Starting phenix.real_space_refine
on Sun Jun 22 04:54:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8f1c_28793/06_2025/8f1c_28793_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8f1c_28793/06_2025/8f1c_28793.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8f1c_28793/06_2025/8f1c_28793.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8f1c_28793/06_2025/8f1c_28793.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8f1c_28793/06_2025/8f1c_28793_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8f1c_28793/06_2025/8f1c_28793_trim.cif"
  }
  resolution = 2.92
  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=   0.011 sd=   0.045
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: 9
    Type Number    sf(0)   Gaussians
     K       4      8.98       5
     Zn      4      6.06       5
     P       4      5.49       5
     S      68      5.16       5
     Cl      4      4.86       5
     C    8520      2.51       5
     N    2120      2.21       5
     O    2208      1.98       5
     H   12184      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 25116
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6194
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 394, 6194
          Classifications: {'peptide': 394}
          Link IDs: {'PTRANS': 21, 'TRANS': 372}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 71
          Unresolved non-hydrogen angles: 85
          Unresolved non-hydrogen dihedrals: 63
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 41
    Chain: "A"
      Number of atoms: 88
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 88
          Unusual residues: {'  K': 4, ' ZN': 1, 'POV': 1, 'X9T': 1}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1518  SG  CYS A 104      63.879  52.710  75.558  1.00 53.86           S

  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 15.78, per 1000 atoms: 0.63
  Number of scatterers: 25116
  At special positions: 0
  Unit cell: (135.24, 135.24, 122.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 9
    Type Number    sf(0)
     Zn      4     29.99
     K       4     19.00
     Cl      4     17.00
     S      68     16.00
     P       4     15.00
     O    2208      8.00
     N    2120      7.00
     C    8520      6.00
     H   12184      1.00
    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: 8.18
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 601 "
        pdb="ZN    ZN A 601 " - pdb=" ND1 HIS A  77 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS A 104 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS D  83 "
      pdb="  ZN B 601 "
        pdb="ZN    ZN B 601 " - pdb=" SG  CYS A  83 "
        pdb="ZN    ZN B 601 " - pdb=" ND1 HIS B  77 "
        pdb="ZN    ZN B 601 " - pdb=" SG  CYS B 104 "
      pdb="  ZN C 601 "
        pdb="ZN    ZN C 601 " - pdb=" SG  CYS B  83 "
        pdb="ZN    ZN C 601 " - pdb=" ND1 HIS C  77 "
        pdb="ZN    ZN C 601 " - pdb=" SG  CYS C 104 "
      pdb="  ZN D 601 "
        pdb="ZN    ZN D 601 " - pdb=" ND1 HIS D  77 "
        pdb="ZN    ZN D 601 " - pdb=" SG  CYS D 104 "
        pdb="ZN    ZN D 601 " - pdb=" SG  CYS C  83 "


