Starting phenix.real_space_refine
on Tue Mar  3 22:22:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wur_32839/03_2026/7wur_32839.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wur_32839/03_2026/7wur_32839.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wur_32839/03_2026/7wur_32839.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wur_32839/03_2026/7wur_32839.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wur_32839/03_2026/7wur_32839.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wur_32839/03_2026/7wur_32839.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 336 atoms to isotropic.
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: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    5636      2.51       5
     N    1528      2.21       5
     O    1706      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 94 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8922
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2725
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2725
          Classifications: {'peptide': 341}
          Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 321}
    Chain: "B"
      Number of atoms: 2725
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2725
          Classifications: {'peptide': 341}
          Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 321}
    Chain: "E"
      Number of atoms: 915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 915
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 2, 'TRANS': 115}
    Chain: "F"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 821
          Classifications: {'peptide': 108}
          Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 96}
    Chain: "G"
      Number of atoms: 915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 915
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 2, 'TRANS': 115}
    Chain: "H"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 821
          Classifications: {'peptide': 108}
          Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 96}
  Time building chain proxies: 2.14, per 1000 atoms: 0.24
  Number of scatterers: 8922
  At special positions: 0
  Unit cell: (84.48, 109.56, 162.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      52     16.00
     O    1706      8.00
     N    1528      7.00
     C    5636      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=16, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   4 " - pdb=" SG  CYS A  15 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  55 " - pdb=" SG  CYS A 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 179 " - pdb=" SG  CYS A 223 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 280 " - pdb=" SG  CYS A 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 313 " - pdb=" SG  CYS A 316 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   4 " - pdb=" SG  CYS B  15 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  55 " - pdb=" SG  CYS B 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 179 " - pdb=" SG  CYS B 223 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 280 " - pdb=" SG  CYS B 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 291 " - pdb=" SG  CYS B 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 313 " - pdb=" SG  CYS B 316 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  23 " - pdb=" SG  CYS F  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  22 " - pdb=" SG  CYS G  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  23 " - pdb=" SG  CYS H  89 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.65
  Conformation dependent library (CDL) restraints added in 365.1 milliseconds
  

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2072

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 20 sheets defined
      12.8% alpha, 24.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 53
      removed outlier: 3.759A  pdb=" N   LEU A  42 " --> pdb=" O   SER A  38 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ILE A  46 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   GLN A  47 " --> pdb=" O   ALA A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 82
      removed outlier: 3.808A  pdb=" N   ASN A  65 " --> pdb=" O   THR A  61 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   LEU A  66 " --> pdb=" O   ARG A  62 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   TRP A  68 " --> pdb=" O   GLU A  64 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   GLN A  70 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
      Proline residue:  A  73  - end of helix
      removed outlier: 3.637A  pdb=" N   HIS A  77 " --> pdb=" O   PRO A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 146
      No H-bonds generated for 'chain 'A' and resid 144 through 146'
    Processing helix  chain 'A' and resid 226 through 230
      removed outlier: 3.592A  pdb=" N   HIS A 229 " --> pdb=" O   PRO A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 248
