Starting phenix.real_space_refine
on Tue Mar 11 23:28:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sh7_40480/03_2025/8sh7_40480.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sh7_40480/03_2025/8sh7_40480.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sh7_40480/03_2025/8sh7_40480.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sh7_40480/03_2025/8sh7_40480.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sh7_40480/03_2025/8sh7_40480.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sh7_40480/03_2025/8sh7_40480.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.001
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: 6
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     Mg      1      5.21       5
     S      48      5.16       5
     C    4283      2.51       5
     N    1164      2.21       5
     O    1318      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6819
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 436, 3410
          Classifications: {'peptide': 436}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 415}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 426, 3348
          Classifications: {'peptide': 426}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405}
    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: "B"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 29
          Unusual residues: {' MG': 1, 'GDP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.62, per 1000 atoms: 0.97
  Number of scatterers: 6819
  At special positions: 0
  Unit cell: (71.24, 71.24, 113.71, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      48     16.00
     P       5     15.00
     Mg      1     11.99
     O    1318      8.00
     N    1164      7.00
     C    4283      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.83
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1590

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 5 sheets defined
      54.4% alpha, 14.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 29
      removed outlier: 3.771A  pdb=" N   ALA A  19 " --> pdb=" O   GLN A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 51
      removed outlier: 4.114A  pdb=" N   THR A  51 " --> pdb=" O   SER A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 79
      removed outlier: 4.811A  pdb=" N   ILE A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLU A  77 " --> pdb=" O   THR A  73 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   VAL A  78 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 90
      No H-bonds generated for 'chain 'A' and resid 88 through 90'
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 110 through 129
      removed outlier: 3.954A  pdb=" N   ILE A 114 " --> pdb=" O   ILE A 110 " (cutoff:3.500A)
      removed outlier: 5.203A  pdb=" N   ASP A 116 " --> pdb=" O   LYS A 112 " (cutoff:3.500A)
      removed outlier: 5.744A  pdb=" N   LEU A 117 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LYS A 124 " --> pdb=" O   ASP A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 161
      removed outlier: 3.991A  pdb=" N   THR A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   VAL A 159 " --> pdb=" O   GLU A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 197
      removed outlier: 3.525A  pdb=" N   ASN A 186 " --> pdb=" O   VAL A 182 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   THR A 191 " --> pdb=" O   SER A 187 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   HIS A 192 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
      removed outlier: 5.338A  pdb=" N   THR A 193 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   THR A 194 " --> pdb=" O   THR A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 216
      removed outlier: 3.571A  pdb=" N   ILE A 209 " --> pdb=" O   ASP A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 239
      removed outlier: 3.551A  pdb=" N   LEU A 227 " --> pdb=" O   THR A 223 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU A 230 " --> pdb=" O   ASN A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 244
      removed outlier: 3.515A  pdb=" N   ARG A 243 " --> pdb=" O   THR A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 258
    Processing helix  chain 'A' and resid 277 through 282
      removed outlier: 3.547A  pdb=" N   TYR A 282 " --> pdb=" O   ALA A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 296
      removed outlier: 3.526A  pdb=" N   CYS A 295 " --> pdb=" O   ILE A 291 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   PHE A 296 " --> pdb=" O   THR A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 301
    Processing helix  chain 'A' and resid 306 through 310
    Processing helix  chain 'A' and resid 324 through 338
      removed outlier: 3.591A  pdb=" N   THR A 337 " --> pdb=" O   ALA A 333 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LYS A 338 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 400
      removed outlier: 3.836A  pdb=" N   TRP A 388 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU A 391 " --> pdb=" O   ALA A 387 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   LYS A 394 " --> pdb=" O   ARG A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 4.112A  pdb=" N   TYR A 408 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 436
      removed outlier: 4.080A  pdb=" N   SER A 419 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLY A 436 " --> pdb=" O   TYR A 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 29
      removed outlier: 3.623A  pdb=" N   LYS B  19 " --> pdb=" O   GLN B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 44
      removed outlier: 3.701A  pdb=" N   LEU B  44 " --> pdb=" O   ASP B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 49
    Processing helix  chain 'B' and resid 70 through 78
      removed outlier: 3.689A  pdb=" N   SER B  75 " --> pdb=" O   GLY B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 84
      removed outlier: 4.366A  pdb=" N   GLN B  83 " --> pdb=" O   PRO B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 88
      No H-bonds generated for 'chain 'B' and resid 86 through 88'
    Processing helix  chain 'B' and resid 100 through 106
    Processing helix  chain 'B' and resid 108 through 125
      removed outlier: 3.699A  pdb=" N   LEU B 112 " --> pdb=" O   GLU B 108 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   ASP B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   SER B 115 " --> pdb=" O   GLU B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 159
      removed outlier: 3.907A  pdb=" N   GLU B 157 " --> pdb=" O   SER B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 196
