Starting phenix.real_space_refine
on Sat Jun 14 13:50:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f2k_50149/06_2025/9f2k_50149_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f2k_50149/06_2025/9f2k_50149.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.48
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9f2k_50149/06_2025/9f2k_50149.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f2k_50149/06_2025/9f2k_50149.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f2k_50149/06_2025/9f2k_50149_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f2k_50149/06_2025/9f2k_50149_neut.cif"
  }
  resolution = 2.48
  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=  -0.001 sd=   0.035
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       8      5.49       5
     S      72      5.16       5
     C   10220      2.51       5
     N    2788      2.21       5
     O    3096      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 16184
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4002
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 513, 3986
          Classifications: {'peptide': 513}
          Link IDs: {'PTRANS': 24, 'TRANS': 488}
      Conformer: "B"
        Number of residues, atoms: 513, 3986
          Classifications: {'peptide': 513}
          Link IDs: {'PTRANS': 24, 'TRANS': 488}
          bond proxies already assigned to first conformer: 4049
    Chain: "A"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'NAD': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C, B, D
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N  AHIS A 167 " occ=0.75
      ... (18 atoms not shown)
      pdb=" NE2BHIS A 167 " occ=0.25
    residue:
      pdb=" N  AHIS B 167 " occ=0.75
      ... (18 atoms not shown)
      pdb=" NE2BHIS B 167 " occ=0.25
    residue:
      pdb=" N  AHIS C 167 " occ=0.75
      ... (18 atoms not shown)
      pdb=" NE2BHIS C 167 " occ=0.25
    residue:
      pdb=" N  AHIS D 167 " occ=0.75
      ... (18 atoms not shown)
      pdb=" NE2BHIS D 167 " occ=0.25
  Time building chain proxies: 12.09, per 1000 atoms: 0.75
  Number of scatterers: 16184
  At special positions: 0
  Unit cell: (105.61, 136.29, 99.71, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      72     16.00
     P       8     15.00
     O    3096      8.00
     N    2788      7.00
     C   10220      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.82
  Conformation dependent library (CDL) restraints added in 3.6 seconds
  

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3832

  Finding SS restraints...
    Secondary structure from input PDB file:
      80 helices and 20 sheets defined
      41.1% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 103 through 119
    Processing helix  chain 'A' and resid 136 through 141
    Processing helix  chain 'A' and resid 160 through 162
      No H-bonds generated for 'chain 'A' and resid 160 through 162'
    Processing helix  chain 'A' and resid 167 through 171
    Processing helix  chain 'A' and resid 182 through 191
    Processing helix  chain 'A' and resid 194 through 206
      removed outlier: 3.541A  pdb=" N   LEU A 200 " --> pdb=" O   SER A 196 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   LYS A 203 " --> pdb=" O   ALA A 199 " (cutoff:3.500A)
      removed outlier: 5.338A  pdb=" N   GLU A 204 " --> pdb=" O   LEU A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 225
      removed outlier: 3.702A  pdb=" N   GLU A 225 " --> pdb=" O   ALA A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 257
      removed outlier: 3.969A  pdb=" N   VAL A 242 " --> pdb=" O   CYS A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 293
      removed outlier: 3.599A  pdb=" N   LYS A 291 " --> pdb=" O   LEU A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 311
    Processing helix  chain 'A' and resid 326 through 335
    Processing helix  chain 'A' and resid 346 through 360
      removed outlier: 3.509A  pdb=" N   ASP A 356 " --> pdb=" O   SER A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 382
    Processing helix  chain 'A' and resid 384 through 397
      removed outlier: 4.377A  pdb=" N   SER A 390 " --> pdb=" O   ARG A 386 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LYS A 391 " --> pdb=" O   GLN A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 406
      removed outlier: 3.555A  pdb=" N   ASN A 406 " --> pdb=" O   MET A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 445
      No H-bonds generated for 'chain 'A' and resid 443 through 445'
    Processing helix  chain 'A' and resid 458 through 477
      Proline residue:  A 464  - end of helix
    Processing helix  chain 'A' and resid 489 through 493
      removed outlier: 3.533A  pdb=" N   TRP A 493 " --> pdb=" O   GLU A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 507
      removed outlier: 3.719A  pdb=" N   LEU A 503 " --> pdb=" O   LEU A 500 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   TYR A 505 " --> pdb=" O   ILE A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 521 through 536
    Processing helix  chain 'B' and resid 103 through 119
    Processing helix  chain 'B' and resid 136 through 141
    Processing helix  chain 'B' and resid 160 through 162
      No H-bonds generated for 'chain 'B' and resid 160 through 162'
    Processing helix  chain 'B' and resid 167 through 171
    Processing helix  chain 'B' and resid 182 through 191
    Processing helix  chain 'B' and resid 194 through 206
      removed outlier: 3.541A  pdb=" N   LEU B 200 " --> pdb=" O   SER B 196 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   LYS B 203 " --> pdb=" O   ALA B 199 " (cutoff:3.500A)
      removed outlier: 5.338A  pdb=" N   GLU B 204 " --> pdb=" O   LEU B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 225
      removed outlier: 3.702A  pdb=" N   GLU B 225 " --> pdb=" O   ALA B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 257
      removed outlier: 3.969A  pdb=" N   VAL B 242 " --> pdb=" O   CYS B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 293
      removed outlier: 3.599A  pdb=" N   LYS B 291 " --> pdb=" O   LEU B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 311
    Processing helix  chain 'B' and resid 326 through 335
    Processing helix  chain 'B' and resid 346 through 360
      removed outlier: 3.509A  pdb=" N   ASP B 356 " --> pdb=" O   SER B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 382
    Processing helix  chain 'B' and resid 384 through 397
      removed outlier: 4.377A  pdb=" N   SER B 390 " --> pdb=" O   ARG B 386 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LYS B 391 " --> pdb=" O   GLN B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 406
      removed outlier: 3.555A  pdb=" N   ASN B 406 " --> pdb=" O   MET B 402 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 445
      No H-bonds generated for 'chain 'B' and resid 443 through 445'
    Processing helix  chain 'B' and resid 458 through 477
      Proline residue:  B 464  - end of helix
    Processing helix  chain 'B' and resid 489 through 493
      removed outlier: 3.533A  pdb=" N   TRP B 493 " --> pdb=" O   GLU B 490 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 500 through 507
      removed outlier: 3.719A  pdb=" N   LEU B 503 " --> pdb=" O   LEU B 500 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   TYR B 505 " --> pdb=" O   ILE B 502 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 521 through 536
    Processing helix  chain 'C' and resid 103 through 119
    Processing helix  chain 'C' and resid 136 through 141
    Processing helix  chain 'C' and resid 160 through 162
      No H-bonds generated for 'chain 'C' and resid 160 through 162'
    Processing helix  chain 'C' and resid 167 through 171
    Processing helix  chain 'C' and resid 182 through 191
    Processing helix  chain 'C' and resid 194 through 206
      removed outlier: 3.541A  pdb=" N   LEU C 200 " --> pdb=" O   SER C 196 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   LYS C 203 " --> pdb=" O   ALA C 199 " (cutoff:3.500A)
      removed outlier: 5.338A  pdb=" N   GLU C 204 " --> pdb=" O   LEU C 200 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 221 through 225
      removed outlier: 3.702A  pdb=" N   GLU C 225 " --> pdb=" O   ALA C 222 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 238 through 257
      removed outlier: 3.969A  pdb=" N   VAL C 242 " --> pdb=" O   CYS C 238 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 282 through 293
      removed outlier: 3.599A  pdb=" N   LYS C 291 " --> pdb=" O   LEU C 287 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 311
    Processing helix  chain 'C' and resid 326 through 335
    Processing helix  chain 'C' and resid 346 through 360
      removed outlier: 3.509A  pdb=" N   ASP C 356 " --> pdb=" O   SER C 352 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 376 through 382
    Processing helix  chain 'C' and resid 384 through 397
      removed outlier: 4.377A  pdb=" N   SER C 390 " --> pdb=" O   ARG C 386 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LYS C 391 " --> pdb=" O   GLN C 387 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 399 through 406
      removed outlier: 3.555A  pdb=" N   ASN C 406 " --> pdb=" O   MET C 402 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 443 through 445
      No H-bonds generated for 'chain 'C' and resid 443 through 445'
    Processing helix  chain 'C' and resid 458 through 477
      Proline residue:  C 464  - end of helix
    Processing helix  chain 'C' and resid 489 through 493
      removed outlier: 3.533A  pdb=" N   TRP C 493 " --> pdb=" O   GLU C 490 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 500 through 507
      removed outlier: 3.719A  pdb=" N   LEU C 503 " --> pdb=" O   LEU C 500 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   TYR C 505 " --> pdb=" O   ILE C 502 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 521 through 536
    Processing helix  chain 'D' and resid 103 through 119
    Processing helix  chain 'D' and resid 136 through 141
    Processing helix  chain 'D' and resid 160 through 162
      No H-bonds generated for 'chain 'D' and resid 160 through 162'
    Processing helix  chain 'D' and resid 167 through 171
    Processing helix  chain 'D' and resid 182 through 191
    Processing helix  chain 'D' and resid 194 through 206
      removed outlier: 3.541A  pdb=" N   LEU D 200 " --> pdb=" O   SER D 196 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   LYS D 203 " --> pdb=" O   ALA D 199 " (cutoff:3.500A)
      removed outlier: 5.338A  pdb=" N   GLU D 204 " --> pdb=" O   LEU D 200 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 221 through 225
      removed outlier: 3.702A  pdb=" N   GLU D 225 " --> pdb=" O   ALA D 222 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 238 through 257
      removed outlier: 3.969A  pdb=" N   VAL D 242 " --> pdb=" O   CYS D 238 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 282 through 293
      removed outlier: 3.599A  pdb=" N   LYS D 291 " --> pdb=" O   LEU D 287 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 298 through 311
    Processing helix  chain 'D' and resid 326 through 335
    Processing helix  chain 'D' and resid 346 through 360
      removed outlier: 3.509A  pdb=" N   ASP D 356 " --> pdb=" O   SER D 352 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 376 through 382
    Processing helix  chain 'D' and resid 384 through 397
      removed outlier: 4.377A  pdb=" N   SER D 390 " --> pdb=" O   ARG D 386 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LYS D 391 " --> pdb=" O   GLN D 387 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 399 through 406
      removed outlier: 3.555A  pdb=" N   ASN D 406 " --> pdb=" O   MET D 402 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 443 through 445
      No H-bonds generated for 'chain 'D' and resid 443 through 445'
    Processing helix  chain 'D' and resid 458 through 477
      Proline residue:  D 464  - end of helix
    Processing helix  chain 'D' and resid 489 through 493
      removed outlier: 3.533A  pdb=" N   TRP D 493 " --> pdb=" O   GLU D 490 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 500 through 507
      removed outlier: 3.719A  pdb=" N   LEU D 503 " --> pdb=" O   LEU D 500 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   TYR D 505 " --> pdb=" O   ILE D 502 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 521 through 536
    Processing sheet with id=1, first strand: chain 'A' and resid 57 through 68
    Processing sheet with id=2, first strand: chain 'A' and resid 172 through 176
    Processing sheet with id=3, first strand: chain 'A' and resid 121 through 124
    Processing sheet with id=4, first strand: chain 'A' and resid 142 through 147
      removed outlier: 5.237A  pdb=" N   LYS A 144 " --> pdb=" O   ILE A 157 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ILE A 157 " --> pdb=" O   LYS A 144 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLY A 146 " --> pdb=" O   ILE A 155 " (cutoff:3.500A)
    Processing sheet with id=5, first strand: chain 'A' and resid 417 through 424
      removed outlier: 5.585A  pdb=" N   LEU A 365 " --> pdb=" O   GLU A 441 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   GLU A 441 " --> pdb=" O   LEU A 365 " (cutoff:3.500A)
    Processing sheet with id=6, first strand: chain 'B' and resid 57 through 68
    Processing sheet with id=7, first strand: chain 'B' and resid 172 through 176
    Processing sheet with id=8, first strand: chain 'B' and resid 121 through 124
    Processing sheet with id=9, first strand: chain 'B' and resid 142 through 147
      removed outlier: 5.237A  pdb=" N   LYS B 144 " --> pdb=" O   ILE B 157 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ILE B 157 " --> pdb=" O   LYS B 144 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLY B 146 " --> pdb=" O   ILE B 155 " (cutoff:3.500A)
    Processing sheet with id=10, first strand: chain 'B' and resid 417 through 424
      removed outlier: 5.585A  pdb=" N   LEU B 365 " --> pdb=" O   GLU B 441 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   GLU B 441 " --> pdb=" O   LEU B 365 " (cutoff:3.500A)
    Processing sheet with id=11, first strand: chain 'C' and resid 57 through 68
    Processing sheet with id=12, first strand: chain 'C' and resid 172 through 176
    Processing sheet with id=13, first strand: chain 'C' and resid 121 through 124
    Processing sheet with id=14, first strand: chain 'C' and resid 142 through 147
      removed outlier: 5.237A  pdb=" N   LYS C 144 " --> pdb=" O   ILE C 157 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ILE C 157 " --> pdb=" O   LYS C 144 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLY C 146 " --> pdb=" O   ILE C 155 " (cutoff:3.500A)
    Processing sheet with id=15, first strand: chain 'C' and resid 417 through 424
      removed outlier: 5.585A  pdb=" N   LEU C 365 " --> pdb=" O   GLU C 441 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   GLU C 441 " --> pdb=" O   LEU C 365 " (cutoff:3.500A)
    Processing sheet with id=16, first strand: chain 'D' and resid 57 through 68
    Processing sheet with id=17, first strand: chain 'D' and resid 172 through 176
    Processing sheet with id=18, first strand: chain 'D' and resid 121 through 124
    Processing sheet with id=19, first strand: chain 'D' and resid 142 through 147
      removed outlier: 5.237A  pdb=" N   LYS D 144 " --> pdb=" O   ILE D 157 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ILE D 157 " --> pdb=" O   LYS D 144 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLY D 146 " --> pdb=" O   ILE D 155 " (cutoff:3.500A)
    Processing sheet with id=20, first strand: chain 'D' and resid 417 through 424
      removed outlier: 5.585A  pdb=" N   LEU D 365 " --> pdb=" O   GLU D 441 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   GLU D 441 " --> pdb=" O   LEU D 365 " (cutoff:3.500A)