    Processing helix  chain 'A' and resid 252 through 256
      removed outlier: 3.501A  pdb=" N   ASN A 255 " --> pdb=" O   SER A 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 53
      removed outlier: 3.675A  pdb=" N   LEU B  42 " --> pdb=" O   SER B  38 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   GLN B  47 " --> pdb=" O   ALA B  43 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LYS B  48 " --> pdb=" O   SER B  44 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ALA B  49 " --> pdb=" O   ALA B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 70
      removed outlier: 3.749A  pdb=" N   ASN B  65 " --> pdb=" O   THR B  61 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   LEU B  66 " --> pdb=" O   ARG B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 82
    Processing helix  chain 'B' and resid 144 through 146
      No H-bonds generated for 'chain 'B' and resid 144 through 146'
    Processing helix  chain 'B' and resid 226 through 230
      removed outlier: 3.552A  pdb=" N   HIS B 229 " --> pdb=" O   PRO B 226 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   THR B 230 " --> pdb=" O   LYS B 227 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 226 through 230'
    Processing helix  chain 'B' and resid 244 through 248
    Processing helix  chain 'B' and resid 252 through 256
      removed outlier: 3.561A  pdb=" N   ASN B 255 " --> pdb=" O   SER B 252 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.665A  pdb=" N   TYR E  32 " --> pdb=" O   PHE E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 65
      removed outlier: 3.716A  pdb=" N   LYS E  65 " --> pdb=" O   ASP E  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 62 through 65'
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.670A  pdb=" N   THR E  91 " --> pdb=" O   ASP E  88 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 80 through 84
      removed outlier: 3.841A  pdb=" N   PHE F  84 " --> pdb=" O   PRO F  81 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 28 through 32
      removed outlier: 3.815A  pdb=" N   TYR G  32 " --> pdb=" O   PHE G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 62 through 65
      removed outlier: 3.822A  pdb=" N   LYS G  65 " --> pdb=" O   ASP G  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 62 through 65'
    Processing helix  chain 'H' and resid 80 through 84
      removed outlier: 3.899A  pdb=" N   PHE H  84 " --> pdb=" O   PRO H  81 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7
    Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58
      removed outlier: 6.598A  pdb=" N   GLY A  56 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 89
      removed outlier: 3.642A  pdb=" N   MET A  89 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 153 through 155
    Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 331
      removed outlier: 4.366A  pdb=" N   PHE A 277 " --> pdb=" O   GLU A 213 " (cutoff:3.500A)
      removed outlier: 9.168A  pdb=" N   GLU A 213 " --> pdb=" O   PHE A 277 " (cutoff:3.500A)
      removed outlier: 5.114A  pdb=" N   ILE A 212 " --> pdb=" O   ALA A 205 " (cutoff:3.500A)
      removed outlier: 5.402A  pdb=" N   ALA A 205 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   SER A 216 " --> pdb=" O   TRP A 201 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ARG A 192 " --> pdb=" O   LYS A 189 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   ARG B 192 " --> pdb=" O   LYS B 189 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   SER B 216 " --> pdb=" O   TRP B 201 " (cutoff:3.500A)
      removed outlier: 5.409A  pdb=" N   ALA B 205 " --> pdb=" O   ILE B 212 " (cutoff:3.500A)
      removed outlier: 5.076A  pdb=" N   ILE B 212 " --> pdb=" O   ALA B 205 " (cutoff:3.500A)
      removed outlier: 9.118A  pdb=" N   GLU B 213 " --> pdb=" O   PHE B 277 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   PHE B 277 " --> pdb=" O   GLU B 213 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 284 through 287
      removed outlier: 5.996A  pdb=" N   THR A 284 " --> pdb=" O   TRP A 311 " (cutoff:3.500A)
      removed outlier: 7.407A  pdb=" N   CYS A 313 " --> pdb=" O   THR A 284 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   VAL A 286 " --> pdb=" O   CYS A 313 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 88 through 89
      removed outlier: 3.563A  pdb=" N   MET B  89 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   GLY B  56 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 153 through 155
    Processing sheet with id=AB1, first strand: chain 'B' and resid 284 through 287
      removed outlier: 5.990A  pdb=" N   THR B 284 " --> pdb=" O   TRP B 311 " (cutoff:3.500A)
      removed outlier: 7.421A  pdb=" N   CYS B 313 " --> pdb=" O   THR B 284 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   VAL B 286 " --> pdb=" O   CYS B 313 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 12
