
   chunk 76 optimal weight:    6.9990
   overall best weight:    2.8000

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.117172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.092069 restraints weight = 13554.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.094227 restraints weight = 8398.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.095633 restraints weight = 6117.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.096749 restraints weight = 4939.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.097342 restraints weight = 4218.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   6466  Z= 0.259
  Angle     :  0.595   6.483   8872  Z= 0.325
  Chirality :  0.043   0.151   1081
  Planarity :  0.004   0.047   1111
  Dihedral  :  9.157 178.630    969
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 16.39 %
    Favored  : 81.01 %
  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:  0.56 (0.29), residues: 878
  helix:  2.05 (0.27), residues: 388
  sheet: -0.97 (0.43), residues: 153
  loop : -0.95 (0.32), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  22 
 TYR   0.014   0.002   TYR R 185 
 PHE   0.017   0.002   PHE B 235 
 TRP   0.016   0.002   TRP R 109 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00600 ( 6464)
  covalent geometry    : angle       0.59468 ( 8868)
  SS BOND              : bond        0.00221 (    2)
  SS BOND              : angle       0.76463 (    4)
  hydrogen bonds       : bond        0.05397 (  325)
  hydrogen bonds       : angle       4.25053 (  954)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A  362 HIS cc_start: 0.8194 (OUTLIER) cc_final: 0.7885 (m-70)
REVERT: G   38 MET cc_start: 0.8346 (ptp) cc_final: 0.7848 (ptp)
  outliers start: 14
  outliers final: 11
  residues processed: 77
  average time/residue: 0.0545
  time to fit residues: 6.3416
Evaluate side-chains
  76 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   93 HIS
Chi-restraints excluded: chain R residue  157 VAL
Chi-restraints excluded: chain R residue  201 ILE
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    1.9990
   chunk 48 optimal weight:    0.3980
   chunk 47 optimal weight:    0.8980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.120157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.094849 restraints weight = 13234.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.097128 restraints weight = 8124.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.098599 restraints weight = 5868.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.099786 restraints weight = 4715.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.100531 restraints weight = 4020.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6466  Z= 0.134
  Angle     :  0.491   6.306   8872  Z= 0.265
  Chirality :  0.040   0.150   1081
  Planarity :  0.003   0.045   1111
  Dihedral  :  8.758 178.465    969
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 18.25 %
    Favored  : 79.89 %
  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:  0.75 (0.29), residues: 878
  helix:  2.24 (0.27), residues: 386
  sheet: -0.97 (0.42), residues: 157
  loop : -0.81 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 347 
 TYR   0.015   0.001   TYR R 308 
 PHE   0.016   0.001   PHE R 289 
 TRP   0.013   0.001   TRP R 109 
 HIS   0.003   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 6464)
  covalent geometry    : angle       0.49090 ( 8868)
  SS BOND              : bond        0.00197 (    2)
  SS BOND              : angle       0.66990 (    4)
  hydrogen bonds       : bond        0.04042 (  325)
  hydrogen bonds       : angle       3.85121 (  954)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A  362 HIS cc_start: 0.8073 (OUTLIER) cc_final: 0.7833 (m-70)
REVERT: G   38 MET cc_start: 0.8290 (ptp) cc_final: 0.7949 (ptp)
  outliers start: 10
  outliers final: 9
  residues processed: 75
  average time/residue: 0.0631
  time to fit residues: 6.9849
Evaluate side-chains
  74 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  133 PHE
Chi-restraints excluded: chain R residue  201 ILE
Chi-restraints excluded: chain R residue  307 VAL
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 78 optimal weight:    0.0970
   chunk 65 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 73 optimal weight:    0.6980
   chunk 57 optimal weight:    6.9990
   chunk 24 optimal weight:    2.9990
   chunk 22 optimal weight:   10.0000
   chunk 74 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.9380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.121061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.095751 restraints weight = 13442.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.098072 restraints weight = 8038.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.099713 restraints weight = 5703.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.100782 restraints weight = 4500.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.101604 restraints weight = 3819.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.2244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6466  Z= 0.112
  Angle     :  0.477   6.864   8872  Z= 0.255
  Chirality :  0.039   0.149   1081
  Planarity :  0.003   0.044   1111
  Dihedral  :  8.400 178.709    969
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 19.55 %
    Favored  : 79.14 %
  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:  0.93 (0.30), residues: 878
  helix:  2.45 (0.27), residues: 385
  sheet: -0.85 (0.43), residues: 157
  loop : -0.82 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 175 
 TYR   0.013   0.001   TYR R 185 
 PHE   0.013   0.001   PHE R 289 
 TRP   0.012   0.001   TRP R 109 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 6464)
  covalent geometry    : angle       0.47717 ( 8868)
  SS BOND              : bond        0.00191 (    2)
  SS BOND              : angle       0.62921 (    4)
  hydrogen bonds       : bond        0.03640 (  325)
  hydrogen bonds       : angle       3.69194 (  954)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A  362 HIS cc_start: 0.7920 (OUTLIER) cc_final: 0.7697 (m-70)
REVERT: G   38 MET cc_start: 0.8332 (ptp) cc_final: 0.7958 (ptp)
  outliers start: 7
  outliers final: 6
  residues processed: 81
  average time/residue: 0.0645
  time to fit residues: 7.6870
Evaluate side-chains
  76 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain R residue  201 ILE
Chi-restraints excluded: chain R residue  275 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 71 optimal weight:    0.0470
   chunk 17 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 27 optimal weight:    5.9990
   chunk 7 optimal weight:    6.9990
   chunk 51 optimal weight:    4.9990
   chunk 64 optimal weight:    3.9990
   chunk 40 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   overall best weight:    1.7284