    740 hydrogen bonds defined for protein.
    2052 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: 5.11

  Time building geometry restraints manager: 4.53 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 5368
        1.34 -     1.46: 3376
        1.46 -     1.58: 7652
        1.58 -     1.69: 16
        1.69 -     1.81: 128
  Bond restraints: 16540
  Sorted by residual:
  bond pdb=" N   ILE D 109 "
       pdb=" CA  ILE D 109 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.032 1.17e-02 7.31e+03 7.65e+00
  bond pdb=" N   ILE A 109 "
       pdb=" CA  ILE A 109 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.032 1.17e-02 7.31e+03 7.65e+00
  bond pdb=" N   ILE C 109 "
       pdb=" CA  ILE C 109 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.032 1.17e-02 7.31e+03 7.65e+00
  bond pdb=" N   ILE B 109 "
       pdb=" CA  ILE B 109 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.032 1.17e-02 7.31e+03 7.65e+00
  bond pdb=" O3  NAD D 601 "
       pdb=" PA  NAD D 601 "
    ideal  model  delta    sigma   weight residual
    1.653  1.600  0.053 2.00e-02 2.50e+03 7.05e+00
  ... (remaining 16535 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 22004
        1.91 -     3.82: 404
        3.82 -     5.74: 68
        5.74 -     7.65: 12
        7.65 -     9.56: 4
  Bond angle restraints: 22492
  Sorted by residual:
  angle pdb=" PA  NAD A 601 "
        pdb=" O3  NAD A 601 "
        pdb=" PN  NAD A 601 "
      ideal   model   delta    sigma   weight residual
     126.50  136.06   -9.56 3.00e+00 1.11e-01 1.02e+01
  angle pdb=" PA  NAD C 601 "
        pdb=" O3  NAD C 601 "
        pdb=" PN  NAD C 601 "
      ideal   model   delta    sigma   weight residual
     126.50  136.06   -9.56 3.00e+00 1.11e-01 1.02e+01
  angle pdb=" PA  NAD D 601 "
        pdb=" O3  NAD D 601 "
        pdb=" PN  NAD D 601 "
      ideal   model   delta    sigma   weight residual
     126.50  136.06   -9.56 3.00e+00 1.11e-01 1.02e+01
  angle pdb=" PA  NAD B 601 "
        pdb=" O3  NAD B 601 "
        pdb=" PN  NAD B 601 "
      ideal   model   delta    sigma   weight residual
     126.50  136.06   -9.56 3.00e+00 1.11e-01 1.02e+01
  angle pdb=" CA  ILE D 109 "
        pdb=" C   ILE D 109 "
        pdb=" O   ILE D 109 "
      ideal   model   delta    sigma   weight residual
     121.17  118.15    3.02 1.06e+00 8.90e-01 8.14e+00
  ... (remaining 22487 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.56: 8744
       17.56 -    35.13: 988
       35.13 -    52.69: 296
       52.69 -    70.26: 48
       70.26 -    87.82: 20
  Dihedral angle restraints: 10096
    sinusoidal: 4140
      harmonic: 5956
  Sorted by residual:
  dihedral pdb=" CB  GLU A 225 "
           pdb=" CG  GLU A 225 "
           pdb=" CD  GLU A 225 "
           pdb=" OE1 GLU A 225 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.82   87.82     1      3.00e+01 1.11e-03 1.03e+01
  dihedral pdb=" CB  GLU D 225 "
           pdb=" CG  GLU D 225 "
           pdb=" CD  GLU D 225 "
           pdb=" OE1 GLU D 225 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.82   87.82     1      3.00e+01 1.11e-03 1.03e+01
  dihedral pdb=" CB  GLU C 225 "
           pdb=" CG  GLU C 225 "
           pdb=" CD  GLU C 225 "
           pdb=" OE1 GLU C 225 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.82   87.82     1      3.00e+01 1.11e-03 1.03e+01
  ... (remaining 10093 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1968
       0.045 -    0.090: 368
       0.090 -    0.135: 204
       0.135 -    0.179: 0
       0.179 -    0.224: 4
  Chirality restraints: 2544
  Sorted by residual:
  chirality pdb=" CA  ILE D 109 "
            pdb=" N   ILE D 109 "
            pdb=" C   ILE D 109 "
            pdb=" CB  ILE D 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CA  ILE A 109 "
            pdb=" N   ILE A 109 "
            pdb=" C   ILE A 109 "
            pdb=" CB  ILE A 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CA  ILE B 109 "
            pdb=" N   ILE B 109 "
            pdb=" C   ILE B 109 "
            pdb=" CB  ILE B 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.22 2.00e-01 2.50e+01 1.26e+00
  ... (remaining 2541 not shown)