      removed outlier: 4.089A  pdb=" N   TYR E 107 " --> pdb=" O   SER E  98 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   GLY E 109 " --> pdb=" O   CYS E  96 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   CYS E  96 " --> pdb=" O   GLY E 109 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   GLY E 111 " --> pdb=" O   TYR E  94 " (cutoff:3.500A)
      removed outlier: 5.157A  pdb=" N   TYR E  94 " --> pdb=" O   GLY E 111 " (cutoff:3.500A)
      removed outlier: 4.935A  pdb=" N   LEU E 113 " --> pdb=" O   ALA E  92 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   ALA E  92 " --> pdb=" O   LEU E 113 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 5 through 6
    Processing sheet with id=AB5, first strand: chain 'F' and resid 10 through 12
    Processing sheet with id=AB6, first strand: chain 'F' and resid 19 through 20
      removed outlier: 3.601A  pdb=" N   ASP F  71 " --> pdb=" O   SER F  68 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'G' and resid 4 through 7
    Processing sheet with id=AB8, first strand: chain 'G' and resid 11 through 12
      removed outlier: 4.135A  pdb=" N   TYR G 107 " --> pdb=" O   SER G  98 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   GLY G 109 " --> pdb=" O   CYS G  96 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   CYS G  96 " --> pdb=" O   GLY G 109 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   GLY G 111 " --> pdb=" O   TYR G  94 " (cutoff:3.500A)
      removed outlier: 5.249A  pdb=" N   TYR G  94 " --> pdb=" O   GLY G 111 " (cutoff:3.500A)
      removed outlier: 4.992A  pdb=" N   LEU G 113 " --> pdb=" O   ALA G  92 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   ALA G  92 " --> pdb=" O   LEU G 113 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   SER G  49 " --> pdb=" O   TRP G  36 " (cutoff:3.500A)
      removed outlier: 5.344A  pdb=" N   ARG G  38 " --> pdb=" O   TRP G  47 " (cutoff:3.500A)
      removed outlier: 5.127A  pdb=" N   TRP G  47 " --> pdb=" O   ARG G  38 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'H' and resid 5 through 7
      removed outlier: 3.680A  pdb=" N   PHE H  72 " --> pdb=" O   CYS H  23 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ALA H  19 " --> pdb=" O   ILE H  76 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'H' and resid 5 through 7
      removed outlier: 3.680A  pdb=" N   PHE H  72 " --> pdb=" O   CYS H  23 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ASP H  71 " --> pdb=" O   SER H  68 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.247A  pdb=" N   LEU H  11 " --> pdb=" O   GLU H 107 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   TYR H  87 " --> pdb=" O   THR H 104 " (cutoff:3.500A)

    224 hydrogen bonds defined for protein.
    564 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.23

  Time building geometry restraints manager: 0.91 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: 2870
        1.34 -     1.46: 2341
        1.46 -     1.58: 3867
        1.58 -     1.70: 0
        1.70 -     1.82: 72
  Bond restraints: 9150
  Sorted by residual:
  bond pdb=" N   GLN B 107 "
       pdb=" CA  GLN B 107 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.66e+00
  bond pdb=" N   GLN A 107 "
       pdb=" CA  GLN A 107 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.90e-02 2.77e+03 2.44e+00
  bond pdb=" CA  ILE B 243 "
       pdb=" CB  ILE B 243 "
    ideal  model  delta    sigma   weight residual
    1.540  1.522  0.018 1.23e-02 6.61e+03 2.11e+00
  bond pdb=" CB  GLN A  70 "
       pdb=" CG  GLN A  70 "
    ideal  model  delta    sigma   weight residual
    1.520  1.560 -0.040 3.00e-02 1.11e+03 1.80e+00
  bond pdb=" C   PRO A 106 "
       pdb=" N   GLN A 107 "
    ideal  model  delta    sigma   weight residual
    1.329  1.347 -0.018 1.40e-02 5.10e+03 1.71e+00
  ... (remaining 9145 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.65: 12279
        2.65 -     5.30: 111
        5.30 -     7.95: 11
        7.95 -    10.60: 5
       10.60 -    13.25: 4
  Bond angle restraints: 12410
  Sorted by residual:
  angle pdb=" C   PRO B 106 "
        pdb=" N   GLN B 107 "
        pdb=" CA  GLN B 107 "
      ideal   model   delta    sigma   weight residual
     121.70  133.13  -11.43 1.80e+00 3.09e-01 4.03e+01
  angle pdb=" C   PRO A 106 "
        pdb=" N   GLN A 107 "
        pdb=" CA  GLN A 107 "
      ideal   model   delta    sigma   weight residual
     121.70  132.97  -11.27 1.80e+00 3.09e-01 3.92e+01
  angle pdb=" CB  MET E  34 "
        pdb=" CG  MET E  34 "
        pdb=" SD  MET E  34 "
      ideal   model   delta    sigma   weight residual
     112.70  125.95  -13.25 3.00e+00 1.11e-01 1.95e+01
  angle pdb=" CA  GLN A  70 "
        pdb=" CB  GLN A  70 "
        pdb=" CG  GLN A  70 "
      ideal   model   delta    sigma   weight residual
     114.10  122.69   -8.59 2.00e+00 2.50e-01 1.84e+01
  angle pdb=" CB  MET B 198 "
        pdb=" CG  MET B 198 "
        pdb=" SD  MET B 198 "
      ideal   model   delta    sigma   weight residual
     112.70  124.65  -11.95 3.00e+00 1.11e-01 1.59e+01