      removed outlier: 3.561A  pdb=" N   ASN B 184 " --> pdb=" O   VAL B 180 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLN B 191 " --> pdb=" O   LEU B 187 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   GLU B 194 " --> pdb=" O   HIS B 190 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ASN B 195 " --> pdb=" O   GLN B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 214
      removed outlier: 3.540A  pdb=" N   ASP B 209 " --> pdb=" O   GLU B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 242
      removed outlier: 3.941A  pdb=" N   THR B 237 " --> pdb=" O   MET B 233 " (cutoff:3.500A)
      removed outlier: 5.078A  pdb=" N   CYS B 239 " --> pdb=" O   GLY B 235 " (cutoff:3.500A)
      removed outlier: 5.833A  pdb=" N   LEU B 240 " --> pdb=" O   VAL B 236 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ARG B 241 " --> pdb=" O   THR B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 258
    Processing helix  chain 'B' and resid 277 through 282
      removed outlier: 3.656A  pdb=" N   GLN B 280 " --> pdb=" O   GLY B 277 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ARG B 282 " --> pdb=" O   GLN B 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 285 through 295
    Processing helix  chain 'B' and resid 296 through 299
    Processing helix  chain 'B' and resid 304 through 308
    Processing helix  chain 'B' and resid 322 through 337
      removed outlier: 3.871A  pdb=" N   GLN B 334 " --> pdb=" O   MET B 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 341
      removed outlier: 3.538A  pdb=" N   PHE B 341 " --> pdb=" O   SER B 338 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 338 through 341'
    Processing helix  chain 'B' and resid 374 through 390
      removed outlier: 3.716A  pdb=" N   PHE B 378 " --> pdb=" O   ILE B 374 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLN B 384 " --> pdb=" O   ARG B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 394 through 400
      removed outlier: 4.081A  pdb=" N   TYR B 398 " --> pdb=" O   PHE B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 424
      removed outlier: 3.521A  pdb=" N   THR B 409 " --> pdb=" O   GLU B 405 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94
      removed outlier: 7.926A  pdb=" N   ILE A  93 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 5.933A  pdb=" N   PHE A  67 " --> pdb=" O   ILE A  93 " (cutoff:3.500A)
      removed outlier: 8.379A  pdb=" N   VAL A  66 " --> pdb=" O   CYS A   4 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   SER A   6 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   VAL A  68 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   HIS A   8 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   ILE A   5 " --> pdb=" O   LEU A 136 " (cutoff:3.500A)
      removed outlier: 7.760A  pdb=" N   PHE A 138 " --> pdb=" O   ILE A   5 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   ILE A   7 " --> pdb=" O   PHE A 138 " (cutoff:3.500A)
      removed outlier: 8.657A  pdb=" N   SER A 140 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
      removed outlier: 8.500A  pdb=" N   VAL A   9 " --> pdb=" O   SER A 140 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   PHE A 135 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   PHE A 169 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   VAL A 137 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 7.891A  pdb=" N   ILE A 171 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 7.484A  pdb=" N   HIS A 139 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   LYS A 166 " --> pdb=" O   CYS A 200 " (cutoff:3.500A)
      removed outlier: 7.979A  pdb=" N   PHE A 202 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   GLU A 168 " --> pdb=" O   PHE A 202 " (cutoff:3.500A)
      removed outlier: 7.360A  pdb=" N   VAL A 204 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
      removed outlier: 6.008A  pdb=" N   SER A 170 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55
    Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273
      removed outlier: 3.613A  pdb=" N   ALA A 314 " --> pdb=" O   ASN A 380 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92
      removed outlier: 8.357A  pdb=" N   VAL B  91 " --> pdb=" O   ALA B  63 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   LEU B  65 " --> pdb=" O   VAL B  91 " (cutoff:3.500A)
      removed outlier: 8.456A  pdb=" N   VAL B  64 " --> pdb=" O   ILE B   4 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   HIS B   6 " --> pdb=" O   VAL B  64 " (cutoff:3.500A)
      removed outlier: 7.778A  pdb=" N   VAL B  66 " --> pdb=" O   HIS B   6 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   GLN B   8 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
      removed outlier: 5.592A  pdb=" N   GLU B   3 " --> pdb=" O   LEU B 130 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLY B 132 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   SER B 138 " --> pdb=" O   ALA B   9 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   MET B 164 " --> pdb=" O   GLU B 198 " (cutoff:3.500A)
      removed outlier: 8.097A  pdb=" N   TYR B 200 " --> pdb=" O   MET B 164 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   THR B 166 " --> pdb=" O   TYR B 200 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   ILE B 202 " --> pdb=" O   THR B 166 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   SER B 168 " --> pdb=" O   ILE B 202 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   THR B 199 " --> pdb=" O   PHE B 266 " (cutoff:3.500A)
      removed outlier: 7.826A  pdb=" N   CYS B 201 " --> pdb=" O   PRO B 268 " (cutoff:3.500A)
      removed outlier: 11.225A  pdb=" N   PHE B 270 " --> pdb=" O   CYS B 201 " (cutoff:3.500A)
      removed outlier: 7.329A  pdb=" N   PHE B 265 " --> pdb=" O   SER B 371 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   SER B 371 " --> pdb=" O   PHE B 265 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   THR B 312 " --> pdb=" O   ASN B 370 " (cutoff:3.500A)
      removed outlier: 8.471A  pdb=" N   LYS B 350 " --> pdb=" O   LEU B 311 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   VAL B 313 " --> pdb=" O   LYS B 350 " (cutoff:3.500A)
      removed outlier: 8.296A  pdb=" N   ALA B 352 " --> pdb=" O   VAL B 313 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ALA B 315 " --> pdb=" O   ALA B 352 " (cutoff:3.500A)
      removed outlier: 7.760A  pdb=" N   CYS B 354 " --> pdb=" O   ALA B 315 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   PHE B 317 " --> pdb=" O   CYS B 354 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 54
      removed outlier: 3.539A  pdb=" N   LYS B  58 " --> pdb=" O   ALA B  54 " (cutoff:3.500A)