  Planarity restraints: 2896
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR D 110 "    0.011 2.00e-02 2.50e+03   2.17e-02 4.70e+00
        pdb=" C   THR D 110 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   THR D 110 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ALA D 111 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR C 110 "    0.011 2.00e-02 2.50e+03   2.17e-02 4.70e+00
        pdb=" C   THR C 110 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   THR C 110 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ALA C 111 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 110 "   -0.011 2.00e-02 2.50e+03   2.17e-02 4.70e+00
        pdb=" C   THR B 110 "    0.038 2.00e-02 2.50e+03
        pdb=" O   THR B 110 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ALA B 111 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 2893 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 144
        2.60 -     3.18: 13076
        3.18 -     3.75: 25460
        3.75 -     4.33: 38548
        4.33 -     4.90: 62840
  Nonbonded interactions: 140068
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN D 347 "
            pdb=" OD1 ASP D 436 "
     model   vdw
     2.026 3.040
  nonbonded pdb=" OE1 GLN B 347 "
            pdb=" OD1 ASP B 436 "
     model   vdw
     2.026 3.040
  nonbonded pdb=" OE1 GLN C 347 "
            pdb=" OD1 ASP C 436 "
     model   vdw
     2.026 3.040
  nonbonded pdb=" OE1 GLN A 347 "
            pdb=" OD1 ASP A 436 "
     model   vdw
     2.026 3.040
  nonbonded pdb=" OG  SER C 136 "
            pdb=" OD1 ASP C 468 "
     model   vdw
     2.131 3.040
  ... (remaining 140063 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: 0.11
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  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=0.25 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:             10.050
  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:             0.020
  Extract box with map and model:          0.660
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     41.410
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.070
  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:14.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   67.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
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   0.053  16540  Z= 0.200
  Angle     :  0.638   9.559  22492  Z= 0.327
  Chirality :  0.044   0.224   2544
  Planarity :  0.005   0.041   2896
  Dihedral  : 16.420  87.819   6264
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 21.00 %
    Favored  : 77.85 %
  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: -0.09 (0.18), residues: 2060
  helix: -0.22 (0.18), residues: 748
  sheet:  0.88 (0.27), residues: 376
  loop : -0.15 (0.19), residues: 936

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 122 
 HIS   0.003   0.001   HIS C 373 
 PHE   0.008   0.001   PHE D 219 
 TYR   0.006   0.001   TYR A  50 
 ARG   0.002   0.000   ARG A 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16328 (  740)
  hydrogen bonds       : angle       5.98026 ( 2052)
  covalent geometry    : bond        0.00411 (16540)
  covalent geometry    : angle       0.63810 (22492)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 192
  time to evaluate  : 1.714 
Fit side-chains
  outliers start: 20
  outliers final: 20
  residues processed: 208
  average time/residue: 1.3967
  time to fit residues: 321.2174
Evaluate side-chains
  208 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 188
  time to evaluate  : 1.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  260 LYS
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  436 ASP
Chi-restraints excluded: chain A residue  456 CYS
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  260 LYS
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  436 ASP
Chi-restraints excluded: chain B residue  456 CYS
Chi-restraints excluded: chain C residue  196 SER
Chi-restraints excluded: chain C residue  260 LYS
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  436 ASP
Chi-restraints excluded: chain C residue  456 CYS
Chi-restraints excluded: chain D residue  196 SER
Chi-restraints excluded: chain D residue  260 LYS
Chi-restraints excluded: chain D residue  398 VAL
Chi-restraints excluded: chain D residue  436 ASP
Chi-restraints excluded: chain D residue  456 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 172 optimal weight:    1.9990
   chunk 154 optimal weight:    6.9990
   chunk 85 optimal weight:    4.9990
   chunk 52 optimal weight:    6.9990
   chunk 104 optimal weight:    4.9990
   chunk 82 optimal weight:    0.7980
   chunk 159 optimal weight:    0.9980
   chunk 61 optimal weight:    6.9990
   chunk 97 optimal weight:    5.9990
   chunk 119 optimal weight:    3.9990
   chunk 185 optimal weight:    6.9990
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 288 ASN
A 316 ASN
A 347 GLN
A 372 ASN
B 288 ASN
B 316 ASN
B 347 GLN
B 372 ASN
C 288 ASN
C 316 ASN
C 347 GLN
C 372 ASN
D 288 ASN
D 316 ASN
D 347 GLN
D 372 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.160113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.141616 restraints weight = 53398.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 2.26
r_work: 0.3515 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3407 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3404
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3404 r_free = 0.3404    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3404 r_free = 0.3404    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3404
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062  16540  Z= 0.256
  Angle     :  0.713   8.113  22492  Z= 0.380
  Chirality :  0.049   0.208   2544
  Planarity :  0.006   0.040   2896
  Dihedral  :  9.126  57.904   2464
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 17.12 %
    Favored  : 79.91 %
  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:  0.27 (0.18), residues: 2060
  helix:  0.12 (0.18), residues: 728
  sheet:  1.04 (0.26), residues: 392
  loop :  0.02 (0.20), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D 101 
 HIS   0.008   0.002   HIS B 549 
 PHE   0.015   0.002   PHE D 552 
 TYR   0.013   0.002   TYR B 134 
 ARG   0.004   0.001   ARG D 482 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06236 (  740)
  hydrogen bonds       : angle       5.16422 ( 2052)
  covalent geometry    : bond        0.00584 (16540)
  covalent geometry    : angle       0.71253 (22492)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 192
  time to evaluate  : 1.931 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7900 (mpt180)
REVERT: A  125 ARG cc_start: 0.7364 (ptm-80) cc_final: 0.7159 (ptm-80)
REVERT: A  223 ASN cc_start: 0.8003 (p0) cc_final: 0.7698 (p0)
REVERT: A  432 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.7969 (tmmm)
REVERT: A  490 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7168 (mp0)
REVERT: B   79 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7883 (mpt180)
REVERT: B  125 ARG cc_start: 0.7373 (ptm-80) cc_final: 0.7165 (ptm-80)
REVERT: B  223 ASN cc_start: 0.8017 (p0) cc_final: 0.7681 (p0)
REVERT: B  432 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.7983 (tmmm)
REVERT: B  490 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7140 (mp0)
REVERT: C   79 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7899 (mpt180)
REVERT: C  125 ARG cc_start: 0.7361 (ptm-80) cc_final: 0.7158 (ptm-80)
REVERT: C  223 ASN cc_start: 0.8002 (p0) cc_final: 0.7695 (p0)
REVERT: C  432 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.7970 (tmmm)
REVERT: C  490 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7166 (mp0)
REVERT: D   79 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7889 (mpt180)
REVERT: D  125 ARG cc_start: 0.7369 (ptm-80) cc_final: 0.7161 (ptm-80)
REVERT: D  223 ASN cc_start: 0.8015 (p0) cc_final: 0.7685 (p0)
REVERT: D  432 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.7975 (tmmm)
REVERT: D  490 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7143 (mp0)
  outliers start: 52
  outliers final: 20
  residues processed: 236
  average time/residue: 1.4201
  time to fit residues: 369.2819
Evaluate side-chains
  196 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 164
  time to evaluate  : 1.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  432 LYS
Chi-restraints excluded: chain A residue  456 CYS
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  490 GLU
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  432 LYS
Chi-restraints excluded: chain B residue  456 CYS
Chi-restraints excluded: chain B residue  489 THR
Chi-restraints excluded: chain B residue  490 GLU
Chi-restraints excluded: chain C residue   79 ARG
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  432 LYS
Chi-restraints excluded: chain C residue  456 CYS
Chi-restraints excluded: chain C residue  489 THR
Chi-restraints excluded: chain C residue  490 GLU
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue  354 LEU
Chi-restraints excluded: chain D residue  370 SER
Chi-restraints excluded: chain D residue  398 VAL
Chi-restraints excluded: chain D residue  432 LYS
Chi-restraints excluded: chain D residue  456 CYS
Chi-restraints excluded: chain D residue  489 THR
Chi-restraints excluded: chain D residue  490 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 175 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 108 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 201 optimal weight:    3.9990
   chunk 185 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 17 optimal weight:    5.9990
   chunk 143 optimal weight:    1.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 288 ASN
A 387 GLN
B 288 ASN
B 387 GLN
C 288 ASN
C 387 GLN
D 288 ASN
D 387 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.160765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.142050 restraints weight = 51061.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 2.23
r_work: 0.3516 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3409 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3406
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3406 r_free = 0.3406    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3406 r_free = 0.3406    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3406
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.1980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  16540  Z= 0.215
  Angle     :  0.651   8.066  22492  Z= 0.347
  Chirality :  0.047   0.167   2544
  Planarity :  0.005   0.040   2896
  Dihedral  :  8.910  59.629   2436
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 15.07 %
    Favored  : 80.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.38 (0.18), residues: 2060
  helix:  0.33 (0.18), residues: 728
  sheet:  0.96 (0.24), residues: 432
  loop : -0.02 (0.20), residues: 900