  ... (remaining 12405 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.32: 4831
       17.32 -    34.64: 478
       34.64 -    51.97: 97
       51.97 -    69.29: 6
       69.29 -    86.61: 14
  Dihedral angle restraints: 5426
    sinusoidal: 2178
      harmonic: 3248
  Sorted by residual:
  dihedral pdb=" CA  LYS A  33 "
           pdb=" C   LYS A  33 "
           pdb=" N   PHE A  34 "
           pdb=" CA  PHE A  34 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.37  -23.63     0      5.00e+00 4.00e-02 2.23e+01
  dihedral pdb=" CB  CYS B  55 "
           pdb=" SG  CYS B  55 "
           pdb=" SG  CYS B 143 "
           pdb=" CB  CYS B 143 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -123.21   37.21     1      1.00e+01 1.00e-02 1.95e+01
  dihedral pdb=" CA  LYS A 189 "
           pdb=" C   LYS A 189 "
           pdb=" N   ASP A 190 "
           pdb=" CA  ASP A 190 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.90   22.10     0      5.00e+00 4.00e-02 1.95e+01
  ... (remaining 5423 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1080
       0.049 -    0.097: 177
       0.097 -    0.146: 71
       0.146 -    0.194: 0
       0.194 -    0.243: 2
  Chirality restraints: 1330
  Sorted by residual:
  chirality pdb=" CA  GLN A 107 "
            pdb=" N   GLN A 107 "
            pdb=" C   GLN A 107 "
            pdb=" CB  GLN A 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CA  GLN B 107 "
            pdb=" N   GLN B 107 "
            pdb=" C   GLN B 107 "
            pdb=" CB  GLN B 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CA  GLN E 110 "
            pdb=" N   GLN E 110 "
            pdb=" C   GLN E 110 "
            pdb=" CB  GLN E 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.22e-01
  ... (remaining 1327 not shown)

  Planarity restraints: 1578
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  20 "   -0.010 2.00e-02 2.50e+03   1.30e-02 2.96e+00
        pdb=" CG  PHE B  20 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  20 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  20 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  20 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  20 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  20 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A  70 "    0.009 2.00e-02 2.50e+03   1.70e-02 2.90e+00
        pdb=" C   GLN A  70 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   GLN A  70 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ILE A  71 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  72 "    0.023 5.00e-02 4.00e+02   3.52e-02 1.98e+00
        pdb=" N   PRO A  73 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A  73 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A  73 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1575 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 925
        2.75 -     3.29: 8826
        3.29 -     3.82: 14527
        3.82 -     4.36: 17416
        4.36 -     4.90: 29740
  Nonbonded interactions: 71434
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 281 "
            pdb=" OG  SER E  52 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OE2 GLU B 281 "
            pdb=" OG  SER G  52 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" OG1 THR A 288 "
            pdb=" OD1 ASP A 290 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" N   GLU E  89 "
            pdb=" OE1 GLU E  89 "
     model   vdw
     2.245 3.120
  nonbonded pdb=" OG  SER B 103 "
            pdb=" OE1 GLN B 175 "
     model   vdw
     2.247 3.040
  ... (remaining 71429 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.350
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
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      :  0.003   0.040   9166  Z= 0.134
  Angle     :  0.680  13.252  12442  Z= 0.386
  Chirality :  0.043   0.243   1330
  Planarity :  0.003   0.035   1578
  Dihedral  : 14.344  86.610   3306
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  9.86 %
    Favored  : 89.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 1.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.48 (0.26), residues: 1122
  helix: -1.02 (0.57), residues: 68
  sheet: -0.59 (0.29), residues: 360
  loop : -1.20 (0.25), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  24 
 TYR   0.011   0.001   TYR B  32 
 PHE   0.030   0.001   PHE B  20 
 TRP   0.017   0.001   TRP E 108 
 HIS   0.001   0.000   HIS B 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 9150)
  covalent geometry    : angle       0.67998 (12410)
  SS BOND              : bond        0.00125 (   16)
  SS BOND              : angle       0.46009 (   32)
  hydrogen bonds       : bond        0.28486 (  219)
  hydrogen bonds       : angle       9.75418 (  564)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8624 (tpp) cc_final: 0.8311 (tpt)
REVERT: A  333 MET cc_start: 0.8412 (mmm) cc_final: 0.7857 (mtt)
REVERT: E  110 GLN cc_start: 0.8509 (mp10) cc_final: 0.7687 (pp30)
  outliers start: 3
  outliers final: 3