  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2976

  Finding SS restraints...
    Secondary structure from input PDB file:
      92 helices and 4 sheets defined
      70.6% alpha, 3.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 27
      removed outlier: 3.975A  pdb=" N   LEU A  26 " --> pdb=" O   TYR A  22 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ARG A  27 " --> pdb=" O   ARG A  23 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 22 through 27'
    Processing helix  chain 'A' and resid 32 through 39
      removed outlier: 3.540A  pdb=" N   GLU A  39 " --> pdb=" O   ALA A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 74
      removed outlier: 3.729A  pdb=" N   PHE A  64 " --> pdb=" O   HIS A  60 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ALA A  65 " --> pdb=" O   PRO A  61 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   HIS A  66 " --> pdb=" O   GLY A  62 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   TYR A  71 " --> pdb=" O   ILE A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 94
    Processing helix  chain 'A' and resid 97 through 101
      removed outlier: 3.703A  pdb=" N   ASP A 100 " --> pdb=" O   ASP A  97 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   VAL A 101 " --> pdb=" O   GLU A  98 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 97 through 101'
    Processing helix  chain 'A' and resid 102 through 104
      No H-bonds generated for 'chain 'A' and resid 102 through 104'
    Processing helix  chain 'A' and resid 105 through 110
      removed outlier: 3.697A  pdb=" N   TYR A 109 " --> pdb=" O   CYS A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 121
      removed outlier: 3.905A  pdb=" N   ALA A 115 " --> pdb=" O   GLN A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 180
      removed outlier: 3.869A  pdb=" N   PHE A 180 " --> pdb=" O   ILE A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 211
      removed outlier: 3.914A  pdb=" N   THR A 211 " --> pdb=" O   PHE A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 266
      removed outlier: 3.620A  pdb=" N   GLU A 249 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 276
    Processing helix  chain 'A' and resid 278 through 285
    Processing helix  chain 'A' and resid 286 through 294
      removed outlier: 3.548A  pdb=" N   TYR A 290 " --> pdb=" O   ILE A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 311
      removed outlier: 4.456A  pdb=" N   ASP A 305 " --> pdb=" O   LYS A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 320
      removed outlier: 3.665A  pdb=" N   ARG A 320 " --> pdb=" O   ARG A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 326
      removed outlier: 3.695A  pdb=" N   ARG A 326 " --> pdb=" O   PHE A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 341
    Processing helix  chain 'A' and resid 341 through 367
    Processing helix  chain 'A' and resid 377 through 381
      removed outlier: 4.179A  pdb=" N   HIS A 381 " --> pdb=" O   ALA A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 399
      removed outlier: 4.363A  pdb=" N   TRP A 392 " --> pdb=" O   PRO A 388 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   TRP A 393 " --> pdb=" O   ILE A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 430
    Processing helix  chain 'A' and resid 431 through 452
      removed outlier: 3.606A  pdb=" N   ILE A 435 " --> pdb=" O   PRO A 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 27
      removed outlier: 3.974A  pdb=" N   LEU B  26 " --> pdb=" O   TYR B  22 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ARG B  27 " --> pdb=" O   ARG B  23 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 22 through 27'
    Processing helix  chain 'B' and resid 32 through 39
      removed outlier: 3.540A  pdb=" N   GLU B  39 " --> pdb=" O   ALA B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 74
      removed outlier: 3.729A  pdb=" N   PHE B  64 " --> pdb=" O   HIS B  60 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   ALA B  65 " --> pdb=" O   PRO B  61 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   HIS B  66 " --> pdb=" O   GLY B  62 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   TYR B  71 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 94
    Processing helix  chain 'B' and resid 97 through 101
      removed outlier: 3.703A  pdb=" N   ASP B 100 " --> pdb=" O   ASP B  97 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   VAL B 101 " --> pdb=" O   GLU B  98 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 97 through 101'
    Processing helix  chain 'B' and resid 102 through 104
      No H-bonds generated for 'chain 'B' and resid 102 through 104'
    Processing helix  chain 'B' and resid 105 through 110
      removed outlier: 3.697A  pdb=" N   TYR B 109 " --> pdb=" O   CYS B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 121
      removed outlier: 3.906A  pdb=" N   ALA B 115 " --> pdb=" O   GLN B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 180
      removed outlier: 3.869A  pdb=" N   PHE B 180 " --> pdb=" O   ILE B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 211
      removed outlier: 3.913A  pdb=" N   THR B 211 " --> pdb=" O   PHE B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 266
      removed outlier: 3.619A  pdb=" N   GLU B 249 " --> pdb=" O   LEU B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 276
    Processing helix  chain 'B' and resid 278 through 285
    Processing helix  chain 'B' and resid 286 through 294
      removed outlier: 3.548A  pdb=" N   TYR B 290 " --> pdb=" O   ILE B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 311
      removed outlier: 4.456A  pdb=" N   ASP B 305 " --> pdb=" O   LYS B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 320
      removed outlier: 3.665A  pdb=" N   ARG B 320 " --> pdb=" O   ARG B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 321 through 326
      removed outlier: 3.695A  pdb=" N   ARG B 326 " --> pdb=" O   PHE B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 328 through 341
    Processing helix  chain 'B' and resid 341 through 367
    Processing helix  chain 'B' and resid 377 through 381
      removed outlier: 4.179A  pdb=" N   HIS B 381 " --> pdb=" O   ALA B 378 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 399
      removed outlier: 4.363A  pdb=" N   TRP B 392 " --> pdb=" O   PRO B 388 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   TRP B 393 " --> pdb=" O   ILE B 389 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 410 through 430
    Processing helix  chain 'B' and resid 431 through 452
      removed outlier: 3.606A  pdb=" N   ILE B 435 " --> pdb=" O   PRO B 431 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 22 through 27
      removed outlier: 3.975A  pdb=" N   LEU C  26 " --> pdb=" O   TYR C  22 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ARG C  27 " --> pdb=" O   ARG C  23 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 22 through 27'
    Processing helix  chain 'C' and resid 32 through 39
      removed outlier: 3.540A  pdb=" N   GLU C  39 " --> pdb=" O   ALA C  35 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 60 through 74
      removed outlier: 3.729A  pdb=" N   PHE C  64 " --> pdb=" O   HIS C  60 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ALA C  65 " --> pdb=" O   PRO C  61 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   HIS C  66 " --> pdb=" O   GLY C  62 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   TYR C  71 " --> pdb=" O   ILE C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 83 through 94
    Processing helix  chain 'C' and resid 97 through 101
      removed outlier: 3.703A  pdb=" N   ASP C 100 " --> pdb=" O   ASP C  97 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   VAL C 101 " --> pdb=" O   GLU C  98 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 97 through 101'
    Processing helix  chain 'C' and resid 102 through 104
      No H-bonds generated for 'chain 'C' and resid 102 through 104'
    Processing helix  chain 'C' and resid 105 through 110
      removed outlier: 3.697A  pdb=" N   TYR C 109 " --> pdb=" O   CYS C 105 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 121
      removed outlier: 3.905A  pdb=" N   ALA C 115 " --> pdb=" O   GLN C 111 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 172 through 180
      removed outlier: 3.869A  pdb=" N   PHE C 180 " --> pdb=" O   ILE C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 188 through 211
      removed outlier: 3.913A  pdb=" N   THR C 211 " --> pdb=" O   PHE C 207 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 243 through 266
      removed outlier: 3.619A  pdb=" N   GLU C 249 " --> pdb=" O   LEU C 245 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 269 through 276
    Processing helix  chain 'C' and resid 278 through 285
    Processing helix  chain 'C' and resid 286 through 294
      removed outlier: 3.548A  pdb=" N   TYR C 290 " --> pdb=" O   ILE C 286 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 299 through 311
      removed outlier: 4.456A  pdb=" N   ASP C 305 " --> pdb=" O   LYS C 301 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 312 through 320
      removed outlier: 3.664A  pdb=" N   ARG C 320 " --> pdb=" O   ARG C 317 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 321 through 326
      removed outlier: 3.695A  pdb=" N   ARG C 326 " --> pdb=" O   PHE C 322 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 328 through 341
    Processing helix  chain 'C' and resid 341 through 367
    Processing helix  chain 'C' and resid 377 through 381
      removed outlier: 4.178A  pdb=" N   HIS C 381 " --> pdb=" O   ALA C 378 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 387 through 399
      removed outlier: 4.364A  pdb=" N   TRP C 392 " --> pdb=" O   PRO C 388 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   TRP C 393 " --> pdb=" O   ILE C 389 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 410 through 430
    Processing helix  chain 'C' and resid 431 through 452
      removed outlier: 3.606A  pdb=" N   ILE C 435 " --> pdb=" O   PRO C 431 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 22 through 27
      removed outlier: 3.974A  pdb=" N   LEU D  26 " --> pdb=" O   TYR D  22 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ARG D  27 " --> pdb=" O   ARG D  23 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 22 through 27'
    Processing helix  chain 'D' and resid 32 through 39
      removed outlier: 3.540A  pdb=" N   GLU D  39 " --> pdb=" O   ALA D  35 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 60 through 74
      removed outlier: 3.729A  pdb=" N   PHE D  64 " --> pdb=" O   HIS D  60 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   ALA D  65 " --> pdb=" O   PRO D  61 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   HIS D  66 " --> pdb=" O   GLY D  62 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   TYR D  71 " --> pdb=" O   ILE D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 83 through 94
    Processing helix  chain 'D' and resid 97 through 101
      removed outlier: 3.705A  pdb=" N   ASP D 100 " --> pdb=" O   ASP D  97 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   VAL D 101 " --> pdb=" O   GLU D  98 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 97 through 101'
    Processing helix  chain 'D' and resid 102 through 104
      No H-bonds generated for 'chain 'D' and resid 102 through 104'
    Processing helix  chain 'D' and resid 105 through 110
      removed outlier: 3.697A  pdb=" N   TYR D 109 " --> pdb=" O   CYS D 105 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 111 through 121
      removed outlier: 3.905A  pdb=" N   ALA D 115 " --> pdb=" O   GLN D 111 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 172 through 180
      removed outlier: 3.869A  pdb=" N   PHE D 180 " --> pdb=" O   ILE D 176 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 188 through 211
      removed outlier: 3.913A  pdb=" N   THR D 211 " --> pdb=" O   PHE D 207 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 243 through 266
      removed outlier: 3.619A  pdb=" N   GLU D 249 " --> pdb=" O   LEU D 245 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 269 through 276
    Processing helix  chain 'D' and resid 278 through 285
    Processing helix  chain 'D' and resid 286 through 294
      removed outlier: 3.548A  pdb=" N   TYR D 290 " --> pdb=" O   ILE D 286 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 299 through 311
      removed outlier: 4.456A  pdb=" N   ASP D 305 " --> pdb=" O   LYS D 301 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 312 through 320
      removed outlier: 3.665A  pdb=" N   ARG D 320 " --> pdb=" O   ARG D 317 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 321 through 326
      removed outlier: 3.695A  pdb=" N   ARG D 326 " --> pdb=" O   PHE D 322 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 328 through 341
    Processing helix  chain 'D' and resid 341 through 367
    Processing helix  chain 'D' and resid 377 through 381
      removed outlier: 4.179A  pdb=" N   HIS D 381 " --> pdb=" O   ALA D 378 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 387 through 399
      removed outlier: 4.363A  pdb=" N   TRP D 392 " --> pdb=" O   PRO D 388 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   TRP D 393 " --> pdb=" O   ILE D 389 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 410 through 430
    Processing helix  chain 'D' and resid 431 through 452
      removed outlier: 3.606A  pdb=" N   ILE D 435 " --> pdb=" O   PRO D 431 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 21
      removed outlier: 3.712A  pdb=" N   THR A  21 " --> pdb=" O   ILE A  10 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ILE A  10 " --> pdb=" O   THR A  21 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   GLU A  54 " --> pdb=" O   ASP A  49 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ASP A  49 " --> pdb=" O   GLU A  54 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 21
      removed outlier: 3.712A  pdb=" N   THR B  21 " --> pdb=" O   ILE B  10 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ILE B  10 " --> pdb=" O   THR B  21 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   GLU B  54 " --> pdb=" O   ASP B  49 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ASP B  49 " --> pdb=" O   GLU B  54 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 17 through 21
      removed outlier: 3.712A  pdb=" N   THR C  21 " --> pdb=" O   ILE C  10 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ILE C  10 " --> pdb=" O   THR C  21 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   GLU C  54 " --> pdb=" O   ASP C  49 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ASP C  49 " --> pdb=" O   GLU C  54 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 17 through 21
      removed outlier: 3.712A  pdb=" N   THR D  21 " --> pdb=" O   ILE D  10 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ILE D  10 " --> pdb=" O   THR D  21 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   GLU D  54 " --> pdb=" O   ASP D  49 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ASP D  49 " --> pdb=" O   GLU D  54 " (cutoff:3.500A)