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C 176 
 HIS   0.006   0.002   HIS C 549 
 PHE   0.013   0.002   PHE D 552 
 TYR   0.009   0.002   TYR D 134 
 ARG   0.003   0.001   ARG A 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05533 (  740)
  hydrogen bonds       : angle       5.03369 ( 2052)
  covalent geometry    : bond        0.00493 (16540)
  covalent geometry    : angle       0.65065 (22492)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 184
  time to evaluate  : 1.922 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7870 (mpt180)
REVERT: A  125 ARG cc_start: 0.7366 (ptm-80) cc_final: 0.7159 (ptm-80)
REVERT: A  194 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7267 (mm-30)
REVERT: A  218 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7308 (p0)
REVERT: A  240 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6556 (mm-30)
REVERT: A  432 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.7996 (tmmm)
REVERT: A  490 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7241 (mp0)
REVERT: B   79 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7867 (mpt180)
REVERT: B  125 ARG cc_start: 0.7372 (ptm-80) cc_final: 0.7159 (ptm-80)
REVERT: B  194 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7257 (mm-30)
REVERT: B  218 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7311 (p0)
REVERT: B  240 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6565 (mm-30)
REVERT: B  432 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8015 (tmmm)
REVERT: B  490 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7231 (mp0)
REVERT: C   79 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7866 (mpt180)
REVERT: C  125 ARG cc_start: 0.7364 (ptm-80) cc_final: 0.7155 (ptm-80)
REVERT: C  218 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7310 (p0)
REVERT: C  240 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6568 (mm-30)
REVERT: C  432 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.7985 (tmmm)
REVERT: C  490 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7239 (mp0)
REVERT: D   79 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7878 (mpt180)
REVERT: D  125 ARG cc_start: 0.7367 (ptm-80) cc_final: 0.7155 (ptm-80)
REVERT: D  194 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7262 (mm-30)
REVERT: D  218 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7318 (p0)
REVERT: D  240 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6577 (mm-30)
REVERT: D  432 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8002 (tmmm)
REVERT: D  490 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7231 (mp0)
  outliers start: 76
  outliers final: 28
  residues processed: 240
  average time/residue: 1.4326
  time to fit residues: 378.0492
Evaluate side-chains
  228 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 177
  time to evaluate  : 1.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  194 GLU
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  432 LYS
Chi-restraints excluded: chain A residue  456 CYS
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  490 GLU
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue  187 MET
Chi-restraints excluded: chain B residue  194 GLU
Chi-restraints excluded: chain B residue  218 ASP
Chi-restraints excluded: chain B residue  240 GLU
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  432 LYS
Chi-restraints excluded: chain B residue  456 CYS
Chi-restraints excluded: chain B residue  489 THR
Chi-restraints excluded: chain B residue  490 GLU
Chi-restraints excluded: chain C residue   79 ARG
Chi-restraints excluded: chain C residue  187 MET
Chi-restraints excluded: chain C residue  218 ASP
Chi-restraints excluded: chain C residue  240 GLU
Chi-restraints excluded: chain C residue  264 LEU
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  432 LYS
Chi-restraints excluded: chain C residue  456 CYS
Chi-restraints excluded: chain C residue  489 THR
Chi-restraints excluded: chain C residue  490 GLU
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue  187 MET
Chi-restraints excluded: chain D residue  194 GLU
Chi-restraints excluded: chain D residue  218 ASP
Chi-restraints excluded: chain D residue  240 GLU
Chi-restraints excluded: chain D residue  264 LEU
Chi-restraints excluded: chain D residue  354 LEU
Chi-restraints excluded: chain D residue  370 SER
Chi-restraints excluded: chain D residue  398 VAL
Chi-restraints excluded: chain D residue  432 LYS
Chi-restraints excluded: chain D residue  456 CYS
Chi-restraints excluded: chain D residue  489 THR
Chi-restraints excluded: chain D residue  490 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 191 optimal weight:    3.9990
   chunk 127 optimal weight:    0.9990
   chunk 174 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 55 optimal weight:    5.9990
   chunk 168 optimal weight:    2.9990
   chunk 145 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0570
   chunk 100 optimal weight:    0.5980
   chunk 10 optimal weight:    8.9990
   overall best weight:    0.6902

-------------------------------------------------------------------------------
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 = 0.3892 r_free = 0.3892 target = 0.166359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.147962 restraints weight = 49852.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.3703 rms_B_bonded: 2.17
r_work: 0.3588 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3483 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3478
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3478 r_free = 0.3478    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3478 r_free = 0.3478    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3478
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  16540  Z= 0.121
  Angle     :  0.525   5.743  22492  Z= 0.279
  Chirality :  0.043   0.124   2544
  Planarity :  0.004   0.036   2896
  Dihedral  :  8.194  62.028   2436
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 14.21 %
    Favored  : 82.42 %
  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:  0.71 (0.18), residues: 2060
  helix:  0.56 (0.18), residues: 768
  sheet:  1.40 (0.27), residues: 348
  loop :  0.18 (0.20), residues: 944