  residues processed: 68
  average time/residue: 0.0863
  time to fit residues: 8.4581
Evaluate side-chains
  67 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue   97 MET
Chi-restraints excluded: chain F residue    3 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.0980
   chunk 106 optimal weight:    0.0030
   overall best weight:    1.0196

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 GLN
** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 175 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.063074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.046168 restraints weight = 42053.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.047660 restraints weight = 20034.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.048680 restraints weight = 13154.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.049295 restraints weight = 10209.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.049635 restraints weight = 8781.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.1120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9166  Z= 0.133
  Angle     :  0.629  12.095  12442  Z= 0.331
  Chirality :  0.043   0.231   1330
  Planarity :  0.004   0.029   1578
  Dihedral  :  4.944  48.360   1237
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  9.96 %
    Favored  : 89.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 1.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.40 (0.26), residues: 1122
  helix: -0.29 (0.59), residues: 72
  sheet: -0.45 (0.29), residues: 348
  loop : -1.28 (0.24), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  72 
 TYR   0.010   0.001   TYR B  32 
 PHE   0.018   0.001   PHE B  34 
 TRP   0.015   0.001   TRP E 108 
 HIS   0.002   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 9150)
  covalent geometry    : angle       0.62863 (12410)
  SS BOND              : bond        0.00186 (   16)
  SS BOND              : angle       0.58223 (   32)
  hydrogen bonds       : bond        0.04380 (  219)
  hydrogen bonds       : angle       6.27252 (  564)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  272 ARG cc_start: 0.8435 (mtt90) cc_final: 0.8190 (ttm110)
REVERT: G   59 ASP cc_start: 0.8907 (t0) cc_final: 0.8706 (t0)
  outliers start: 10
  outliers final: 6
  residues processed: 73
  average time/residue: 0.0850
  time to fit residues: 9.1528
Evaluate side-chains
  70 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain F residue    2 ILE
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 59 optimal weight:    5.9990
   chunk 39 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   chunk 101 optimal weight:    1.9990
   chunk 95 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 74 optimal weight:    0.5980
   chunk 69 optimal weight:    9.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.061982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.044990 restraints weight = 41746.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.046496 restraints weight = 20002.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.047380 restraints weight = 13161.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.048060 restraints weight = 10353.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.048385 restraints weight = 8917.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.1462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9166  Z= 0.166
  Angle     :  0.627  11.969  12442  Z= 0.328
  Chirality :  0.043   0.233   1330
  Planarity :  0.003   0.029   1578
  Dihedral  :  4.959  57.921   1234
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 11.81 %
    Favored  : 87.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 1.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.39 (0.26), residues: 1122
  helix:  0.16 (0.60), residues: 72
  sheet: -0.58 (0.29), residues: 364
  loop : -1.25 (0.25), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  72 
 TYR   0.011   0.001   TYR H  87 
 PHE   0.019   0.001   PHE A  34 
 TRP   0.016   0.001   TRP E 108 
 HIS   0.003   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 9150)
  covalent geometry    : angle       0.62725 (12410)
  SS BOND              : bond        0.00205 (   16)
  SS BOND              : angle       0.60081 (   32)
  hydrogen bonds       : bond        0.04080 (  219)
  hydrogen bonds       : angle       5.66197 (  564)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 GLN cc_start: 0.9037 (pm20) cc_final: 0.8659 (pm20)
REVERT: B   34 PHE cc_start: 0.6508 (m-80) cc_final: 0.6214 (m-10)
REVERT: B   67 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8292 (tmm)
REVERT: B  272 ARG cc_start: 0.8446 (mtt90) cc_final: 0.8177 (ttm110)
REVERT: E   59 ASP cc_start: 0.8386 (t0) cc_final: 0.8151 (t0)
REVERT: E   76 LYS cc_start: 0.9462 (ptpp) cc_final: 0.9222 (ptpp)
REVERT: E  110 GLN cc_start: 0.8637 (mp10) cc_final: 0.7742 (pp30)
REVERT: G    1 GLN cc_start: 0.7967 (tp-100) cc_final: 0.7517 (tm-30)
  outliers start: 6
  outliers final: 4
  residues processed: 71