    308 hydrogen bonds defined for protein.
    879 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: 2.12

  Time building geometry restraints manager: 2.17 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1435
        1.33 -     1.45: 1626
        1.45 -     1.57: 3829
        1.57 -     1.69: 8
        1.69 -     1.81: 76
  Bond restraints: 6974
  Sorted by residual:
  bond pdb=" N   VAL A  74 "
       pdb=" CA  VAL A  74 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.036 1.21e-02 6.83e+03 9.02e+00
  bond pdb=" N   VAL A  68 "
       pdb=" CA  VAL A  68 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.19e-02 7.06e+03 8.91e+00
  bond pdb=" N   CYS B 354 "
       pdb=" CA  CYS B 354 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.035 1.18e-02 7.18e+03 8.58e+00
  bond pdb=" N   VAL B 353 "
       pdb=" CA  VAL B 353 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.24e-02 6.50e+03 7.57e+00
  bond pdb=" N   ASP A  98 "
       pdb=" CA  ASP A  98 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.037 1.34e-02 5.57e+03 7.50e+00
  ... (remaining 6969 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 9207
        2.36 -     4.72: 239
        4.72 -     7.09: 13
        7.09 -     9.45: 7
        9.45 -    11.81: 5
  Bond angle restraints: 9471
  Sorted by residual:
  angle pdb=" CA  GLY B 319 "
        pdb=" C   GLY B 319 "
        pdb=" O   GLY B 319 "
      ideal   model   delta    sigma   weight residual
     121.66  118.05    3.61 8.80e-01 1.29e+00 1.68e+01
  angle pdb=" PA  GTP A 501 "
        pdb=" O3A GTP A 501 "
        pdb=" PB  GTP A 501 "
      ideal   model   delta    sigma   weight residual
     120.50  132.31  -11.81 3.00e+00 1.11e-01 1.55e+01
  angle pdb=" C1' GTP A 501 "
        pdb=" C2' GTP A 501 "
        pdb=" C3' GTP A 501 "
      ideal   model   delta    sigma   weight residual
     111.00   99.71   11.29 3.00e+00 1.11e-01 1.42e+01
  angle pdb=" PB  GTP A 501 "
        pdb=" O3B GTP A 501 "
        pdb=" PG  GTP A 501 "
      ideal   model   delta    sigma   weight residual
     120.50  131.68  -11.18 3.00e+00 1.11e-01 1.39e+01
  angle pdb=" N   ALA A  99 "
        pdb=" CA  ALA A  99 "
        pdb=" C   ALA A  99 "
      ideal   model   delta    sigma   weight residual
     112.87  108.73    4.14 1.20e+00 6.94e-01 1.19e+01
  ... (remaining 9466 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.73: 4002
       28.73 -    57.46: 117
       57.46 -    86.19: 18
       86.19 -   114.93: 3
      114.93 -   143.66: 3
  Dihedral angle restraints: 4143
    sinusoidal: 1660
      harmonic: 2483
  Sorted by residual:
  dihedral pdb=" C8  GTP A 501 "
           pdb=" C1' GTP A 501 "
           pdb=" N9  GTP A 501 "
           pdb=" O4' GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -39.06  143.66     1      2.00e+01 2.50e-03 4.33e+01
  dihedral pdb=" C5' GTP A 501 "
           pdb=" O5' GTP A 501 "
           pdb=" PA  GTP A 501 "
           pdb=" O3A GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -157.71 -133.02     1      2.00e+01 2.50e-03 4.04e+01
  dihedral pdb=" O3B GTP A 501 "
           pdb=" O3A GTP A 501 "
           pdb=" PB  GTP A 501 "
           pdb=" PA  GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     291.08  172.67  118.41     1      2.00e+01 2.50e-03 3.54e+01
  ... (remaining 4140 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 588
       0.045 -    0.091: 311
       0.091 -    0.136: 105
       0.136 -    0.182: 27
       0.182 -    0.227: 3
  Chirality restraints: 1034
  Sorted by residual:
  chirality pdb=" CA  ILE A  93 "
            pdb=" N   ILE A  93 "
            pdb=" C   ILE A  93 "
            pdb=" CB  ILE A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" C3' GTP A 501 "
            pdb=" C2' GTP A 501 "
            pdb=" C4' GTP A 501 "
            pdb=" O3' GTP A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.69    0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CA  ARG B 241 "
            pdb=" N   ARG B 241 "
            pdb=" C   ARG B 241 "
            pdb=" CB  ARG B 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.99e-01
  ... (remaining 1031 not shown)

  Planarity restraints: 1234
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 320 "    0.280 9.50e-02 1.11e+02   1.25e-01 9.68e+00
        pdb=" NE  ARG B 320 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 320 "    0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 320 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 320 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 215 "   -0.275 9.50e-02 1.11e+02   1.23e-01 9.33e+00
        pdb=" NE  ARG A 215 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 215 "    0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 215 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 215 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 241 "   -0.234 9.50e-02 1.11e+02   1.05e-01 7.60e+00
        pdb=" NE  ARG B 241 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 241 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 241 "    0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 241 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1231 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 19
        2.53 -     3.12: 5264
        3.12 -     3.72: 9792
        3.72 -     4.31: 14981
        4.31 -     4.90: 25284
  Nonbonded interactions: 55340
  Sorted by model distance:
  nonbonded pdb=" O3G GTP A 501 "
            pdb="MG    MG B 501 "
     model   vdw
     1.939 2.170
  nonbonded pdb=" NZ  LYS B 174 "
            pdb=" OE2 GLU B 205 "
     model   vdw
     2.300 3.120
  nonbonded pdb=" NH1 ARG B 282 "
            pdb=" OE2 GLU B 288 "
     model   vdw
     2.310 3.120
  nonbonded pdb=" NZ  LYS A 311 "
            pdb=" O   GLY A 436 "
     model   vdw
     2.400 3.120
  nonbonded pdb=" N   GLY B 142 "
            pdb=" O1B GDP B 502 "
     model   vdw
     2.453 3.120
  ... (remaining 55335 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             9.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.660
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  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:13.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8708
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      :  0.008   0.061   6974  Z= 0.530
  Angle     :  0.923  11.812   9471  Z= 0.544
  Chirality :  0.060   0.227   1034
  Planarity :  0.010   0.125   1234
  Dihedral  : 14.910 143.657   2553
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 2.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.25), residues: 856
  helix: -1.38 (0.22), residues: 365
  sheet:  0.55 (0.41), residues: 145
  loop : -0.77 (0.31), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.004   TRP B 101 
 HIS   0.008   0.002   HIS A   8 
 PHE   0.017   0.003   PHE A  53 
 TYR   0.025   0.004   TYR A 319 
 ARG   0.021   0.003   ARG B 156 