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 176 
 HIS   0.006   0.001   HIS C 373 
 PHE   0.007   0.001   PHE B 552 
 TYR   0.004   0.001   TYR B 216 
 ARG   0.001   0.000   ARG D 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03965 (  740)
  hydrogen bonds       : angle       4.72040 ( 2052)
  covalent geometry    : bond        0.00267 (16540)
  covalent geometry    : angle       0.52469 (22492)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 213
  time to evaluate  : 1.847 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7931 (mpt180)
REVERT: A  194 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7170 (mm-30)
REVERT: A  218 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7202 (p0)
REVERT: A  350 MET cc_start: 0.8798 (ttm) cc_final: 0.8485 (ttp)
REVERT: A  354 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7995 (tt)
REVERT: A  378 ASP cc_start: 0.8308 (t70) cc_final: 0.8075 (t70)
REVERT: A  437 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7626 (tm-30)
REVERT: A  490 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7249 (mp0)
REVERT: B   79 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7932 (mpt180)
REVERT: B  194 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7169 (mm-30)
REVERT: B  218 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.7205 (p0)
REVERT: B  350 MET cc_start: 0.8801 (ttm) cc_final: 0.8489 (ttp)
REVERT: B  354 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7987 (tt)
REVERT: B  378 ASP cc_start: 0.8309 (t70) cc_final: 0.8074 (t70)
REVERT: B  437 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7621 (tm-30)
REVERT: B  490 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7268 (mp0)
REVERT: C   79 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7930 (mpt180)
REVERT: C  218 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7213 (p0)
REVERT: C  350 MET cc_start: 0.8797 (ttm) cc_final: 0.8486 (ttp)
REVERT: C  354 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.8002 (tt)
REVERT: C  378 ASP cc_start: 0.8307 (t70) cc_final: 0.8073 (t70)
REVERT: C  437 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7640 (tm-30)
REVERT: C  490 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7249 (mp0)
REVERT: D   79 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7932 (mpt180)
REVERT: D  194 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7179 (mm-30)
REVERT: D  218 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7207 (p0)
REVERT: D  350 MET cc_start: 0.8813 (ttm) cc_final: 0.8497 (ttp)
REVERT: D  354 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7984 (tt)
REVERT: D  378 ASP cc_start: 0.8318 (t70) cc_final: 0.8076 (t70)
REVERT: D  437 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7617 (tm-30)
REVERT: D  490 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7263 (mp0)
  outliers start: 59
  outliers final: 20
  residues processed: 256
  average time/residue: 1.4920
  time to fit residues: 417.7524
Evaluate side-chains
  248 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 205
  time to evaluate  : 1.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  194 GLU
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  238 CYS
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  437 GLU
Chi-restraints excluded: chain A residue  490 GLU
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue  194 GLU
Chi-restraints excluded: chain B residue  218 ASP
Chi-restraints excluded: chain B residue  238 CYS
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  437 GLU
Chi-restraints excluded: chain B residue  490 GLU
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue   79 ARG
Chi-restraints excluded: chain C residue  218 ASP
Chi-restraints excluded: chain C residue  238 CYS
Chi-restraints excluded: chain C residue  264 LEU
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  437 GLU
Chi-restraints excluded: chain C residue  490 GLU
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue  194 GLU
Chi-restraints excluded: chain D residue  218 ASP
Chi-restraints excluded: chain D residue  238 CYS
Chi-restraints excluded: chain D residue  264 LEU
Chi-restraints excluded: chain D residue  354 LEU
Chi-restraints excluded: chain D residue  370 SER
Chi-restraints excluded: chain D residue  398 VAL
Chi-restraints excluded: chain D residue  437 GLU
Chi-restraints excluded: chain D residue  490 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 69 optimal weight:    6.9990
   chunk 11 optimal weight:    0.7980
   chunk 67 optimal weight:    2.9990
   chunk 91 optimal weight:    4.9990
   chunk 169 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 78 optimal weight:    0.7980
   chunk 56 optimal weight:    6.9990
   chunk 194 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 387 GLN
B 387 GLN
C 387 GLN
D 387 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.162484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.143316 restraints weight = 56966.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3653 rms_B_bonded: 2.34
r_work: 0.3528 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3523
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3523 r_free = 0.3523    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3523 r_free = 0.3523    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3523
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  16540  Z= 0.178
  Angle     :  0.594   7.365  22492  Z= 0.315
  Chirality :  0.044   0.124   2544
  Planarity :  0.004   0.036   2896
  Dihedral  :  8.539  60.277   2432
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 15.53 %
    Favored  : 80.82 %
  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:  0.64 (0.18), residues: 2060
  helix:  0.43 (0.18), residues: 776
  sheet:  1.17 (0.27), residues: 356
  loop :  0.29 (0.20), residues: 928

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 176 
 HIS   0.006   0.001   HIS A 373 
 PHE   0.010   0.001   PHE C 552 
 TYR   0.006   0.001   TYR B 505 
 ARG   0.002   0.001   ARG D 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04960 (  740)
  hydrogen bonds       : angle       4.88004 ( 2052)
  covalent geometry    : bond        0.00402 (16540)
  covalent geometry    : angle       0.59395 (22492)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 181
  time to evaluate  : 1.764 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7761 (mpt180)
REVERT: A  194 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6979 (mm-30)
REVERT: A  218 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7223 (p0)
REVERT: A  240 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6331 (mm-30)
REVERT: A  350 MET cc_start: 0.8792 (ttm) cc_final: 0.8475 (ttp)
REVERT: A  354 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8056 (tt)
REVERT: A  437 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7562 (tm-30)
REVERT: A  490 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7247 (mp0)
REVERT: B   79 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7769 (mpt180)
REVERT: B  194 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6982 (mm-30)
REVERT: B  218 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7216 (p0)
REVERT: B  240 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6361 (mm-30)
REVERT: B  350 MET cc_start: 0.8792 (ttm) cc_final: 0.8477 (ttp)
REVERT: B  354 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8047 (tt)
REVERT: B  437 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7558 (tm-30)
REVERT: B  490 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7244 (mp0)
REVERT: C   79 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7738 (mpt180)
REVERT: C  194 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.7014 (mm-30)
REVERT: C  218 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7224 (p0)
REVERT: C  240 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6332 (mm-30)
REVERT: C  350 MET cc_start: 0.8793 (ttm) cc_final: 0.8477 (ttp)
REVERT: C  354 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8055 (tt)
REVERT: C  437 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7562 (tm-30)
REVERT: C  490 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7253 (mp0)
REVERT: D   79 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7772 (mpt180)
REVERT: D  194 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6979 (mm-30)
REVERT: D  218 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.7217 (p0)
REVERT: D  240 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6358 (mm-30)
REVERT: D  350 MET cc_start: 0.8792 (ttm) cc_final: 0.8474 (ttp)
REVERT: D  354 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8045 (tt)
REVERT: D  437 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7559 (tm-30)
REVERT: D  490 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7254 (mp0)
  outliers start: 64
  outliers final: 20
  residues processed: 225
  average time/residue: 1.4723
  time to fit residues: 365.4557
Evaluate side-chains
  229 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 181
  time to evaluate  : 2.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  194 GLU
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  238 CYS
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  437 GLU
Chi-restraints excluded: chain A residue  490 GLU
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue  194 GLU
Chi-restraints excluded: chain B residue  218 ASP
Chi-restraints excluded: chain B residue  238 CYS
Chi-restraints excluded: chain B residue  240 GLU
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  437 GLU
Chi-restraints excluded: chain B residue  490 GLU
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue   79 ARG
Chi-restraints excluded: chain C residue  194 GLU
Chi-restraints excluded: chain C residue  218 ASP
Chi-restraints excluded: chain C residue  238 CYS
Chi-restraints excluded: chain C residue  240 GLU
Chi-restraints excluded: chain C residue  264 LEU
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  437 GLU
Chi-restraints excluded: chain C residue  490 GLU
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue  194 GLU
Chi-restraints excluded: chain D residue  218 ASP
Chi-restraints excluded: chain D residue  238 CYS
Chi-restraints excluded: chain D residue  240 GLU
Chi-restraints excluded: chain D residue  264 LEU
Chi-restraints excluded: chain D residue  354 LEU
Chi-restraints excluded: chain D residue  370 SER
Chi-restraints excluded: chain D residue  398 VAL
Chi-restraints excluded: chain D residue  437 GLU
Chi-restraints excluded: chain D residue  490 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 116 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 154 optimal weight:    5.9990
   chunk 123 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   chunk 10 optimal weight:    8.9990
   chunk 95 optimal weight:    5.9990
   chunk 126 optimal weight:    0.9980
   chunk 131 optimal weight:    6.9990
   chunk 85 optimal weight:    2.9990
   chunk 198 optimal weight:    8.9990
   overall best weight:    2.5586

-------------------------------------------------------------------------------
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 = 0.3820 r_free = 0.3820 target = 0.159531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.140630 restraints weight = 52455.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3622 rms_B_bonded: 2.29
r_work: 0.3500 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3390 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3384
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3384 r_free = 0.3384    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3384 r_free = 0.3384    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3384
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.2218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.074  16540  Z= 0.256
  Angle     :  0.690   8.307  22492  Z= 0.366
  Chirality :  0.048   0.149   2544
  Planarity :  0.005   0.038   2896
  Dihedral  :  8.867  59.481   2432
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 15.30 %
    Favored  : 80.82 %
  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:  0.51 (0.18), residues: 2060
  helix:  0.37 (0.18), residues: 740
  sheet:  0.99 (0.25), residues: 404
  loop :  0.17 (0.20), residues: 916