    700 hydrogen bonds defined for protein.
    2016 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: 9.35

  Time building geometry restraints manager: 8.21 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 12160
        1.03 -     1.23: 36
        1.23 -     1.42: 5800
        1.42 -     1.61: 7400
        1.61 -     1.81: 108
  Bond restraints: 25504
  Sorted by residual:
  bond pdb=" O12 POV A 603 "
       pdb=" P   POV A 603 "
    ideal  model  delta    sigma   weight residual
    1.657  1.606  0.051 2.00e-02 2.50e+03 6.47e+00
  bond pdb=" O12 POV C 603 "
       pdb=" P   POV C 603 "
    ideal  model  delta    sigma   weight residual
    1.657  1.606  0.051 2.00e-02 2.50e+03 6.47e+00
  bond pdb=" O12 POV D 603 "
       pdb=" P   POV D 603 "
    ideal  model  delta    sigma   weight residual
    1.657  1.607  0.050 2.00e-02 2.50e+03 6.29e+00
  bond pdb=" O12 POV B 603 "
       pdb=" P   POV B 603 "
    ideal  model  delta    sigma   weight residual
    1.657  1.607  0.050 2.00e-02 2.50e+03 6.20e+00
  bond pdb=" C11 POV A 603 "
       pdb=" O12 POV A 603 "
    ideal  model  delta    sigma   weight residual
    1.408  1.455 -0.047 2.00e-02 2.50e+03 5.49e+00
  ... (remaining 25499 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.25: 43919
        1.25 -     2.49: 1664
        2.49 -     3.74: 119
        3.74 -     4.99: 34
        4.99 -     6.23: 8
  Bond angle restraints: 45744
  Sorted by residual:
  angle pdb=" O11 POV A 603 "
        pdb=" P   POV A 603 "
        pdb=" O12 POV A 603 "
      ideal   model   delta    sigma   weight residual
      97.67  103.90   -6.23 3.00e+00 1.11e-01 4.32e+00
  angle pdb=" O11 POV C 603 "
        pdb=" P   POV C 603 "
        pdb=" O12 POV C 603 "
      ideal   model   delta    sigma   weight residual
      97.67  103.89   -6.22 3.00e+00 1.11e-01 4.30e+00
  angle pdb=" O11 POV B 603 "
        pdb=" P   POV B 603 "
        pdb=" O12 POV B 603 "
      ideal   model   delta    sigma   weight residual
      97.67  103.87   -6.20 3.00e+00 1.11e-01 4.27e+00
  angle pdb=" O11 POV D 603 "
        pdb=" P   POV D 603 "
        pdb=" O12 POV D 603 "
      ideal   model   delta    sigma   weight residual
      97.67  103.84   -6.17 3.00e+00 1.11e-01 4.23e+00
  angle pdb=" N   GLU B 181 "
        pdb=" CA  GLU B 181 "
        pdb=" CB  GLU B 181 "
      ideal   model   delta    sigma   weight residual
     113.65  110.94    2.71 1.47e+00 4.63e-01 3.39e+00
  ... (remaining 45739 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.07: 11211
       16.07 -    32.13: 717
       32.13 -    48.20: 168
       48.20 -    64.27: 88
       64.27 -    80.33: 16
  Dihedral angle restraints: 12200
    sinusoidal: 6400
      harmonic: 5800
  Sorted by residual:
  dihedral pdb=" CA  ILE A 318 "
           pdb=" CB  ILE A 318 "
           pdb=" CG1 ILE A 318 "
           pdb=" CD1 ILE A 318 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  133.72   46.28     3      1.50e+01 4.44e-03 8.31e+00
  dihedral pdb=" CA  ILE D 318 "
           pdb=" CB  ILE D 318 "
           pdb=" CG1 ILE D 318 "
           pdb=" CD1 ILE D 318 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  133.74   46.26     3      1.50e+01 4.44e-03 8.31e+00
  dihedral pdb=" CA  ILE B 318 "
           pdb=" CB  ILE B 318 "
           pdb=" CG1 ILE B 318 "
           pdb=" CD1 ILE B 318 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  133.74   46.26     3      1.50e+01 4.44e-03 8.31e+00
  ... (remaining 12197 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 1135
       0.024 -    0.049: 502
       0.049 -    0.073: 192
       0.073 -    0.097: 90
       0.097 -    0.121: 41
  Chirality restraints: 1960
  Sorted by residual:
  chirality pdb=" CA  ILE D  12 "
            pdb=" N   ILE D  12 "
            pdb=" C   ILE D  12 "
            pdb=" CB  ILE D  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.68e-01
  chirality pdb=" CA  ILE C  12 "
            pdb=" N   ILE C  12 "
            pdb=" C   ILE C  12 "
            pdb=" CB  ILE C  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.57e-01
  chirality pdb=" CA  ILE B  12 "
            pdb=" N   ILE B  12 "
            pdb=" C   ILE B  12 "
            pdb=" CB  ILE B  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.56e-01
  ... (remaining 1957 not shown)

  Planarity restraints: 3732
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 102 "   -0.023 5.00e-02 4.00e+02   3.51e-02 1.97e+00
        pdb=" N   PRO B 103 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO B 103 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 103 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU D 102 "    0.023 5.00e-02 4.00e+02   3.50e-02 1.96e+00
        pdb=" N   PRO D 103 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO D 103 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO D 103 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C 102 "   -0.023 5.00e-02 4.00e+02   3.49e-02 1.95e+00
        pdb=" N   PRO C 103 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO C 103 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO C 103 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 3729 not shown)