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.776 
Fit side-chains
REVERT: A  254 GLU cc_start: 0.8708 (tt0) cc_final: 0.8099 (tp30)
REVERT: A  302 MET cc_start: 0.8632 (mtt) cc_final: 0.7950 (mtt)
REVERT: A  423 GLU cc_start: 0.8354 (tp30) cc_final: 0.7776 (tm-30)
REVERT: B   26 ASP cc_start: 0.8404 (t0) cc_final: 0.8078 (t0)
REVERT: B   31 ASP cc_start: 0.8289 (m-30) cc_final: 0.7603 (m-30)
REVERT: B   37 HIS cc_start: 0.8695 (m-70) cc_final: 0.7585 (m-70)
REVERT: B  114 ASP cc_start: 0.8332 (m-30) cc_final: 0.7783 (m-30)
REVERT: B  122 LYS cc_start: 0.8850 (ttpt) cc_final: 0.8586 (tptt)
REVERT: B  145 SER cc_start: 0.8765 (t) cc_final: 0.8541 (p)
REVERT: B  213 ARG cc_start: 0.8911 (ttm-80) cc_final: 0.8701 (ttm170)
REVERT: B  299 MET cc_start: 0.9437 (mmp) cc_final: 0.9033 (mmp)
REVERT: B  324 LYS cc_start: 0.8726 (tttp) cc_final: 0.8345 (tttt)
REVERT: B  388 MET cc_start: 0.8318 (mtp) cc_final: 0.8113 (mtp)
REVERT: B  390 ARG cc_start: 0.8087 (ptm-80) cc_final: 0.7524 (tpt170)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 1.6406
  time to fit residues: 240.3042
Evaluate side-chains
  97 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 34 optimal weight:    0.4980
   chunk 66 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 77 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 133 GLN
A 139 HIS
A 293 ASN
A 356 ASN
A 406 HIS
B  43 GLN
B 137 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.091964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.079968 restraints weight = 9979.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.2933 rms_B_bonded: 2.13
r_work: 0.2811 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2690 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8674
moved from start:          0.1896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   6974  Z= 0.302
  Angle     :  0.626   7.819   9471  Z= 0.333
  Chirality :  0.046   0.164   1034
  Planarity :  0.005   0.039   1234
  Dihedral  : 11.111 151.410    961
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 10.23 %
    Favored  : 88.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.27), residues: 856
  helix:  0.37 (0.26), residues: 381
  sheet:  0.61 (0.42), residues: 145
  loop : -0.66 (0.31), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  21 
 HIS   0.004   0.001   HIS A  88 
 PHE   0.018   0.002   PHE A 255 
 TYR   0.011   0.001   TYR A 103 
 ARG   0.005   0.001   ARG A 402 

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.755 
Fit side-chains
REVERT: A   24 TYR cc_start: 0.8835 (m-10) cc_final: 0.8578 (m-10)
REVERT: A   26 LEU cc_start: 0.9000 (tp) cc_final: 0.8740 (mt)
REVERT: A  176 GLN cc_start: 0.8295 (mt0) cc_final: 0.8056 (mm-40)
REVERT: A  254 GLU cc_start: 0.8253 (tt0) cc_final: 0.7614 (tp30)
REVERT: A  290 GLU cc_start: 0.8874 (tt0) cc_final: 0.8639 (mt-10)
REVERT: A  302 MET cc_start: 0.8618 (mtt) cc_final: 0.7897 (mtt)
REVERT: A  377 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.7839 (tmm)
REVERT: A  393 HIS cc_start: 0.9062 (t70) cc_final: 0.8846 (t70)
REVERT: A  423 GLU cc_start: 0.8578 (tp30) cc_final: 0.8352 (mt-10)
REVERT: B   26 ASP cc_start: 0.8796 (t0) cc_final: 0.8526 (t0)
REVERT: B   31 ASP cc_start: 0.8452 (m-30) cc_final: 0.7768 (m-30)
REVERT: B   37 HIS cc_start: 0.8705 (m-70) cc_final: 0.7807 (m-70)
REVERT: B  114 ASP cc_start: 0.8214 (m-30) cc_final: 0.7787 (m-30)
REVERT: B  122 LYS cc_start: 0.8940 (ttpt) cc_final: 0.8654 (tptt)
REVERT: B  157 GLU cc_start: 0.8328 (mp0) cc_final: 0.8008 (mp0)
REVERT: B  282 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8133 (mmt180)
REVERT: B  299 MET cc_start: 0.9330 (mmp) cc_final: 0.8983 (mmp)
REVERT: B  324 LYS cc_start: 0.8824 (tttp) cc_final: 0.8408 (tttm)
REVERT: B  374 ILE cc_start: 0.9124 (tp) cc_final: 0.8880 (tt)
REVERT: B  388 MET cc_start: 0.8439 (mtp) cc_final: 0.8237 (mtp)
REVERT: B  390 ARG cc_start: 0.8376 (ptm-80) cc_final: 0.7511 (tpt170)
REVERT: B  421 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8067 (mt-10)
  outliers start: 12
  outliers final: 2
  residues processed: 121
  average time/residue: 1.5395
  time to fit residues: 194.1833
Evaluate side-chains
  104 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  282 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 14 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0040
   chunk 33 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 81 optimal weight:    0.5980
   overall best weight:    0.5192

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

Flipped N/Q/H residues before XYZ refinement:
A 107 HIS
B   6 HIS
B   8 GLN
B 264 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.093778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.081524 restraints weight = 10003.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.2956 rms_B_bonded: 2.16
r_work: 0.2836 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2713 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.2432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6974  Z= 0.220
  Angle     :  0.545   6.858   9471  Z= 0.284
  Chirality :  0.043   0.133   1034
  Planarity :  0.004   0.041   1234
  Dihedral  : 10.516 158.445    961
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 11.87 %
    Favored  : 86.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.28), residues: 856
  helix:  0.85 (0.27), residues: 380
  sheet:  0.61 (0.42), residues: 148
  loop : -0.65 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  21 
 HIS   0.003   0.001   HIS A  88 
 PHE   0.019   0.001   PHE A 255 
 TYR   0.009   0.001   TYR B 310 
 ARG   0.005   0.000   ARG A 402 