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 176 
 HIS   0.006   0.002   HIS A 373 
 PHE   0.013   0.002   PHE C 552 
 TYR   0.008   0.002   TYR D 505 
 ARG   0.003   0.001   ARG C 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05866 (  740)
  hydrogen bonds       : angle       5.07703 ( 2052)
  covalent geometry    : bond        0.00588 (16540)
  covalent geometry    : angle       0.68976 (22492)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 168
  time to evaluate  : 1.709 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7859 (mpt180)
REVERT: A  194 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7243 (mm-30)
REVERT: A  218 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7353 (p0)
REVERT: A  240 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6685 (mm-30)
REVERT: A  437 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7795 (tm-30)
REVERT: A  490 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7196 (mp0)
REVERT: B   79 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7896 (mpt180)
REVERT: B  194 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7244 (mm-30)
REVERT: B  218 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.7342 (p0)
REVERT: B  240 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6714 (mm-30)
REVERT: B  437 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7784 (tm-30)
REVERT: B  490 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7217 (mp0)
REVERT: C   79 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7851 (mpt180)
REVERT: C  194 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7236 (mm-30)
REVERT: C  218 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7344 (p0)
REVERT: C  240 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6694 (mm-30)
REVERT: C  437 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7799 (tm-30)
REVERT: C  490 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7209 (mp0)
REVERT: D   79 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7871 (mpt180)
REVERT: D  194 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7255 (mm-30)
REVERT: D  218 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7342 (p0)
REVERT: D  240 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6695 (mm-30)
REVERT: D  437 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7785 (tm-30)
REVERT: D  490 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7215 (mp0)
  outliers start: 68
  outliers final: 32
  residues processed: 212
  average time/residue: 1.3714
  time to fit residues: 320.5785
Evaluate side-chains
  220 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 164
  time to evaluate  : 1.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  194 GLU
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  238 CYS
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  437 GLU
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  490 GLU
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue  187 MET
Chi-restraints excluded: chain B residue  194 GLU
Chi-restraints excluded: chain B residue  218 ASP
Chi-restraints excluded: chain B residue  238 CYS
Chi-restraints excluded: chain B residue  240 GLU
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  437 GLU
Chi-restraints excluded: chain B residue  489 THR
Chi-restraints excluded: chain B residue  490 GLU
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue   79 ARG
Chi-restraints excluded: chain C residue  187 MET
Chi-restraints excluded: chain C residue  194 GLU
Chi-restraints excluded: chain C residue  218 ASP
Chi-restraints excluded: chain C residue  238 CYS
Chi-restraints excluded: chain C residue  240 GLU
Chi-restraints excluded: chain C residue  264 LEU
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  437 GLU
Chi-restraints excluded: chain C residue  489 THR
Chi-restraints excluded: chain C residue  490 GLU
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue  187 MET
Chi-restraints excluded: chain D residue  194 GLU
Chi-restraints excluded: chain D residue  218 ASP
Chi-restraints excluded: chain D residue  238 CYS
Chi-restraints excluded: chain D residue  240 GLU
Chi-restraints excluded: chain D residue  264 LEU
Chi-restraints excluded: chain D residue  354 LEU
Chi-restraints excluded: chain D residue  370 SER
Chi-restraints excluded: chain D residue  398 VAL
Chi-restraints excluded: chain D residue  437 GLU
Chi-restraints excluded: chain D residue  489 THR
Chi-restraints excluded: chain D residue  490 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 117 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9990
   chunk 121 optimal weight:    0.0370
   chunk 69 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 116 optimal weight:    1.9990
   chunk 203 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 193 optimal weight:    2.9990
   overall best weight:    1.1864

-------------------------------------------------------------------------------
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 = 0.3858 r_free = 0.3858 target = 0.163118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.144859 restraints weight = 46855.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3669 rms_B_bonded: 2.15
r_work: 0.3555 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3448 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3444
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3444 r_free = 0.3444    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3444 r_free = 0.3444    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3444
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.2213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  16540  Z= 0.155
  Angle     :  0.571   6.587  22492  Z= 0.304
  Chirality :  0.043   0.125   2544
  Planarity :  0.004   0.038   2896
  Dihedral  :  8.501  61.300   2432
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 15.98 %
    Favored  : 81.05 %
  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:  0.56 (0.18), residues: 2060
  helix:  0.41 (0.18), residues: 776
  sheet:  1.10 (0.25), residues: 396
  loop :  0.17 (0.20), residues: 888