  Histogram of nonbonded interaction distances:
        1.67 -     2.36: 8096
        2.36 -     3.06: 68417
        3.06 -     3.75: 85403
        3.75 -     4.45: 132921
        4.45 -     5.14: 203943
  Nonbonded interactions: 498780
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 100 "
            pdb=" HZ1 LYS D 458 "
     model   vdw
     1.667 2.450
  nonbonded pdb=" HZ1 LYS A 458 "
            pdb=" OD2 ASP B 100 "
     model   vdw
     1.668 2.450
  nonbonded pdb=" HZ1 LYS B 458 "
            pdb=" OD2 ASP C 100 "
     model   vdw
     1.672 2.450
  nonbonded pdb=" HZ1 LYS C 458 "
            pdb=" OD2 ASP D 100 "
     model   vdw
     1.673 2.450
  nonbonded pdb=" O   GLU B 210 "
            pdb="HD21 ASN B 216 "
     model   vdw
     1.693 2.450
  ... (remaining 498775 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 7 through 463 or resid 601 through 603))
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.020
  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:             0.400
  Extract box with map and model:          0.870
  Check model and map are aligned:         0.160
  Set scattering table:                    0.200
  Process input model:                     66.910
  Find NCS groups from input model:        0.850
  Set up NCS constraints:                  0.060
  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:             0.010
  Load rotamer database and sin/cos tables:14.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   84.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
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      :  0.004   0.051  13332  Z= 0.183
  Angle     :  0.527   6.232  18136  Z= 0.247
  Chirality :  0.036   0.121   1960
  Planarity :  0.004   0.035   2252
  Dihedral  : 11.032  80.333   4768
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  3.36 %
    Favored  : 96.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.84 (0.22), residues: 1552
  helix:  1.68 (0.18), residues: 908
  sheet: -2.91 (0.85), residues: 40
  loop : -0.95 (0.26), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 255 
 HIS   0.001   0.000   HIS A  60 
 PHE   0.006   0.001   PHE C 328 
 TYR   0.005   0.001   TYR C  71 
 ARG   0.003   0.000   ARG A 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16365 (  700)
  hydrogen bonds       : angle       5.51583 ( 2016)
  metal coordination   : bond        0.00255 (   12)
  covalent geometry    : bond        0.00395 (13320)
  covalent geometry    : angle       0.52698 (18136)

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

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

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Evaluate side-chains
  213 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 205
  time to evaluate  : 1.765 
Fit side-chains
REVERT: A  412 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.7712 (p)
REVERT: A  447 MET cc_start: 0.8507 (mmm) cc_final: 0.8121 (mmt)
REVERT: B  412 SER cc_start: 0.8471 (OUTLIER) cc_final: 0.7695 (p)
REVERT: B  447 MET cc_start: 0.8497 (mmm) cc_final: 0.8107 (mmt)
REVERT: C  412 SER cc_start: 0.8477 (OUTLIER) cc_final: 0.7690 (p)
REVERT: C  447 MET cc_start: 0.8499 (mmm) cc_final: 0.8109 (mmt)
REVERT: D  412 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.7681 (p)
REVERT: D  447 MET cc_start: 0.8499 (mmm) cc_final: 0.8112 (mmt)
  outliers start: 8
  outliers final: 0
  residues processed: 213
  average time/residue: 2.4034
  time to fit residues: 563.8891
Evaluate side-chains
  145 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 141
  time to evaluate  : 1.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  412 SER
Chi-restraints excluded: chain B residue  412 SER
Chi-restraints excluded: chain C residue  412 SER
Chi-restraints excluded: chain D residue  412 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    2.9990
   chunk 118 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   chunk 40 optimal weight:    9.9990
   chunk 79 optimal weight:    9.9990
   chunk 63 optimal weight:    1.9990
   chunk 122 optimal weight:    7.9990
   chunk 47 optimal weight:    8.9990
   chunk 74 optimal weight:    3.9990
   chunk 91 optimal weight:    7.9990
   chunk 141 optimal weight:    1.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
D 276 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.183328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.143502 restraints weight = 37249.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 1.27
r_work: 0.3140 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  13332  Z= 0.219
  Angle     :  0.580   6.779  18136  Z= 0.301
  Chirality :  0.042   0.149   1960
  Planarity :  0.005   0.045   2252
  Dihedral  :  8.822  85.302   1980
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 10.09 %
    Favored  : 88.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.47 (0.22), residues: 1552
  helix:  1.29 (0.17), residues: 932
  sheet: -2.44 (0.74), residues: 40
  loop : -1.08 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 255 
 HIS   0.004   0.001   HIS C  60 
 PHE   0.016   0.002   PHE A 384 
 TYR   0.009   0.001   TYR C  48 
 ARG   0.002   0.000   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06620 (  700)
  hydrogen bonds       : angle       4.60788 ( 2016)
  metal coordination   : bond        0.00614 (   12)
  covalent geometry    : bond        0.00533 (13320)
  covalent geometry    : angle       0.57980 (18136)