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.119170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.093932 restraints weight = 13640.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.096172 restraints weight = 8159.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.097808 restraints weight = 5826.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.098878 restraints weight = 4610.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.099501 restraints weight = 3925.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6466  Z= 0.168
  Angle     :  0.526   6.971   8872  Z= 0.280
  Chirality :  0.041   0.149   1081
  Planarity :  0.003   0.046   1111
  Dihedral  :  8.342 178.596    969
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 19.93 %
    Favored  : 78.03 %
  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:  0.81 (0.29), residues: 878
  helix:  2.34 (0.27), residues: 386
  sheet: -0.95 (0.43), residues: 156
  loop : -0.84 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 175 
 TYR   0.023   0.001   TYR R 185 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.013   0.001   TRP R 109 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 6464)
  covalent geometry    : angle       0.52544 ( 8868)
  SS BOND              : bond        0.00160 (    2)
  SS BOND              : angle       0.69264 (    4)
  hydrogen bonds       : bond        0.04288 (  325)
  hydrogen bonds       : angle       3.91054 (  954)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A  362 HIS cc_start: 0.8055 (OUTLIER) cc_final: 0.7762 (m-70)
REVERT: G   38 MET cc_start: 0.8355 (ptp) cc_final: 0.8005 (ptp)
  outliers start: 11
  outliers final: 8
  residues processed: 79
  average time/residue: 0.0616
  time to fit residues: 7.2773
Evaluate side-chains
  77 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  201 ILE
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 78 optimal weight:    0.0670
   chunk 39 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 59 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.6918

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

Flipped N/Q/H residues before XYZ refinement:
R  69 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.121886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.096565 restraints weight = 13252.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.098918 restraints weight = 7945.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.100466 restraints weight = 5625.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.101665 restraints weight = 4477.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.102388 restraints weight = 3790.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6466  Z= 0.098
  Angle     :  0.477   9.422   8872  Z= 0.250
  Chirality :  0.039   0.153   1081
  Planarity :  0.003   0.043   1111
  Dihedral  :  8.075 178.894    969
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 2.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 20.86 %
    Favored  : 77.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.30), residues: 878
  helix:  2.46 (0.27), residues: 387
  sheet: -0.86 (0.43), residues: 156
  loop : -0.82 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  49 
 TYR   0.025   0.001   TYR R 185 
 PHE   0.013   0.001   PHE R 289 
 TRP   0.012   0.001   TRP R 109 
 HIS   0.002   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 6464)
  covalent geometry    : angle       0.47730 ( 8868)
  SS BOND              : bond        0.00190 (    2)
  SS BOND              : angle       0.65780 (    4)
  hydrogen bonds       : bond        0.03359 (  325)
  hydrogen bonds       : angle       3.69088 (  954)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  362 HIS cc_start: 0.7938 (OUTLIER) cc_final: 0.7722 (m-70)
REVERT: B  233 CYS cc_start: 0.9007 (t) cc_final: 0.8796 (t)
REVERT: G   38 MET cc_start: 0.8335 (ptp) cc_final: 0.7944 (ptp)
  outliers start: 9
  outliers final: 7
  residues processed: 79
  average time/residue: 0.0591
  time to fit residues: 6.9934
Evaluate side-chains
  80 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 80 optimal weight:    6.9990
   chunk 53 optimal weight:    0.2980
   chunk 27 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   chunk 24 optimal weight:    8.9990
   chunk 29 optimal weight:    0.0970
   chunk 84 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 13 optimal weight:    6.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
R  69 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.120302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.095063 restraints weight = 13523.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.097345 restraints weight = 8105.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.098941 restraints weight = 5772.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.100020 restraints weight = 4566.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.100871 restraints weight = 3893.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.2384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6466  Z= 0.134
  Angle     :  0.499   8.717   8872  Z= 0.263
  Chirality :  0.040   0.152   1081
  Planarity :  0.003   0.044   1111
  Dihedral  :  8.037 179.322    969
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 21.04 %
    Favored  : 77.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.30), residues: 878
  helix:  2.37 (0.27), residues: 393
  sheet: -0.89 (0.43), residues: 156
  loop : -0.84 (0.33), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  49 
 TYR   0.027   0.001   TYR R 185 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.011   0.001   TRP R 109 
 HIS   0.003   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 6464)
  covalent geometry    : angle       0.49929 ( 8868)
  SS BOND              : bond        0.00182 (    2)
  SS BOND              : angle       0.66901 (    4)
  hydrogen bonds       : bond        0.03767 (  325)
  hydrogen bonds       : angle       3.73500 (  954)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1173.78 seconds
wall clock time: 20 minutes 55.33 seconds (1255.33 seconds total)