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D 176 
 HIS   0.007   0.001   HIS D 373 
 PHE   0.008   0.001   PHE D 443 
 TYR   0.006   0.001   TYR C 505 
 ARG   0.003   0.000   ARG C 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04572 (  740)
  hydrogen bonds       : angle       4.88280 ( 2052)
  covalent geometry    : bond        0.00350 (16540)
  covalent geometry    : angle       0.57134 (22492)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 177
  time to evaluate  : 1.622 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7886 (mpt180)
REVERT: A  194 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7180 (mm-30)
REVERT: A  218 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7328 (p0)
REVERT: A  350 MET cc_start: 0.8851 (ttm) cc_final: 0.8528 (ttp)
REVERT: A  354 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8050 (tt)
REVERT: A  437 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7715 (tm-30)
REVERT: A  490 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7282 (mp0)
REVERT: B   79 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7864 (mpt180)
REVERT: B  194 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7179 (mm-30)
REVERT: B  218 ASP cc_start: 0.7545 (OUTLIER) cc_final: 0.7321 (p0)
REVERT: B  350 MET cc_start: 0.8860 (ttm) cc_final: 0.8536 (ttp)
REVERT: B  354 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8044 (tt)
REVERT: B  437 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7720 (tm-30)
REVERT: B  490 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7278 (mp0)
REVERT: C   79 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7868 (mpt180)
REVERT: C  194 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7191 (mm-30)
REVERT: C  218 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7321 (p0)
REVERT: C  350 MET cc_start: 0.8859 (ttm) cc_final: 0.8533 (ttp)
REVERT: C  354 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8049 (tt)
REVERT: C  437 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7714 (tm-30)
REVERT: C  490 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7273 (mp0)
REVERT: D   79 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7869 (mpt180)
REVERT: D  194 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7186 (mm-30)
REVERT: D  218 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7319 (p0)
REVERT: D  350 MET cc_start: 0.8868 (ttm) cc_final: 0.8540 (ttp)
REVERT: D  354 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8039 (tt)
REVERT: D  437 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7713 (tm-30)
REVERT: D  490 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7279 (mp0)
  outliers start: 52
  outliers final: 24
  residues processed: 209
  average time/residue: 1.4941
  time to fit residues: 343.4979
Evaluate side-chains
  221 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 173
  time to evaluate  : 1.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  194 GLU
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  238 CYS
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  437 GLU
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  490 GLU
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue  194 GLU
Chi-restraints excluded: chain B residue  218 ASP
Chi-restraints excluded: chain B residue  238 CYS
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  437 GLU
Chi-restraints excluded: chain B residue  489 THR
Chi-restraints excluded: chain B residue  490 GLU
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue   79 ARG
Chi-restraints excluded: chain C residue  194 GLU
Chi-restraints excluded: chain C residue  218 ASP
Chi-restraints excluded: chain C residue  238 CYS
Chi-restraints excluded: chain C residue  264 LEU
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  437 GLU
Chi-restraints excluded: chain C residue  489 THR
Chi-restraints excluded: chain C residue  490 GLU
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue  194 GLU
Chi-restraints excluded: chain D residue  218 ASP
Chi-restraints excluded: chain D residue  238 CYS
Chi-restraints excluded: chain D residue  264 LEU
Chi-restraints excluded: chain D residue  354 LEU
Chi-restraints excluded: chain D residue  370 SER
Chi-restraints excluded: chain D residue  398 VAL
Chi-restraints excluded: chain D residue  437 GLU
Chi-restraints excluded: chain D residue  489 THR
Chi-restraints excluded: chain D residue  490 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 88 optimal weight:    5.9990
   chunk 132 optimal weight:    0.7980
   chunk 48 optimal weight:    7.9990
   chunk 200 optimal weight:    0.0970
   chunk 172 optimal weight:    3.9990
   chunk 129 optimal weight:    2.9990
   chunk 118 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 127 optimal weight:    0.6980
   chunk 171 optimal weight:    5.9990
   chunk 167 optimal weight:    0.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 256 ASN
B 256 ASN
C 256 ASN
D 256 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.164547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.145597 restraints weight = 55885.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 2.32
r_work: 0.3552 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3548
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3548 r_free = 0.3548    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3548 r_free = 0.3548    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3548
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.2241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  16540  Z= 0.136
  Angle     :  0.543   6.379  22492  Z= 0.288
  Chirality :  0.043   0.123   2544
  Planarity :  0.004   0.036   2896
  Dihedral  :  8.295  61.716   2432
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 14.84 %
    Favored  : 81.96 %
  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:  0.80 (0.18), residues: 2060
  helix:  0.68 (0.18), residues: 764
  sheet:  1.14 (0.27), residues: 356
  loop :  0.32 (0.20), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 176 
 HIS   0.006   0.001   HIS D 373 
 PHE   0.007   0.001   PHE C 443 
 TYR   0.005   0.001   TYR A 505 
 ARG   0.003   0.000   ARG C 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04268 (  740)
  hydrogen bonds       : angle       4.76731 ( 2052)
  covalent geometry    : bond        0.00302 (16540)
  covalent geometry    : angle       0.54332 (22492)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 192
  time to evaluate  : 1.918 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7789 (mpt180)
REVERT: A  194 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6944 (mm-30)
REVERT: A  218 ASP cc_start: 0.7489 (OUTLIER) cc_final: 0.7283 (p0)
REVERT: A  240 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6249 (mm-30)
REVERT: A  350 MET cc_start: 0.8778 (ttm) cc_final: 0.8417 (ttp)
REVERT: A  354 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.8025 (tt)
REVERT: A  437 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7514 (tm-30)
REVERT: A  490 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7262 (mp0)
REVERT: B   79 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7805 (mpt180)
REVERT: B  194 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6947 (mm-30)
REVERT: B  218 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7282 (p0)
REVERT: B  240 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6253 (mm-30)
REVERT: B  350 MET cc_start: 0.8785 (ttm) cc_final: 0.8425 (ttp)
REVERT: B  354 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.8012 (tt)
REVERT: B  437 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7513 (tm-30)
REVERT: B  490 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7270 (mp0)
REVERT: C   79 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7784 (mpt180)
REVERT: C  194 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6983 (mm-30)
REVERT: C  218 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7279 (p0)
REVERT: C  240 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6244 (mm-30)
REVERT: C  350 MET cc_start: 0.8777 (ttm) cc_final: 0.8415 (ttp)
REVERT: C  354 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.8023 (tt)
REVERT: C  437 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7513 (tm-30)
REVERT: C  490 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7264 (mp0)
REVERT: D   79 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7808 (mpt180)
REVERT: D  194 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6952 (mm-30)
REVERT: D  218 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7279 (p0)
REVERT: D  240 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6242 (mm-30)
REVERT: D  350 MET cc_start: 0.8783 (ttm) cc_final: 0.8420 (ttp)
REVERT: D  354 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.8012 (tt)
REVERT: D  437 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7517 (tm-30)
REVERT: D  490 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7275 (mp0)
  outliers start: 56
  outliers final: 24
  residues processed: 228
  average time/residue: 1.4607
  time to fit residues: 366.5756
Evaluate side-chains
  236 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 184
  time to evaluate  : 1.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  194 GLU
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  238 CYS
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  437 GLU
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  490 GLU
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue  194 GLU
Chi-restraints excluded: chain B residue  218 ASP
Chi-restraints excluded: chain B residue  238 CYS
Chi-restraints excluded: chain B residue  240 GLU
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  437 GLU
Chi-restraints excluded: chain B residue  489 THR
Chi-restraints excluded: chain B residue  490 GLU
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue   79 ARG
Chi-restraints excluded: chain C residue  194 GLU
Chi-restraints excluded: chain C residue  218 ASP
Chi-restraints excluded: chain C residue  238 CYS
Chi-restraints excluded: chain C residue  240 GLU
Chi-restraints excluded: chain C residue  264 LEU
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  437 GLU
Chi-restraints excluded: chain C residue  489 THR
Chi-restraints excluded: chain C residue  490 GLU
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue  194 GLU
Chi-restraints excluded: chain D residue  218 ASP
Chi-restraints excluded: chain D residue  238 CYS
Chi-restraints excluded: chain D residue  240 GLU
Chi-restraints excluded: chain D residue  264 LEU
Chi-restraints excluded: chain D residue  354 LEU
Chi-restraints excluded: chain D residue  370 SER
Chi-restraints excluded: chain D residue  398 VAL
Chi-restraints excluded: chain D residue  437 GLU
Chi-restraints excluded: chain D residue  489 THR
Chi-restraints excluded: chain D residue  490 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 99 optimal weight:    6.9990
   chunk 123 optimal weight:    5.9990
   chunk 184 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 120 optimal weight:    6.9990
   chunk 128 optimal weight:    3.9990
   chunk 113 optimal weight:    6.9990
   chunk 109 optimal weight:    0.9980
   chunk 129 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 202 optimal weight:    1.9990
   overall best weight:    2.1786

-------------------------------------------------------------------------------
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 = 0.3787 r_free = 0.3787 target = 0.157975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.137739 restraints weight = 56677.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 2.65
r_work: 0.3405 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3411
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3411 r_free = 0.3411    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3411 r_free = 0.3411    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3411
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.2301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065  16540  Z= 0.227
  Angle     :  0.660   8.863  22492  Z= 0.349
  Chirality :  0.046   0.141   2544
  Planarity :  0.005   0.036   2896
  Dihedral  :  8.760  59.201   2432
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 15.30 %
    Favored  : 81.51 %
  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:  0.49 (0.18), residues: 2060
  helix:  0.31 (0.18), residues: 772
  sheet:  1.01 (0.25), residues: 404
  loop :  0.20 (0.20), residues: 884

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 176 
 HIS   0.006   0.001   HIS A 373 
 PHE   0.012   0.002   PHE B 443 
 TYR   0.008   0.001   TYR B 505 
 ARG   0.005   0.001   ARG C 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05518 (  740)
  hydrogen bonds       : angle       5.01355 ( 2052)
  covalent geometry    : bond        0.00519 (16540)
  covalent geometry    : angle       0.65957 (22492)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 176
  time to evaluate  : 1.770 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7745 (mpt180)
REVERT: A  194 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6876 (mm-30)
REVERT: A  209 LYS cc_start: 0.7359 (tptm) cc_final: 0.6638 (mptt)
REVERT: A  218 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7178 (p0)
REVERT: A  240 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6266 (mm-30)
REVERT: A  350 MET cc_start: 0.8776 (ttm) cc_final: 0.8385 (ttp)
REVERT: A  354 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8009 (tt)
REVERT: A  437 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7656 (tm-30)
REVERT: A  490 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7161 (mp0)
REVERT: B   79 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7761 (mpt180)
REVERT: B  194 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6874 (mm-30)
REVERT: B  209 LYS cc_start: 0.7362 (tptm) cc_final: 0.6641 (mptt)
REVERT: B  218 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7172 (p0)
REVERT: B  240 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6275 (mm-30)
REVERT: B  350 MET cc_start: 0.8784 (ttm) cc_final: 0.8394 (ttp)
REVERT: B  354 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8008 (tt)
REVERT: B  437 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7651 (tm-30)
REVERT: B  490 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7151 (mp0)
REVERT: C   79 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7741 (mpt180)
REVERT: C  194 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6893 (mm-30)
REVERT: C  209 LYS cc_start: 0.7361 (tptm) cc_final: 0.6643 (mptt)
REVERT: C  218 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7179 (p0)
REVERT: C  240 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6262 (mm-30)
REVERT: C  350 MET cc_start: 0.8779 (ttm) cc_final: 0.8386 (ttp)
REVERT: C  354 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8008 (tt)
REVERT: C  437 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7647 (tm-30)
REVERT: C  490 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7162 (mp0)
REVERT: D   79 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7756 (mpt180)
REVERT: D  194 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6875 (mm-30)
REVERT: D  209 LYS cc_start: 0.7365 (tptm) cc_final: 0.6645 (mptt)
REVERT: D  218 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7175 (p0)
REVERT: D  240 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6269 (mm-30)
REVERT: D  350 MET cc_start: 0.8782 (ttm) cc_final: 0.8389 (ttp)
REVERT: D  354 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8006 (tt)
REVERT: D  437 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7648 (tm-30)
REVERT: D  490 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7155 (mp0)
  outliers start: 56
  outliers final: 28
  residues processed: 208
  average time/residue: 1.5185
  time to fit residues: 346.4093
Evaluate side-chains
  232 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 176
  time to evaluate  : 2.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  194 GLU
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  238 CYS
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  437 GLU
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  490 GLU
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue  187 MET
Chi-restraints excluded: chain B residue  194 GLU
Chi-restraints excluded: chain B residue  218 ASP
Chi-restraints excluded: chain B residue  238 CYS
Chi-restraints excluded: chain B residue  240 GLU
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  437 GLU
Chi-restraints excluded: chain B residue  489 THR
Chi-restraints excluded: chain B residue  490 GLU
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue   79 ARG
Chi-restraints excluded: chain C residue  187 MET
Chi-restraints excluded: chain C residue  194 GLU
Chi-restraints excluded: chain C residue  218 ASP
Chi-restraints excluded: chain C residue  238 CYS
Chi-restraints excluded: chain C residue  240 GLU
Chi-restraints excluded: chain C residue  264 LEU
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  437 GLU
Chi-restraints excluded: chain C residue  489 THR
Chi-restraints excluded: chain C residue  490 GLU
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue  187 MET
Chi-restraints excluded: chain D residue  194 GLU
Chi-restraints excluded: chain D residue  218 ASP
Chi-restraints excluded: chain D residue  238 CYS
Chi-restraints excluded: chain D residue  240 GLU
Chi-restraints excluded: chain D residue  264 LEU
Chi-restraints excluded: chain D residue  354 LEU
Chi-restraints excluded: chain D residue  370 SER
Chi-restraints excluded: chain D residue  398 VAL
Chi-restraints excluded: chain D residue  437 GLU
Chi-restraints excluded: chain D residue  489 THR
Chi-restraints excluded: chain D residue  490 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 172 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 169 optimal weight:    0.9990
   chunk 154 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 182 optimal weight:    4.9990
   chunk 140 optimal weight:    3.9990
   overall best weight:    1.1986