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

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

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Evaluate side-chains
  153 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 138
  time to evaluate  : 1.827 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 ARG cc_start: 0.8304 (tpp80) cc_final: 0.7764 (ttm-80)
REVERT: A  120 ASP cc_start: 0.5067 (m-30) cc_final: 0.4853 (m-30)
REVERT: A  172 TRP cc_start: 0.7151 (m100) cc_final: 0.6745 (m100)
REVERT: A  262 MET cc_start: 0.8440 (mmp) cc_final: 0.7984 (mmp)
REVERT: A  412 SER cc_start: 0.8764 (OUTLIER) cc_final: 0.8271 (p)
REVERT: B   23 ARG cc_start: 0.8316 (tpp80) cc_final: 0.7769 (ttm-80)
REVERT: B  120 ASP cc_start: 0.5085 (m-30) cc_final: 0.4868 (m-30)
REVERT: B  172 TRP cc_start: 0.6813 (m100) cc_final: 0.6524 (m100)
REVERT: B  412 SER cc_start: 0.8763 (OUTLIER) cc_final: 0.8272 (p)
REVERT: B  447 MET cc_start: 0.8525 (mmm) cc_final: 0.8047 (mmt)
REVERT: C   23 ARG cc_start: 0.8294 (tpp80) cc_final: 0.7731 (ttm-80)
REVERT: C  120 ASP cc_start: 0.5091 (m-30) cc_final: 0.4870 (m-30)
REVERT: C  172 TRP cc_start: 0.6816 (m100) cc_final: 0.6529 (m100)
REVERT: C  412 SER cc_start: 0.8766 (OUTLIER) cc_final: 0.8268 (p)
REVERT: D   23 ARG cc_start: 0.8294 (tpp80) cc_final: 0.7733 (ttm-80)
REVERT: D  120 ASP cc_start: 0.5077 (m-30) cc_final: 0.4862 (m-30)
REVERT: D  172 TRP cc_start: 0.6825 (m100) cc_final: 0.6534 (m100)
REVERT: D  412 SER cc_start: 0.8768 (OUTLIER) cc_final: 0.8274 (p)
  outliers start: 15
  outliers final: 10
  residues processed: 150
  average time/residue: 2.1478
  time to fit residues: 367.8151
Evaluate side-chains
  139 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 1.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ILE
Chi-restraints excluded: chain A residue  412 SER
Chi-restraints excluded: chain B residue   10 ILE
Chi-restraints excluded: chain B residue  293 VAL
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  412 SER
Chi-restraints excluded: chain C residue   10 ILE
Chi-restraints excluded: chain C residue  293 VAL
Chi-restraints excluded: chain C residue  324 LEU
Chi-restraints excluded: chain C residue  412 SER
Chi-restraints excluded: chain D residue   10 ILE
Chi-restraints excluded: chain D residue  293 VAL
Chi-restraints excluded: chain D residue  324 LEU
Chi-restraints excluded: chain D residue  412 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 127 optimal weight:    7.9990
   chunk 34 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 79 optimal weight:    0.0980
   chunk 55 optimal weight:    2.9990
   chunk 84 optimal weight:    5.9990
   chunk 108 optimal weight:    3.9990
   chunk 146 optimal weight:    1.9990
   chunk 113 optimal weight:    0.6980
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
B 276 ASN
D 276 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.184982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.144932 restraints weight = 37217.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.3651 rms_B_bonded: 1.25
r_work: 0.3161 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.2276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  13332  Z= 0.129
  Angle     :  0.483   5.366  18136  Z= 0.245
  Chirality :  0.038   0.134   1960
  Planarity :  0.005   0.041   2252
  Dihedral  :  8.259  88.525   1980
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 1.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 10.63 %
    Favored  : 88.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.72 (0.22), residues: 1552
  helix:  1.55 (0.17), residues: 936
  sheet: -2.26 (0.74), residues: 40
  loop : -1.11 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 255 
 HIS   0.002   0.000   HIS A  60 
 PHE   0.014   0.001   PHE B  56 
 TYR   0.006   0.001   TYR A 407 
 ARG   0.001   0.000   ARG B 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05438 (  700)
  hydrogen bonds       : angle       4.34410 ( 2016)
  metal coordination   : bond        0.00314 (   12)
  covalent geometry    : bond        0.00299 (13320)
  covalent geometry    : angle       0.48300 (18136)

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

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

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Evaluate side-chains
  158 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 142
  time to evaluate  : 3.036 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 ARG cc_start: 0.8286 (tpp80) cc_final: 0.7716 (ttm-80)
REVERT: A  120 ASP cc_start: 0.5077 (m-30) cc_final: 0.4869 (m-30)
REVERT: A  172 TRP cc_start: 0.7153 (m100) cc_final: 0.6793 (m100)
REVERT: A  262 MET cc_start: 0.8425 (mmp) cc_final: 0.8043 (mmp)
REVERT: A  447 MET cc_start: 0.8523 (mmm) cc_final: 0.8110 (mmt)
REVERT: B   23 ARG cc_start: 0.8279 (tpp80) cc_final: 0.7707 (ttm-80)
REVERT: B  120 ASP cc_start: 0.5047 (m-30) cc_final: 0.4839 (m-30)
REVERT: B  262 MET cc_start: 0.8427 (mmp) cc_final: 0.8038 (mmp)
REVERT: B  324 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8145 (mp)
REVERT: C   23 ARG cc_start: 0.8280 (tpp80) cc_final: 0.7704 (ttm-80)
REVERT: C  120 ASP cc_start: 0.5060 (m-30) cc_final: 0.4853 (m-30)
REVERT: C  262 MET cc_start: 0.8435 (mmp) cc_final: 0.8047 (mmp)
REVERT: C  324 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8143 (mp)
REVERT: C  447 MET cc_start: 0.8511 (mmm) cc_final: 0.8106 (mmt)
REVERT: D   23 ARG cc_start: 0.8275 (tpp80) cc_final: 0.7706 (ttm-80)
REVERT: D  120 ASP cc_start: 0.5058 (m-30) cc_final: 0.4845 (m-30)
REVERT: D  262 MET cc_start: 0.8415 (mmp) cc_final: 0.8031 (mmp)
REVERT: D  324 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8150 (mp)
REVERT: D  447 MET cc_start: 0.8506 (mmm) cc_final: 0.8110 (mmt)
  outliers start: 16
  outliers final: 7
  residues processed: 154
  average time/residue: 2.5775
  time to fit residues: 456.3264
Evaluate side-chains
  141 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 1.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ILE
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain B residue   10 ILE
Chi-restraints excluded: chain B residue  293 VAL
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain C residue   10 ILE
Chi-restraints excluded: chain C residue  293 VAL
Chi-restraints excluded: chain C residue  324 LEU
Chi-restraints excluded: chain D residue  293 VAL
Chi-restraints excluded: chain D residue  324 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 6 optimal weight:    6.9990
   chunk 146 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 91 optimal weight:    6.9990
   chunk 36 optimal weight:    0.7980
   chunk 44 optimal weight:    6.9990
   chunk 118 optimal weight:   10.0000
   chunk 39 optimal weight:    7.9990
   chunk 58 optimal weight:    4.9990
   chunk 82 optimal weight:    8.9990
   chunk 89 optimal weight:    9.9990
   overall best weight:    3.5588

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

Flipped N/Q/H residues before XYZ refinement:
C 276 ASN
D 276 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.181727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.139563 restraints weight = 37471.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3591 rms_B_bonded: 1.23
r_work: 0.3189 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.2945 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.2637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  13332  Z= 0.249
  Angle     :  0.597   7.153  18136  Z= 0.306
  Chirality :  0.043   0.148   1960
  Planarity :  0.005   0.049   2252
  Dihedral  :  8.320  70.202   1976
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  9.48 %
    Favored  : 89.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.28 (0.21), residues: 1552
  helix:  1.17 (0.17), residues: 940
  sheet: -2.26 (0.72), residues: 40
  loop : -1.29 (0.25), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 392 
 HIS   0.004   0.001   HIS C  60 
 PHE   0.019   0.002   PHE A 384 
 TYR   0.011   0.001   TYR C 365 
 ARG   0.001   0.000   ARG B 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06901 (  700)
  hydrogen bonds       : angle       4.48719 ( 2016)
  metal coordination   : bond        0.00710 (   12)
  covalent geometry    : bond        0.00621 (13320)
  covalent geometry    : angle       0.59656 (18136)