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.728 
Fit side-chains
REVERT: A   24 TYR cc_start: 0.8881 (m-10) cc_final: 0.8593 (m-10)
REVERT: A   26 LEU cc_start: 0.9014 (tp) cc_final: 0.8723 (mt)
REVERT: A  176 GLN cc_start: 0.8258 (mt0) cc_final: 0.8027 (mm-40)
REVERT: A  254 GLU cc_start: 0.8199 (tt0) cc_final: 0.7609 (tp30)
REVERT: A  302 MET cc_start: 0.8317 (mtt) cc_final: 0.7868 (mtt)
REVERT: A  411 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7211 (mt-10)
REVERT: A  434 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8036 (tp30)
REVERT: B   26 ASP cc_start: 0.8801 (t0) cc_final: 0.8583 (t0)
REVERT: B   31 ASP cc_start: 0.8474 (m-30) cc_final: 0.7772 (m-30)
REVERT: B   37 HIS cc_start: 0.8716 (m-70) cc_final: 0.7709 (m-70)
REVERT: B  114 ASP cc_start: 0.8242 (m-30) cc_final: 0.7943 (m-30)
REVERT: B  122 LYS cc_start: 0.8891 (ttpt) cc_final: 0.8639 (tptt)
REVERT: B  157 GLU cc_start: 0.8375 (mp0) cc_final: 0.8125 (mp0)
REVERT: B  203 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8331 (m-30)
REVERT: B  299 MET cc_start: 0.9290 (mmp) cc_final: 0.8937 (mmp)
REVERT: B  324 LYS cc_start: 0.8845 (tttp) cc_final: 0.8441 (tttm)
REVERT: B  388 MET cc_start: 0.8434 (mtp) cc_final: 0.7939 (mtm)
REVERT: B  390 ARG cc_start: 0.8362 (ptm-80) cc_final: 0.7534 (tpt170)
REVERT: B  421 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8163 (mt-10)
  outliers start: 14
  outliers final: 4
  residues processed: 119
  average time/residue: 1.4944
  time to fit residues: 185.5832
Evaluate side-chains
  103 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  203 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9980
   chunk 67 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 82 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B   6 HIS
B   8 GLN
B  48 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.093000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.080875 restraints weight = 9985.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.2943 rms_B_bonded: 2.13
r_work: 0.2823 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2702 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8666
moved from start:          0.2549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6974  Z= 0.262
  Angle     :  0.552   7.517   9471  Z= 0.285
  Chirality :  0.044   0.133   1034
  Planarity :  0.004   0.042   1234
  Dihedral  : 10.384 162.075    961
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 12.96 %
    Favored  : 84.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.28), residues: 856
  helix:  0.98 (0.28), residues: 377
  sheet:  0.67 (0.41), residues: 148
  loop : -0.71 (0.31), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A  21 
 HIS   0.004   0.001   HIS B 264 
 PHE   0.019   0.002   PHE A 255 
 TYR   0.010   0.001   TYR A 103 
 ARG   0.004   0.000   ARG A 221 

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.740 
Fit side-chains
REVERT: A   24 TYR cc_start: 0.8900 (m-10) cc_final: 0.8580 (m-10)
REVERT: A   26 LEU cc_start: 0.8990 (tp) cc_final: 0.8666 (mt)
REVERT: A  176 GLN cc_start: 0.8255 (mt0) cc_final: 0.8015 (mm-40)
REVERT: A  254 GLU cc_start: 0.8228 (tt0) cc_final: 0.7625 (tp30)
REVERT: A  302 MET cc_start: 0.8330 (mtt) cc_final: 0.7859 (mtt)
REVERT: A  377 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.7846 (tmm)
REVERT: A  411 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7273 (mt-10)
REVERT: A  413 MET cc_start: 0.8480 (ttp) cc_final: 0.8241 (ttp)
REVERT: A  423 GLU cc_start: 0.7442 (mt-10) cc_final: 0.6936 (mt-10)
REVERT: A  434 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7878 (tp30)
REVERT: B   26 ASP cc_start: 0.8829 (t0) cc_final: 0.8608 (t0)
REVERT: B   31 ASP cc_start: 0.8258 (m-30) cc_final: 0.7620 (m-30)
REVERT: B   37 HIS cc_start: 0.8760 (m-70) cc_final: 0.7757 (m-70)
REVERT: B  114 ASP cc_start: 0.8236 (m-30) cc_final: 0.7959 (m-30)
REVERT: B  122 LYS cc_start: 0.8908 (ttpt) cc_final: 0.8657 (tptt)
REVERT: B  157 GLU cc_start: 0.8395 (mp0) cc_final: 0.8123 (mp0)
REVERT: B  203 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8495 (m-30)
REVERT: B  324 LYS cc_start: 0.8780 (tttp) cc_final: 0.8425 (tttm)
REVERT: B  388 MET cc_start: 0.8425 (mtp) cc_final: 0.8056 (mtm)
REVERT: B  390 ARG cc_start: 0.8348 (ptm-80) cc_final: 0.7464 (tpt170)
REVERT: B  421 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8144 (mt-10)
  outliers start: 15
  outliers final: 5
  residues processed: 118
  average time/residue: 1.4647
  time to fit residues: 180.7389
Evaluate side-chains
  107 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  203 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 72 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 59 optimal weight:    0.2980
   chunk 36 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 197 HIS
B   6 HIS
B   8 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.092567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.080456 restraints weight = 9977.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.2938 rms_B_bonded: 2.14
r_work: 0.2817 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2697 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8672
moved from start:          0.2662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6974  Z= 0.273
  Angle     :  0.550   7.057   9471  Z= 0.284
  Chirality :  0.044   0.136   1034
  Planarity :  0.004   0.040   1234
  Dihedral  : 10.340 165.692    961
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 14.60 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.28), residues: 856
  helix:  0.97 (0.28), residues: 374
  sheet:  0.78 (0.41), residues: 148
  loop : -0.80 (0.31), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  21 
 HIS   0.004   0.001   HIS A  88 
 PHE   0.019   0.002   PHE A 255 
 TYR   0.010   0.001   TYR A 103 
 ARG   0.004   0.000   ARG B 282 