  average time/residue: 0.0897
  time to fit residues: 9.3589
Evaluate side-chains
  70 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue   97 MET
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 45 optimal weight:    0.0170
   chunk 76 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 108 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9980
   chunk 72 optimal weight:    6.9990
   chunk 44 optimal weight:    4.9990
   chunk 28 optimal weight:    0.7980
   chunk 7 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 73 optimal weight:    4.9990
   overall best weight:    0.7418

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 GLN
B 254 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.062969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.045991 restraints weight = 42076.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.047460 restraints weight = 19834.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.048489 restraints weight = 13006.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.049130 restraints weight = 10084.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.049464 restraints weight = 8655.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9166  Z= 0.113
  Angle     :  0.601  11.846  12442  Z= 0.314
  Chirality :  0.042   0.235   1330
  Planarity :  0.003   0.030   1578
  Dihedral  :  4.724  52.277   1233
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 12.83 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 1.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.41 (0.26), residues: 1122
  helix:  0.20 (0.59), residues: 72
  sheet: -0.58 (0.29), residues: 350
  loop : -1.27 (0.24), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  72 
 TYR   0.009   0.001   TYR A  32 
 PHE   0.029   0.001   PHE A  34 
 TRP   0.013   0.001   TRP E 108 
 HIS   0.002   0.000   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 9150)
  covalent geometry    : angle       0.60093 (12410)
  SS BOND              : bond        0.00156 (   16)
  SS BOND              : angle       0.50233 (   32)
  hydrogen bonds       : bond        0.03471 (  219)
  hydrogen bonds       : angle       5.44110 (  564)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 GLN cc_start: 0.8991 (pm20) cc_final: 0.8622 (pm20)
REVERT: A   67 MET cc_start: 0.8421 (tpp) cc_final: 0.8198 (tpp)
REVERT: A   68 TRP cc_start: 0.9376 (m100) cc_final: 0.9170 (m100)
REVERT: A  184 MET cc_start: 0.8482 (tpp) cc_final: 0.8176 (ttt)
REVERT: B   67 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8183 (tmm)
REVERT: B  174 ARG cc_start: 0.8619 (ptp90) cc_final: 0.8182 (pmt-80)
REVERT: B  272 ARG cc_start: 0.8369 (mtt90) cc_final: 0.8076 (ttm110)
REVERT: E   59 ASP cc_start: 0.8209 (t0) cc_final: 0.7907 (t0)
REVERT: E   76 LYS cc_start: 0.9475 (ptpp) cc_final: 0.9229 (ptpp)
REVERT: G    3 GLN cc_start: 0.8039 (mp10) cc_final: 0.7756 (mp10)
REVERT: G   59 ASP cc_start: 0.8879 (t0) cc_final: 0.8612 (t0)
  outliers start: 10
  outliers final: 5
  residues processed: 74
  average time/residue: 0.1008
  time to fit residues: 10.6219
Evaluate side-chains
  73 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue   97 MET
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 95 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   chunk 63 optimal weight:    0.2980
   chunk 13 optimal weight:    6.9990
   chunk 97 optimal weight:    6.9990
   chunk 43 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.062827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.045802 restraints weight = 42084.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.047279 restraints weight = 19961.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.048292 restraints weight = 13098.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.048929 restraints weight = 10214.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.049244 restraints weight = 8807.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.1741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9166  Z= 0.123
  Angle     :  0.611  11.806  12442  Z= 0.316
  Chirality :  0.042   0.233   1330
  Planarity :  0.003   0.032   1578
  Dihedral  :  4.594  45.582   1233
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 13.35 %
    Favored  : 85.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 1.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.26), residues: 1122
  helix:  0.34 (0.59), residues: 72
  sheet: -0.62 (0.29), residues: 362
  loop : -1.14 (0.25), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  72 
 TYR   0.016   0.001   TYR A  32 
 PHE   0.012   0.001   PHE A  34 
 TRP   0.013   0.001   TRP E 108 
 HIS   0.002   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 9150)
  covalent geometry    : angle       0.61122 (12410)
  SS BOND              : bond        0.00165 (   16)
  SS BOND              : angle       0.49137 (   32)
  hydrogen bonds       : bond        0.03386 (  219)
  hydrogen bonds       : angle       5.34866 (  564)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8652 (pm20)