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

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

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Evaluate side-chains
  147 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 1.853 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 ARG cc_start: 0.8362 (tpp80) cc_final: 0.7820 (ttm-80)
REVERT: A  172 TRP cc_start: 0.7149 (m100) cc_final: 0.6806 (m100)
REVERT: A  262 MET cc_start: 0.8563 (mmp) cc_final: 0.8202 (mmp)
REVERT: A  412 SER cc_start: 0.8811 (OUTLIER) cc_final: 0.8356 (p)
REVERT: B   23 ARG cc_start: 0.8368 (tpp80) cc_final: 0.7820 (ttm-80)
REVERT: B  262 MET cc_start: 0.8568 (mmp) cc_final: 0.8182 (mmp)
REVERT: B  324 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8083 (mp)
REVERT: B  412 SER cc_start: 0.8812 (OUTLIER) cc_final: 0.8333 (p)
REVERT: C   23 ARG cc_start: 0.8367 (tpp80) cc_final: 0.7817 (ttm-80)
REVERT: C  262 MET cc_start: 0.8567 (mmp) cc_final: 0.8186 (mmp)
REVERT: C  324 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8085 (mp)
REVERT: C  412 SER cc_start: 0.8808 (OUTLIER) cc_final: 0.8352 (p)
REVERT: D   23 ARG cc_start: 0.8403 (tpp80) cc_final: 0.7847 (ttm-80)
REVERT: D  262 MET cc_start: 0.8564 (mmp) cc_final: 0.8205 (mmp)
REVERT: D  324 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8093 (mp)
REVERT: D  412 SER cc_start: 0.8817 (OUTLIER) cc_final: 0.8357 (p)
  outliers start: 19
  outliers final: 11
  residues processed: 143
  average time/residue: 1.9779
  time to fit residues: 318.4969
Evaluate side-chains
  135 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 1.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ILE
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain A residue  412 SER
Chi-restraints excluded: chain B residue   10 ILE
Chi-restraints excluded: chain B residue  293 VAL
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  412 SER
Chi-restraints excluded: chain C residue   10 ILE
Chi-restraints excluded: chain C residue  293 VAL
Chi-restraints excluded: chain C residue  324 LEU
Chi-restraints excluded: chain C residue  352 LEU
Chi-restraints excluded: chain C residue  412 SER
Chi-restraints excluded: chain D residue  293 VAL
Chi-restraints excluded: chain D residue  324 LEU
Chi-restraints excluded: chain D residue  352 LEU
Chi-restraints excluded: chain D residue  412 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0000
   chunk 79 optimal weight:   10.0000
   chunk 92 optimal weight:    2.9990
   chunk 125 optimal weight:    8.9990
   chunk 7 optimal weight:    0.8980
   chunk 144 optimal weight:    3.9990
   chunk 90 optimal weight:    0.2980
   chunk 143 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 139 optimal weight:    6.9990
   overall best weight:    0.5984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.185933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.145863 restraints weight = 37469.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 1.25
r_work: 0.3239 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3022 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.2622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  13332  Z= 0.097
  Angle     :  0.459   4.421  18136  Z= 0.231
  Chirality :  0.037   0.126   1960
  Planarity :  0.004   0.041   2252
  Dihedral  :  6.750  48.743   1976
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 2.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 10.70 %
    Favored  : 88.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.88 (0.22), residues: 1552
  helix:  1.58 (0.17), residues: 956
  sheet: -1.93 (0.77), residues: 40
  loop : -0.97 (0.26), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 255 
 HIS   0.002   0.000   HIS B 383 
 PHE   0.020   0.001   PHE D  56 
 TYR   0.005   0.001   TYR A 407 
 ARG   0.001   0.000   ARG A 311 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04715 (  700)
  hydrogen bonds       : angle       4.17555 ( 2016)
  metal coordination   : bond        0.00200 (   12)
  covalent geometry    : bond        0.00204 (13320)
  covalent geometry    : angle       0.45852 (18136)

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

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

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Evaluate side-chains
  139 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 1.762 
Fit side-chains
REVERT: A   23 ARG cc_start: 0.8379 (tpp80) cc_final: 0.7813 (ttm-80)
REVERT: A  172 TRP cc_start: 0.7038 (m100) cc_final: 0.6789 (m100)
REVERT: A  447 MET cc_start: 0.8674 (mmm) cc_final: 0.8392 (mmt)
REVERT: B   23 ARG cc_start: 0.8369 (tpp80) cc_final: 0.7796 (ttm-80)
REVERT: B  324 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8084 (mp)
REVERT: B  447 MET cc_start: 0.8657 (mmm) cc_final: 0.8362 (mmt)
REVERT: C   23 ARG cc_start: 0.8373 (tpp80) cc_final: 0.7795 (ttm-80)
REVERT: C  324 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8080 (mp)
REVERT: D  324 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8089 (mp)
REVERT: D  447 MET cc_start: 0.8651 (mmm) cc_final: 0.8359 (mmt)
  outliers start: 16
  outliers final: 8
  residues processed: 135
  average time/residue: 2.0404
  time to fit residues: 308.9544
Evaluate side-chains
  132 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 121
  time to evaluate  : 1.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain B residue  293 VAL
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain C residue  293 VAL
Chi-restraints excluded: chain C residue  324 LEU
Chi-restraints excluded: chain C residue  352 LEU
Chi-restraints excluded: chain D residue  293 VAL
Chi-restraints excluded: chain D residue  324 LEU
Chi-restraints excluded: chain D residue  352 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 132 optimal weight:    1.9990
   chunk 150 optimal weight:    1.9990
   chunk 148 optimal weight:    0.4980
   chunk 42 optimal weight:    8.9990
   chunk 98 optimal weight:    0.9980
   chunk 125 optimal weight:    8.9990
   chunk 107 optimal weight:    1.9990
   chunk 130 optimal weight:    7.9990
   chunk 76 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    1.4986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.184803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.141759 restraints weight = 37335.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 1.33
r_work: 0.3159 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2973 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.2676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  13332  Z= 0.130
  Angle     :  0.490   4.995  18136  Z= 0.246
  Chirality :  0.038   0.128   1960
  Planarity :  0.004   0.041   2252
  Dihedral  :  6.424  50.227   1976
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 2.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 11.31 %
    Favored  : 87.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.94 (0.22), residues: 1552
  helix:  1.61 (0.17), residues: 956
  sheet: -1.75 (0.79), residues: 40
  loop : -0.93 (0.27), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 392 
 HIS   0.002   0.000   HIS D  60 
 PHE   0.016   0.001   PHE D  56 
 TYR   0.007   0.001   TYR C 365 
 ARG   0.001   0.000   ARG B 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05204 (  700)
  hydrogen bonds       : angle       4.13341 ( 2016)
  metal coordination   : bond        0.00319 (   12)
  covalent geometry    : bond        0.00304 (13320)
  covalent geometry    : angle       0.49048 (18136)