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.724 
Fit side-chains
REVERT: A   24 TYR cc_start: 0.8900 (m-10) cc_final: 0.8571 (m-10)
REVERT: A  176 GLN cc_start: 0.8250 (mt0) cc_final: 0.8016 (mm-40)
REVERT: A  254 GLU cc_start: 0.8238 (tt0) cc_final: 0.7593 (tp30)
REVERT: A  302 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7962 (mtt)
REVERT: A  377 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.7888 (tmm)
REVERT: A  411 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7243 (mt-10)
REVERT: A  413 MET cc_start: 0.8582 (ttp) cc_final: 0.8313 (ttp)
REVERT: A  423 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7018 (mt-10)
REVERT: A  434 GLU cc_start: 0.8527 (mm-30) cc_final: 0.7976 (tp30)
REVERT: B   26 ASP cc_start: 0.8836 (t0) cc_final: 0.8618 (t0)
REVERT: B   31 ASP cc_start: 0.8247 (m-30) cc_final: 0.7573 (m-30)
REVERT: B   37 HIS cc_start: 0.8778 (m-70) cc_final: 0.7706 (m-70)
REVERT: B  114 ASP cc_start: 0.8308 (m-30) cc_final: 0.7984 (m-30)
REVERT: B  157 GLU cc_start: 0.8454 (mp0) cc_final: 0.8086 (mp0)
REVERT: B  203 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.8485 (m-30)
REVERT: B  388 MET cc_start: 0.8446 (mtp) cc_final: 0.8057 (mtm)
REVERT: B  390 ARG cc_start: 0.8318 (ptm-80) cc_final: 0.7437 (tpt170)
REVERT: B  421 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8165 (mt-10)
  outliers start: 12
  outliers final: 5
  residues processed: 113
  average time/residue: 1.4279
  time to fit residues: 168.5395
Evaluate side-chains
  109 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  203 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 74 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9990
   chunk 67 optimal weight:    0.8980
   chunk 77 optimal weight:    0.4980
   chunk 11 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0970
   chunk 78 optimal weight:    0.0570
   chunk 51 optimal weight:    0.9990
   chunk 3 optimal weight:    0.3980
   overall best weight:    0.3296

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

Flipped N/Q/H residues before XYZ refinement:
B   6 HIS
B   8 GLN
B 280 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.095120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.083096 restraints weight = 9928.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 2.12
r_work: 0.2860 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2738 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.2929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6974  Z= 0.163
  Angle     :  0.499   6.582   9471  Z= 0.255
  Chirality :  0.042   0.136   1034
  Planarity :  0.004   0.041   1234
  Dihedral  : 10.085 168.084    961
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 14.19 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.28), residues: 856
  helix:  1.13 (0.28), residues: 379
  sheet:  0.93 (0.42), residues: 149
  loop : -0.69 (0.32), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  21 
 HIS   0.002   0.001   HIS A  28 
 PHE   0.018   0.001   PHE A 255 
 TYR   0.006   0.001   TYR B 310 
 ARG   0.003   0.000   ARG B 282 

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.730 
Fit side-chains
REVERT: A   15 GLN cc_start: 0.9042 (mt0) cc_final: 0.8747 (mt0)
REVERT: A   24 TYR cc_start: 0.8887 (m-10) cc_final: 0.8592 (m-10)
REVERT: A  176 GLN cc_start: 0.8236 (mt0) cc_final: 0.8016 (mm-40)
REVERT: A  254 GLU cc_start: 0.8099 (tt0) cc_final: 0.7578 (tp30)
REVERT: A  302 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7870 (mtt)
REVERT: A  411 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7388 (mt-10)
REVERT: A  413 MET cc_start: 0.8585 (ttp) cc_final: 0.8337 (ttp)
REVERT: A  423 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6992 (mt-10)
REVERT: A  434 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8020 (tp30)
REVERT: A  437 VAL cc_start: 0.8343 (t) cc_final: 0.8124 (p)
REVERT: B   26 ASP cc_start: 0.8869 (t0) cc_final: 0.8632 (t0)
REVERT: B   31 ASP cc_start: 0.8256 (m-30) cc_final: 0.7526 (m-30)
REVERT: B   37 HIS cc_start: 0.8778 (m-70) cc_final: 0.7956 (m170)
REVERT: B  114 ASP cc_start: 0.8233 (m-30) cc_final: 0.7872 (m-30)
REVERT: B  157 GLU cc_start: 0.8369 (mp0) cc_final: 0.8148 (mp0)
REVERT: B  197 ASP cc_start: 0.8674 (m-30) cc_final: 0.8425 (m-30)
REVERT: B  203 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8414 (m-30)
REVERT: B  324 LYS cc_start: 0.8694 (tttp) cc_final: 0.8362 (tttm)
REVERT: B  388 MET cc_start: 0.8436 (mtp) cc_final: 0.8013 (mtm)
REVERT: B  390 ARG cc_start: 0.8293 (ptm-80) cc_final: 0.7524 (tpt170)
REVERT: B  421 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8144 (mt-10)
  outliers start: 13
  outliers final: 4
  residues processed: 119
  average time/residue: 1.5422
  time to fit residues: 191.3319
Evaluate side-chains
  112 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 106
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 GLU
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  203 ASP
Chi-restraints excluded: chain B residue  218 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 82 optimal weight:    0.0870
   chunk 31 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   chunk 72 optimal weight:    0.3980
   chunk 35 optimal weight:    0.9980
   chunk 8 optimal weight:    0.4980
   chunk 28 optimal weight:    0.3980
   chunk 66 optimal weight:    0.4980
   chunk 5 optimal weight:    0.6980
   chunk 63 optimal weight:    0.0980
   overall best weight:    0.2958

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

Flipped N/Q/H residues before XYZ refinement:
A 256 GLN
B   6 HIS
B   8 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.095902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.083891 restraints weight = 9925.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 2.13
r_work: 0.2876 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2755 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.3065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6974  Z= 0.157
  Angle     :  0.490   6.475   9471  Z= 0.248
  Chirality :  0.041   0.136   1034
  Planarity :  0.004   0.039   1234
  Dihedral  :  9.987 168.297    961
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 15.69 %
    Favored  : 83.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.29), residues: 856
  helix:  1.30 (0.28), residues: 372
  sheet:  1.03 (0.42), residues: 149
  loop : -0.52 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  21 
 HIS   0.002   0.001   HIS B 264 
 PHE   0.019   0.001   PHE A 255 
 TYR   0.006   0.001   TYR B 310 
 ARG   0.004   0.000   ARG B 282 