REVERT: A   67 MET cc_start: 0.8412 (tpp) cc_final: 0.8148 (tpp)
REVERT: A  184 MET cc_start: 0.8468 (tpp) cc_final: 0.7948 (ttt)
REVERT: B   67 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.7562 (tpp)
REVERT: B  123 MET cc_start: 0.8383 (tpp) cc_final: 0.8126 (tpt)
REVERT: B  174 ARG cc_start: 0.8668 (ptp90) cc_final: 0.8218 (pmt-80)
REVERT: B  272 ARG cc_start: 0.8428 (mtt90) cc_final: 0.8131 (ttm110)
REVERT: E   59 ASP cc_start: 0.8322 (t0) cc_final: 0.7987 (t0)
REVERT: E   76 LYS cc_start: 0.9480 (ptpp) cc_final: 0.9243 (ptpp)
REVERT: E  110 GLN cc_start: 0.8527 (mp10) cc_final: 0.7769 (pp30)
REVERT: F   79 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8697 (mm)
REVERT: G    1 GLN cc_start: 0.8010 (tp-100) cc_final: 0.7588 (tm-30)
REVERT: G    3 GLN cc_start: 0.8118 (mp10) cc_final: 0.7068 (mp10)
REVERT: G   59 ASP cc_start: 0.8835 (t0) cc_final: 0.8543 (t0)
  outliers start: 16
  outliers final: 6
  residues processed: 77
  average time/residue: 0.0953
  time to fit residues: 10.6050
Evaluate side-chains
  75 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 GLN
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue   97 MET
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue   79 LEU
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 105 optimal weight:    0.2980
   chunk 109 optimal weight:    1.9990
   chunk 8 optimal weight:    7.9990
   chunk 41 optimal weight:    7.9990
   chunk 2 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0870
   chunk 100 optimal weight:    1.9990
   overall best weight:    0.8160

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.063098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.046118 restraints weight = 41734.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.047627 restraints weight = 19857.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.048629 restraints weight = 13007.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.049270 restraints weight = 10087.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.049594 restraints weight = 8686.516|
|-----------------------------------------------------------------------------|
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.1909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9166  Z= 0.114
  Angle     :  0.606  11.786  12442  Z= 0.313
  Chirality :  0.043   0.233   1330
  Planarity :  0.003   0.032   1578
  Dihedral  :  4.478  41.824   1233
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 14.37 %
    Favored  : 84.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 1.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.27 (0.26), residues: 1122
  helix:  0.35 (0.60), residues: 72
  sheet: -0.57 (0.29), residues: 362
  loop : -1.14 (0.25), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  62 
 TYR   0.016   0.001   TYR A  32 
 PHE   0.026   0.001   PHE B  20 
 TRP   0.011   0.001   TRP E 108 
 HIS   0.002   0.000   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 9150)
  covalent geometry    : angle       0.60607 (12410)
  SS BOND              : bond        0.00156 (   16)
  SS BOND              : angle       0.47392 (   32)
  hydrogen bonds       : bond        0.03230 (  219)
  hydrogen bonds       : angle       5.21161 (  564)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8654 (pm20)
REVERT: A   97 MET cc_start: 0.8759 (tpp) cc_final: 0.8487 (mmt)
REVERT: A  184 MET cc_start: 0.8405 (tpp) cc_final: 0.8162 (ttt)
REVERT: B   67 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7480 (tpp)
REVERT: B  123 MET cc_start: 0.8486 (tpp) cc_final: 0.8258 (tpt)
REVERT: B  174 ARG cc_start: 0.8695 (ptp90) cc_final: 0.8181 (pmt-80)
REVERT: B  272 ARG cc_start: 0.8453 (mtt90) cc_final: 0.8151 (ttm110)
REVERT: E   59 ASP cc_start: 0.8267 (t0) cc_final: 0.7905 (t0)
REVERT: E   65 LYS cc_start: 0.9374 (mmmm) cc_final: 0.9166 (mmmm)
REVERT: F   79 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8768 (mm)
REVERT: G    3 GLN cc_start: 0.8099 (mp10) cc_final: 0.7343 (mp10)
REVERT: G   59 ASP cc_start: 0.8856 (t0) cc_final: 0.8544 (t0)
  outliers start: 12
  outliers final: 6
  residues processed: 77
  average time/residue: 0.1001
  time to fit residues: 10.8527
Evaluate side-chains
  76 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 GLN
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue   97 MET
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain F residue   79 LEU
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 50 optimal weight:    8.9990
   chunk 15 optimal weight:   10.0000
   chunk 90 optimal weight:    9.9990
   chunk 61 optimal weight:    5.9990
   chunk 105 optimal weight:    0.0030
   chunk 37 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   chunk 102 optimal weight:   10.0000
   chunk 85 optimal weight:    0.4980
   chunk 97 optimal weight:    1.9990
   chunk 70 optimal weight:    5.9990
   overall best weight:    2.0996