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

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

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Evaluate side-chains
  147 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 2.111 
Fit side-chains
REVERT: A   23 ARG cc_start: 0.8301 (tpp80) cc_final: 0.7738 (ttm-80)
REVERT: A  172 TRP cc_start: 0.6976 (m100) cc_final: 0.6753 (m100)
REVERT: A  447 MET cc_start: 0.8572 (mmm) cc_final: 0.8244 (mmt)
REVERT: B   23 ARG cc_start: 0.8310 (tpp80) cc_final: 0.7740 (ttm-80)
REVERT: B  324 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8091 (mp)
REVERT: B  447 MET cc_start: 0.8566 (mmm) cc_final: 0.8226 (mmt)
REVERT: C   23 ARG cc_start: 0.8301 (tpp80) cc_final: 0.7725 (ttm-80)
REVERT: C  324 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8091 (mp)
REVERT: C  447 MET cc_start: 0.8578 (mmm) cc_final: 0.8349 (mmt)
REVERT: D  324 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8094 (mp)
REVERT: D  447 MET cc_start: 0.8553 (mmm) cc_final: 0.8219 (mmt)
  outliers start: 19
  outliers final: 12
  residues processed: 139
  average time/residue: 2.3801
  time to fit residues: 374.7171
Evaluate side-chains
  144 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 1.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain B residue  293 VAL
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  430 MET
Chi-restraints excluded: chain C residue  293 VAL
Chi-restraints excluded: chain C residue  324 LEU
Chi-restraints excluded: chain C residue  352 LEU
Chi-restraints excluded: chain C residue  430 MET
Chi-restraints excluded: chain D residue  293 VAL
Chi-restraints excluded: chain D residue  324 LEU
Chi-restraints excluded: chain D residue  352 LEU
Chi-restraints excluded: chain D residue  430 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 45 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   chunk 132 optimal weight:    1.9990
   chunk 129 optimal weight:    0.9980
   chunk 155 optimal weight:   10.0000
   chunk 122 optimal weight:    7.9990
   chunk 121 optimal weight:    7.9990
   chunk 125 optimal weight:    0.7980
   chunk 117 optimal weight:    2.9990
   overall best weight:    1.2984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.185505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.145195 restraints weight = 37255.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3653 rms_B_bonded: 1.42
r_work: 0.3154 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.2759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  13332  Z= 0.117
  Angle     :  0.480   4.574  18136  Z= 0.242
  Chirality :  0.038   0.125   1960
  Planarity :  0.004   0.041   2252
  Dihedral  :  6.256  49.294   1976
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 2.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 12.46 %
    Favored  : 86.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.11 (0.22), residues: 1552
  helix:  1.68 (0.17), residues: 956
  sheet:  None (None), residues: 0
  loop : -0.83 (0.26), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 392 
 HIS   0.002   0.000   HIS A  60 
 PHE   0.016   0.001   PHE C  56 
 TYR   0.006   0.001   TYR C  48 
 ARG   0.001   0.000   ARG C 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04980 (  700)
  hydrogen bonds       : angle       4.04687 ( 2016)
  metal coordination   : bond        0.00269 (   12)
  covalent geometry    : bond        0.00270 (13320)
  covalent geometry    : angle       0.48045 (18136)

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

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

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Evaluate side-chains
  146 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 1.754 
Fit side-chains
REVERT: A   23 ARG cc_start: 0.8362 (tpp80) cc_final: 0.7782 (ttm-80)
REVERT: A  447 MET cc_start: 0.8634 (mmm) cc_final: 0.8348 (mmt)
REVERT: B   23 ARG cc_start: 0.8350 (tpp80) cc_final: 0.7764 (ttm-80)
REVERT: B  324 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8076 (mp)
REVERT: B  447 MET cc_start: 0.8628 (mmm) cc_final: 0.8330 (mmt)
REVERT: C   23 ARG cc_start: 0.8352 (tpp80) cc_final: 0.7764 (ttm-80)
REVERT: C  324 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8074 (mp)
REVERT: D  324 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8078 (mp)
REVERT: D  447 MET cc_start: 0.8614 (mmm) cc_final: 0.8318 (mmt)
  outliers start: 15
  outliers final: 12
  residues processed: 138
  average time/residue: 2.1263
  time to fit residues: 326.9841
Evaluate side-chains
  146 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 1.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain B residue  293 VAL
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  430 MET
Chi-restraints excluded: chain C residue  293 VAL
Chi-restraints excluded: chain C residue  324 LEU
Chi-restraints excluded: chain C residue  352 LEU
Chi-restraints excluded: chain C residue  430 MET
Chi-restraints excluded: chain D residue  293 VAL
Chi-restraints excluded: chain D residue  324 LEU
Chi-restraints excluded: chain D residue  352 LEU
Chi-restraints excluded: chain D residue  430 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 104 optimal weight:    2.9990
   chunk 147 optimal weight:    3.9990
   chunk 120 optimal weight:    6.9990
   chunk 115 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 61 optimal weight:    6.9990
   chunk 99 optimal weight:    2.9990
   chunk 125 optimal weight:    6.9990
   chunk 151 optimal weight:    0.7980
   chunk 144 optimal weight:    1.9990
   overall best weight:    2.1588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.183931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.141404 restraints weight = 37279.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 1.31
r_work: 0.3125 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
moved from start:          0.2834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13332  Z= 0.161
  Angle     :  0.518   5.558  18136  Z= 0.262
  Chirality :  0.039   0.126   1960
  Planarity :  0.005   0.042   2252
  Dihedral  :  6.635  53.322   1976
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 2.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 12.84 %
    Favored  : 86.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.95 (0.22), residues: 1552
  helix:  1.64 (0.17), residues: 940
  sheet:  None (None), residues: 0
  loop : -0.98 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 392 
 HIS   0.003   0.001   HIS C  60 
 PHE   0.015   0.001   PHE B 384 
 TYR   0.008   0.001   TYR D 365 
 ARG   0.001   0.000   ARG C 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05647 (  700)
  hydrogen bonds       : angle       4.09144 ( 2016)
  metal coordination   : bond        0.00441 (   12)
  covalent geometry    : bond        0.00389 (13320)
  covalent geometry    : angle       0.51833 (18136)

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

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

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Evaluate side-chains
  146 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 1.824 
Fit side-chains
REVERT: A   23 ARG cc_start: 0.8322 (tpp80) cc_final: 0.7752 (ttm-80)
REVERT: A  447 MET cc_start: 0.8546 (mmm) cc_final: 0.8216 (mmt)
REVERT: B   23 ARG cc_start: 0.8327 (tpp80) cc_final: 0.7753 (ttm-80)
REVERT: B  324 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8081 (mp)
REVERT: B  447 MET cc_start: 0.8528 (mmm) cc_final: 0.8191 (mmt)
REVERT: C   23 ARG cc_start: 0.8334 (tpp80) cc_final: 0.7760 (ttm-80)
REVERT: C  324 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8081 (mp)
REVERT: D  324 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8083 (mp)
REVERT: D  447 MET cc_start: 0.8531 (mmm) cc_final: 0.8202 (mmt)
  outliers start: 15
  outliers final: 12
  residues processed: 138
  average time/residue: 2.1565
  time to fit residues: 331.2291
Evaluate side-chains
  144 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 1.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain B residue  293 VAL
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  430 MET
Chi-restraints excluded: chain C residue  293 VAL
Chi-restraints excluded: chain C residue  324 LEU
Chi-restraints excluded: chain C residue  352 LEU
Chi-restraints excluded: chain C residue  430 MET
Chi-restraints excluded: chain D residue  293 VAL
Chi-restraints excluded: chain D residue  324 LEU
Chi-restraints excluded: chain D residue  352 LEU
Chi-restraints excluded: chain D residue  430 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 45 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   chunk 94 optimal weight:    3.9990
   chunk 148 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 64 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 105 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    1.5588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.185007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.144696 restraints weight = 37350.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 1.27
r_work: 0.3172 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3015 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.2883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  13332  Z= 0.129
  Angle     :  0.490   4.616  18136  Z= 0.246
  Chirality :  0.038   0.124   1960
  Planarity :  0.005   0.041   2252
  Dihedral  :  6.483  51.103   1976
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 2.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 12.77 %
    Favored  : 85.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.11 (0.22), residues: 1552
  helix:  1.66 (0.17), residues: 956
  sheet:  None (None), residues: 0
  loop : -0.78 (0.26), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 255 
 HIS   0.003   0.000   HIS A  60 
 PHE   0.013   0.001   PHE A  93 
 TYR   0.006   0.001   TYR A 365 
 ARG   0.001   0.000   ARG C 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05184 (  700)
  hydrogen bonds       : angle       4.03035 ( 2016)
  metal coordination   : bond        0.00338 (   12)
  covalent geometry    : bond        0.00301 (13320)
  covalent geometry    : angle       0.48971 (18136)