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 111
  time to evaluate  : 0.712 
Fit side-chains
REVERT: A   24 TYR cc_start: 0.8911 (m-10) cc_final: 0.8599 (m-10)
REVERT: A   71 GLU cc_start: 0.8062 (tt0) cc_final: 0.7818 (tm-30)
REVERT: A  176 GLN cc_start: 0.8092 (mt0) cc_final: 0.7853 (mm-40)
REVERT: A  254 GLU cc_start: 0.7915 (tt0) cc_final: 0.7465 (tp30)
REVERT: A  302 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7786 (mtt)
REVERT: A  411 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7389 (mt-10)
REVERT: A  414 GLU cc_start: 0.8726 (pt0) cc_final: 0.8413 (pt0)
REVERT: A  423 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7009 (mt-10)
REVERT: A  434 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7894 (tp30)
REVERT: A  437 VAL cc_start: 0.8354 (t) cc_final: 0.8126 (p)
REVERT: B   26 ASP cc_start: 0.8859 (t0) cc_final: 0.8618 (t0)
REVERT: B   31 ASP cc_start: 0.8255 (m-30) cc_final: 0.7524 (m-30)
REVERT: B   37 HIS cc_start: 0.8768 (m-70) cc_final: 0.7961 (m170)
REVERT: B  114 ASP cc_start: 0.8212 (m-30) cc_final: 0.7870 (m-30)
REVERT: B  147 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8123 (tpp)
REVERT: B  157 GLU cc_start: 0.8307 (mp0) cc_final: 0.8075 (mp0)
REVERT: B  197 ASP cc_start: 0.8693 (m-30) cc_final: 0.8469 (m-30)
REVERT: B  203 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8389 (m-30)
REVERT: B  324 LYS cc_start: 0.8804 (tttp) cc_final: 0.8486 (tttm)
REVERT: B  388 MET cc_start: 0.8437 (mtp) cc_final: 0.7932 (mtm)
REVERT: B  390 ARG cc_start: 0.8287 (ptm-80) cc_final: 0.7568 (tpt170)
REVERT: B  421 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8180 (mt-10)
  outliers start: 7
  outliers final: 4
  residues processed: 115
  average time/residue: 1.4829
  time to fit residues: 177.8999
Evaluate side-chains
  115 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 108
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  203 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0040
   chunk 54 optimal weight:    0.2980
   chunk 78 optimal weight:    0.0000
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0970
   overall best weight:    0.2394

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

Flipped N/Q/H residues before XYZ refinement:
B   6 HIS
B   8 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.096972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.084906 restraints weight = 9914.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 2.13
r_work: 0.2892 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2771 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8605
moved from start:          0.3155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6974  Z= 0.142
  Angle     :  0.481   6.308   9471  Z= 0.244
  Chirality :  0.041   0.135   1034
  Planarity :  0.004   0.039   1234
  Dihedral  :  9.920 168.726    961
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 15.69 %
    Favored  : 83.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.29), residues: 856
  helix:  1.30 (0.28), residues: 378
  sheet:  1.09 (0.42), residues: 149
  loop : -0.55 (0.32), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  21 
 HIS   0.002   0.001   HIS B 396 
 PHE   0.019   0.001   PHE A 255 
 TYR   0.006   0.001   TYR B 310 
 ARG   0.004   0.000   ARG B 282 

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 114
  time to evaluate  : 0.728 
Fit side-chains
REVERT: A   24 TYR cc_start: 0.8866 (m-10) cc_final: 0.8545 (m-10)
REVERT: A  176 GLN cc_start: 0.8093 (mt0) cc_final: 0.7860 (mm-40)
REVERT: A  254 GLU cc_start: 0.7893 (tt0) cc_final: 0.7450 (tp30)
REVERT: A  302 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7763 (mtt)
REVERT: A  390 ARG cc_start: 0.8295 (ttp-170) cc_final: 0.8022 (mtm-85)
REVERT: A  411 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7371 (mt-10)
REVERT: A  414 GLU cc_start: 0.8685 (pt0) cc_final: 0.8330 (pt0)
REVERT: A  423 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7084 (mt-10)
REVERT: A  434 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7889 (tp30)
REVERT: A  437 VAL cc_start: 0.8375 (t) cc_final: 0.7984 (p)
REVERT: B   26 ASP cc_start: 0.8863 (t0) cc_final: 0.8618 (t0)
REVERT: B   31 ASP cc_start: 0.8264 (m-30) cc_final: 0.7533 (m-30)
REVERT: B   37 HIS cc_start: 0.8742 (m-70) cc_final: 0.7919 (m170)
REVERT: B  114 ASP cc_start: 0.8486 (m-30) cc_final: 0.8200 (m-30)
REVERT: B  147 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8200 (tpp)
REVERT: B  157 GLU cc_start: 0.8324 (mp0) cc_final: 0.8082 (mp0)
REVERT: B  197 ASP cc_start: 0.8651 (m-30) cc_final: 0.8440 (m-30)
REVERT: B  203 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8387 (m-30)
REVERT: B  332 ASN cc_start: 0.8712 (t0) cc_final: 0.8454 (t0)
REVERT: B  388 MET cc_start: 0.8414 (mtp) cc_final: 0.7988 (mtm)
REVERT: B  390 ARG cc_start: 0.8308 (ptm-80) cc_final: 0.7571 (tpt170)
REVERT: B  421 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8136 (mt-10)
  outliers start: 7
  outliers final: 5
  residues processed: 118
  average time/residue: 1.4155
  time to fit residues: 174.4476
Evaluate side-chains
  115 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  203 ASP
Chi-restraints excluded: chain B residue  363 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   chunk 52 optimal weight:    0.7980
   chunk 67 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 81 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 33 optimal weight:    0.0030
   overall best weight:    0.6190

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

Flipped N/Q/H residues before XYZ refinement:
A 309 HIS
B   6 HIS
B   8 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.093867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.081777 restraints weight = 10032.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 2.14
r_work: 0.2838 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2718 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.3023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6974  Z= 0.245
  Angle     :  0.532   6.710   9471  Z= 0.273
  Chirality :  0.043   0.130   1034
  Planarity :  0.004   0.039   1234
  Dihedral  : 10.131 169.297    961
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 16.23 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.29), residues: 856
  helix:  1.25 (0.28), residues: 378
  sheet:  1.09 (0.42), residues: 148
  loop : -0.63 (0.32), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  21 
 HIS   0.003   0.001   HIS A  88 
 PHE   0.021   0.001   PHE A 255 
 TYR   0.011   0.001   TYR A 103 
 ARG   0.013   0.001   ARG A 422 