-------------------------------------------------------------------------------
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 = 0.3815 r_free = 0.3815 target = 0.160450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.140671 restraints weight = 53504.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3584 rms_B_bonded: 2.59
r_work: 0.3444 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3450
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3450 r_free = 0.3450    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3450 r_free = 0.3450    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3450
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  16540  Z= 0.159
  Angle     :  0.592  10.419  22492  Z= 0.312
  Chirality :  0.044   0.130   2544
  Planarity :  0.004   0.035   2896
  Dihedral  :  8.538  60.493   2432
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 14.84 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.65 (0.18), residues: 2060
  helix:  0.45 (0.18), residues: 776
  sheet:  1.09 (0.27), residues: 356
  loop :  0.33 (0.20), residues: 928

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 176 
 HIS   0.006   0.001   HIS A 373 
 PHE   0.008   0.001   PHE A 443 
 TYR   0.006   0.001   TYR C 505 
 ARG   0.004   0.000   ARG A 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04616 (  740)
  hydrogen bonds       : angle       4.89545 ( 2052)
  covalent geometry    : bond        0.00357 (16540)
  covalent geometry    : angle       0.59208 (22492)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 180
  time to evaluate  : 1.732 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7791 (mpt180)
REVERT: A  194 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6831 (mm-30)
REVERT: A  218 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7117 (p0)
REVERT: A  240 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6168 (mm-30)
REVERT: A  350 MET cc_start: 0.8743 (ttm) cc_final: 0.8326 (ttp)
REVERT: A  354 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7909 (tt)
REVERT: A  437 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7603 (tm-30)
REVERT: A  490 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7179 (mp0)
REVERT: B   79 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7805 (mpt180)
REVERT: B  194 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6834 (mm-30)
REVERT: B  218 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7108 (p0)
REVERT: B  240 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6173 (mm-30)
REVERT: B  350 MET cc_start: 0.8748 (ttm) cc_final: 0.8332 (ttp)
REVERT: B  354 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7908 (tt)
REVERT: B  437 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7607 (tm-30)
REVERT: B  490 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7171 (mp0)
REVERT: C   79 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7788 (mpt180)
REVERT: C  194 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6843 (mm-30)
REVERT: C  218 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7112 (p0)
REVERT: C  240 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6171 (mm-30)
REVERT: C  350 MET cc_start: 0.8743 (ttm) cc_final: 0.8324 (ttp)
REVERT: C  354 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7908 (tt)
REVERT: C  437 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7596 (tm-30)
REVERT: C  490 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7178 (mp0)
REVERT: D   79 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7796 (mpt180)
REVERT: D  194 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6829 (mm-30)
REVERT: D  218 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7113 (p0)
REVERT: D  240 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6171 (mm-30)
REVERT: D  350 MET cc_start: 0.8744 (ttm) cc_final: 0.8323 (ttp)
REVERT: D  354 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7908 (tt)
REVERT: D  437 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7592 (tm-30)
REVERT: D  490 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7174 (mp0)
  outliers start: 60
  outliers final: 24
  residues processed: 212
  average time/residue: 1.4899
  time to fit residues: 345.6661
Evaluate side-chains
  227 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 175
  time to evaluate  : 1.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  194 GLU
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  238 CYS
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  437 GLU
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  490 GLU
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   79 ARG
Chi-restraints excluded: chain B residue  194 GLU
Chi-restraints excluded: chain B residue  218 ASP
Chi-restraints excluded: chain B residue  238 CYS
Chi-restraints excluded: chain B residue  240 GLU
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  437 GLU
Chi-restraints excluded: chain B residue  489 THR
Chi-restraints excluded: chain B residue  490 GLU
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue   79 ARG
Chi-restraints excluded: chain C residue  194 GLU
Chi-restraints excluded: chain C residue  218 ASP
Chi-restraints excluded: chain C residue  238 CYS
Chi-restraints excluded: chain C residue  240 GLU
Chi-restraints excluded: chain C residue  264 LEU
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  437 GLU
Chi-restraints excluded: chain C residue  489 THR
Chi-restraints excluded: chain C residue  490 GLU
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue  194 GLU
Chi-restraints excluded: chain D residue  218 ASP
Chi-restraints excluded: chain D residue  238 CYS
Chi-restraints excluded: chain D residue  240 GLU
Chi-restraints excluded: chain D residue  264 LEU
Chi-restraints excluded: chain D residue  354 LEU
Chi-restraints excluded: chain D residue  370 SER
Chi-restraints excluded: chain D residue  398 VAL
Chi-restraints excluded: chain D residue  437 GLU
Chi-restraints excluded: chain D residue  489 THR
Chi-restraints excluded: chain D residue  490 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 186 optimal weight:    2.9990
   chunk 98 optimal weight:    0.5980
   chunk 29 optimal weight:    5.9990
   chunk 126 optimal weight:    1.9990
   chunk 185 optimal weight:    5.9990
   chunk 145 optimal weight:    2.9990
   chunk 54 optimal weight:   10.0000
   chunk 166 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 151 optimal weight:    2.9990
   overall best weight:    1.7188

-------------------------------------------------------------------------------
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 = 0.3799 r_free = 0.3799 target = 0.158953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.139089 restraints weight = 40131.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 2.30
r_work: 0.3451 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3333
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3333 r_free = 0.3333    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3333 r_free = 0.3333    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3333
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.2306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  16540  Z= 0.192
  Angle     :  0.614   7.511  22492  Z= 0.326
  Chirality :  0.045   0.131   2544
  Planarity :  0.004   0.035   2896
  Dihedral  :  8.682  59.818   2432
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 15.70 %
    Favored  : 81.34 %
  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:  0.57 (0.18), residues: 2060
  helix:  0.38 (0.18), residues: 772
  sheet:  1.00 (0.25), residues: 404
  loop :  0.27 (0.20), residues: 884

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 176 
 HIS   0.006   0.001   HIS A 373 
 PHE   0.010   0.002   PHE B 443 
 TYR   0.007   0.001   TYR D 505 
 ARG   0.005   0.001   ARG A 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05128 (  740)
  hydrogen bonds       : angle       4.96608 ( 2052)
  covalent geometry    : bond        0.00437 (16540)
  covalent geometry    : angle       0.61402 (22492)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 13345.48 seconds
wall clock time: 228 minutes 44.94 seconds (13724.94 seconds total)