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

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

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Evaluate side-chains
  154 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 137
  time to evaluate  : 1.843 
Fit side-chains
REVERT: A   23 ARG cc_start: 0.8366 (tpp80) cc_final: 0.7815 (ttm-80)
REVERT: A  447 MET cc_start: 0.8614 (mmm) cc_final: 0.8312 (mmt)
REVERT: B   23 ARG cc_start: 0.8377 (tpp80) cc_final: 0.7811 (ttm-80)
REVERT: B  324 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8060 (mp)
REVERT: B  447 MET cc_start: 0.8588 (mmm) cc_final: 0.8275 (mmt)
REVERT: C   23 ARG cc_start: 0.8368 (tpp80) cc_final: 0.7800 (ttm-80)
REVERT: C  324 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8064 (mp)
REVERT: D  324 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8062 (mp)
REVERT: D  447 MET cc_start: 0.8598 (mmm) cc_final: 0.8288 (mmt)
  outliers start: 17
  outliers final: 12
  residues processed: 144
  average time/residue: 2.0921
  time to fit residues: 337.8324
Evaluate side-chains
  149 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 134
  time to evaluate  : 1.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain B residue  293 VAL
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  430 MET
Chi-restraints excluded: chain C residue  293 VAL
Chi-restraints excluded: chain C residue  324 LEU
Chi-restraints excluded: chain C residue  352 LEU
Chi-restraints excluded: chain C residue  430 MET
Chi-restraints excluded: chain D residue  293 VAL
Chi-restraints excluded: chain D residue  324 LEU
Chi-restraints excluded: chain D residue  352 LEU
Chi-restraints excluded: chain D residue  430 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 5 optimal weight:    7.9990
   chunk 54 optimal weight:    2.9990
   chunk 115 optimal weight:    3.9990
   chunk 107 optimal weight:    0.5980
   chunk 104 optimal weight:    0.5980
   chunk 3 optimal weight:    9.9990
   chunk 151 optimal weight:    0.9990
   chunk 144 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 140 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.6386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.184798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.144106 restraints weight = 37216.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 1.22
r_work: 0.3159 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.2903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  13332  Z= 0.135
  Angle     :  0.497   4.811  18136  Z= 0.250
  Chirality :  0.038   0.124   1960
  Planarity :  0.005   0.041   2252
  Dihedral  :  6.512  51.077   1976
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 13.00 %
    Favored  : 85.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.06 (0.22), residues: 1552
  helix:  1.74 (0.18), residues: 928
  sheet:  None (None), residues: 0
  loop : -0.92 (0.25), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 392 
 HIS   0.003   0.000   HIS B  60 
 PHE   0.013   0.001   PHE A 384 
 TYR   0.006   0.001   TYR B 365 
 ARG   0.001   0.000   ARG C 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05259 (  700)
  hydrogen bonds       : angle       4.02151 ( 2016)
  metal coordination   : bond        0.00347 (   12)
  covalent geometry    : bond        0.00318 (13320)
  covalent geometry    : angle       0.49694 (18136)

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

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

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Residue TYR  235 is missing expected H atoms. Skipping.
Residue TYR  236 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue LYS  454 is missing expected H atoms. Skipping.
Residue LYS  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue LYS  457 is missing expected H atoms. Skipping.
Evaluate side-chains
  154 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 138
  time to evaluate  : 1.839 
Fit side-chains
REVERT: A  447 MET cc_start: 0.8534 (mmm) cc_final: 0.8226 (mmt)
REVERT: B   23 ARG cc_start: 0.8335 (tpp80) cc_final: 0.7763 (ttm-80)
REVERT: B  324 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8043 (mp)
REVERT: B  447 MET cc_start: 0.8529 (mmm) cc_final: 0.8211 (mmt)
REVERT: C   23 ARG cc_start: 0.8325 (tpp80) cc_final: 0.7747 (ttm-80)
REVERT: C  324 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8045 (mp)
REVERT: D  324 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8054 (mp)
REVERT: D  447 MET cc_start: 0.8514 (mmm) cc_final: 0.8200 (mmt)
  outliers start: 16
  outliers final: 12
  residues processed: 145
  average time/residue: 2.0929
  time to fit residues: 340.0146
Evaluate side-chains
  152 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 137
  time to evaluate  : 1.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain B residue  293 VAL
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  430 MET
Chi-restraints excluded: chain C residue  293 VAL
Chi-restraints excluded: chain C residue  324 LEU
Chi-restraints excluded: chain C residue  352 LEU
Chi-restraints excluded: chain C residue  430 MET
Chi-restraints excluded: chain D residue  293 VAL
Chi-restraints excluded: chain D residue  324 LEU
Chi-restraints excluded: chain D residue  352 LEU
Chi-restraints excluded: chain D residue  430 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 5 optimal weight:    7.9990
   chunk 126 optimal weight:    2.9990
   chunk 144 optimal weight:    0.9990
   chunk 125 optimal weight:    6.9990
   chunk 77 optimal weight:   10.0000
   chunk 96 optimal weight:    2.9990
   chunk 122 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 88 optimal weight:    6.9990
   chunk 135 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    1.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.184251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.141449 restraints weight = 37189.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 1.28
r_work: 0.3158 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.2942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  13332  Z= 0.153
  Angle     :  0.514   5.338  18136  Z= 0.259
  Chirality :  0.039   0.124   1960
  Planarity :  0.005   0.042   2252
  Dihedral  :  6.685  52.166   1976
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 2.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 13.30 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.99 (0.22), residues: 1552
  helix:  1.69 (0.18), residues: 928
  sheet:  None (None), residues: 0
  loop : -0.94 (0.25), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 392 
 HIS   0.003   0.000   HIS C  60 
 PHE   0.015   0.001   PHE D 384 
 TYR   0.007   0.001   TYR C 365 
 ARG   0.001   0.000   ARG C 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05501 (  700)
  hydrogen bonds       : angle       4.04304 ( 2016)
  metal coordination   : bond        0.00414 (   12)
  covalent geometry    : bond        0.00368 (13320)
  covalent geometry    : angle       0.51436 (18136)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 15931.22 seconds
wall clock time: 278 minutes 48.50 seconds (16728.50 seconds total)