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.748 
Fit side-chains
REVERT: A   24 TYR cc_start: 0.8865 (m-10) cc_final: 0.8528 (m-10)
REVERT: A  176 GLN cc_start: 0.8145 (mt0) cc_final: 0.7896 (mm-40)
REVERT: A  254 GLU cc_start: 0.8089 (tt0) cc_final: 0.7556 (tp30)
REVERT: A  302 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7916 (mtt)
REVERT: A  390 ARG cc_start: 0.8202 (ttp-170) cc_final: 0.7950 (mtm-85)
REVERT: A  411 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7386 (mt-10)
REVERT: A  414 GLU cc_start: 0.8667 (pt0) cc_final: 0.8347 (pt0)
REVERT: A  423 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7127 (mt-10)
REVERT: A  434 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7884 (tp30)
REVERT: A  437 VAL cc_start: 0.8485 (t) cc_final: 0.8035 (p)
REVERT: B   26 ASP cc_start: 0.8867 (t0) cc_final: 0.8628 (t0)
REVERT: B   37 HIS cc_start: 0.8759 (m-70) cc_final: 0.8525 (m170)
REVERT: B  114 ASP cc_start: 0.8229 (m-30) cc_final: 0.7955 (m-30)
REVERT: B  147 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8405 (tpp)
REVERT: B  197 ASP cc_start: 0.8724 (m-30) cc_final: 0.8460 (m-30)
REVERT: B  203 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8472 (m-30)
REVERT: B  388 MET cc_start: 0.8406 (mtp) cc_final: 0.7928 (mtm)
REVERT: B  390 ARG cc_start: 0.8306 (ptm-80) cc_final: 0.7519 (tpt170)
REVERT: B  421 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8186 (mt-10)
  outliers start: 9
  outliers final: 4
  residues processed: 111
  average time/residue: 1.4597
  time to fit residues: 169.3949
Evaluate side-chains
  111 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  203 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0770
   chunk 34 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 2 optimal weight:    0.4980
   chunk 45 optimal weight:    0.2980
   chunk 77 optimal weight:    0.1980
   overall best weight:    0.3538

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

Flipped N/Q/H residues before XYZ refinement:
A 309 HIS
B   6 HIS
B   8 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.095631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.083517 restraints weight = 10095.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 2.14
r_work: 0.2866 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2746 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.3138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6974  Z= 0.171
  Angle     :  0.505   6.437   9471  Z= 0.258
  Chirality :  0.042   0.135   1034
  Planarity :  0.004   0.039   1234
  Dihedral  : 10.030 169.191    961
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 15.96 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.29), residues: 856
  helix:  1.33 (0.28), residues: 373
  sheet:  1.07 (0.42), residues: 149
  loop : -0.55 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  21 
 HIS   0.002   0.001   HIS A 309 
 PHE   0.020   0.001   PHE A 255 
 TYR   0.006   0.001   TYR A 103 
 ARG   0.011   0.000   ARG A 422 

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.708 
Fit side-chains
REVERT: A   24 TYR cc_start: 0.8921 (m-10) cc_final: 0.8625 (m-10)
REVERT: A   71 GLU cc_start: 0.8017 (tt0) cc_final: 0.7695 (tm-30)
REVERT: A  176 GLN cc_start: 0.8117 (mt0) cc_final: 0.7883 (mm-40)
REVERT: A  254 GLU cc_start: 0.7940 (tt0) cc_final: 0.7463 (tp30)
REVERT: A  302 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7843 (mtt)
REVERT: A  390 ARG cc_start: 0.8177 (ttp-170) cc_final: 0.7927 (mtm-85)
REVERT: A  391 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8486 (tt)
REVERT: A  411 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7380 (mt-10)
REVERT: A  414 GLU cc_start: 0.8633 (pt0) cc_final: 0.8335 (pt0)
REVERT: A  423 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7189 (mt-10)
REVERT: A  434 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7868 (tp30)
REVERT: A  437 VAL cc_start: 0.8529 (t) cc_final: 0.8100 (p)
REVERT: B   26 ASP cc_start: 0.8847 (t0) cc_final: 0.8608 (t0)
REVERT: B   37 HIS cc_start: 0.8751 (m-70) cc_final: 0.8515 (m170)
REVERT: B  114 ASP cc_start: 0.8162 (m-30) cc_final: 0.7912 (m-30)
REVERT: B  147 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8345 (tpp)
REVERT: B  157 GLU cc_start: 0.8233 (mp0) cc_final: 0.8023 (pm20)
REVERT: B  197 ASP cc_start: 0.8690 (m-30) cc_final: 0.8427 (m-30)
REVERT: B  388 MET cc_start: 0.8407 (mtp) cc_final: 0.8043 (mtm)
REVERT: B  390 ARG cc_start: 0.8273 (ptm-80) cc_final: 0.7562 (tpt170)
REVERT: B  421 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8155 (mt-10)
  outliers start: 10
  outliers final: 6
  residues processed: 112
  average time/residue: 1.4868
  time to fit residues: 173.9393
Evaluate side-chains
  115 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  257 MET
Chi-restraints excluded: chain B residue  363 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 74 optimal weight:    0.0980
   chunk 0 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0050
   chunk 15 optimal weight:    0.0970
   chunk 11 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.2792

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

Flipped N/Q/H residues before XYZ refinement:
A 309 HIS
B   6 HIS
B   8 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.096731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.084678 restraints weight = 9947.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.2995 rms_B_bonded: 2.13
r_work: 0.2872 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2748 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.3254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6974  Z= 0.154
  Angle     :  0.494   6.271   9471  Z= 0.251
  Chirality :  0.041   0.135   1034
  Planarity :  0.004   0.039   1234
  Dihedral  :  9.930 168.654    961
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 16.23 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.29), residues: 856
  helix:  1.42 (0.28), residues: 372
  sheet:  1.06 (0.42), residues: 150
  loop : -0.53 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  21 
 HIS   0.002   0.001   HIS A 309 
 PHE   0.019   0.001   PHE A 255 
 TYR   0.006   0.001   TYR B 310 
 ARG   0.010   0.000   ARG A 422 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5184.15 seconds
wall clock time: 89 minutes 1.31 seconds (5341.31 seconds total)