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.061554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.044475 restraints weight = 42262.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.045954 restraints weight = 20193.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.046925 restraints weight = 13308.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.047527 restraints weight = 10400.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.047834 restraints weight = 8983.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9166  Z= 0.191
  Angle     :  0.650  11.847  12442  Z= 0.334
  Chirality :  0.043   0.234   1330
  Planarity :  0.003   0.032   1578
  Dihedral  :  4.765  42.541   1233
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 15.50 %
    Favored  : 83.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 1.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.23 (0.26), residues: 1122
  helix:  0.57 (0.62), residues: 72
  sheet: -0.58 (0.30), residues: 340
  loop : -1.10 (0.24), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  18 
 TYR   0.013   0.001   TYR A 323 
 PHE   0.008   0.001   PHE A 279 
 TRP   0.012   0.001   TRP E 108 
 HIS   0.004   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 9150)
  covalent geometry    : angle       0.65040 (12410)
  SS BOND              : bond        0.00239 (   16)
  SS BOND              : angle       0.53639 (   32)
  hydrogen bonds       : bond        0.03541 (  219)
  hydrogen bonds       : angle       5.26192 (  564)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8684 (pm20)
REVERT: A  184 MET cc_start: 0.8582 (tpp) cc_final: 0.8228 (ttt)
REVERT: B   67 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.7368 (tpp)
REVERT: B  123 MET cc_start: 0.8638 (tpp) cc_final: 0.8424 (tpt)
REVERT: B  241 MET cc_start: 0.8847 (mtp) cc_final: 0.8586 (mtp)
REVERT: B  272 ARG cc_start: 0.8481 (mtt90) cc_final: 0.8172 (ttm110)
REVERT: E   59 ASP cc_start: 0.8553 (t0) cc_final: 0.8100 (t0)
REVERT: E   65 LYS cc_start: 0.9460 (mmmm) cc_final: 0.9222 (mmmm)
REVERT: E   76 LYS cc_start: 0.9464 (ptpp) cc_final: 0.9262 (ptpp)
REVERT: E  110 GLN cc_start: 0.8516 (mp10) cc_final: 0.7813 (pp30)
REVERT: F   79 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8790 (mm)
REVERT: G    3 GLN cc_start: 0.8046 (mp10) cc_final: 0.7024 (mp10)
REVERT: G   59 ASP cc_start: 0.8928 (t0) cc_final: 0.8270 (t0)
  outliers start: 14
  outliers final: 8
  residues processed: 73
  average time/residue: 0.0896
  time to fit residues: 9.5975
Evaluate side-chains
  76 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 GLN
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue   97 MET
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain E residue  114 VAL
Chi-restraints excluded: chain F residue   79 LEU
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 37 optimal weight:    0.0030
   chunk 29 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   chunk 42 optimal weight:    9.9990
   chunk 81 optimal weight:    9.9990
   chunk 20 optimal weight:    4.9990
   chunk 71 optimal weight:    6.9990
   chunk 28 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   overall best weight:    1.7996

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.061592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.044612 restraints weight = 42079.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.046065 restraints weight = 20218.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.047051 restraints weight = 13341.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.047596 restraints weight = 10453.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.047999 restraints weight = 9067.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9166  Z= 0.172
  Angle     :  0.654  11.839  12442  Z= 0.335
  Chirality :  0.043   0.234   1330
  Planarity :  0.003   0.033   1578
  Dihedral  :  4.749  40.498   1233
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.40 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 15.50 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 1.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.19 (0.26), residues: 1122
  helix:  0.71 (0.62), residues: 72
  sheet: -0.58 (0.30), residues: 344
  loop : -1.06 (0.25), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  72 
 TYR   0.012   0.001   TYR A  32 
 PHE   0.027   0.001   PHE B  20 
 TRP   0.011   0.001   TRP E 108 
 HIS   0.004   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 9150)
  covalent geometry    : angle       0.65422 (12410)
  SS BOND              : bond        0.00212 (   16)
  SS BOND              : angle       0.51731 (   32)
  hydrogen bonds       : bond        0.03425 (  219)
  hydrogen bonds       : angle       5.30346 (  564)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8683 (pm20)
REVERT: A  184 MET cc_start: 0.8450 (tpp) cc_final: 0.8120 (ttt)
REVERT: B   67 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.7507 (tpp)
REVERT: B  123 MET cc_start: 0.8723 (tpp) cc_final: 0.8491 (tpt)
REVERT: B  272 ARG cc_start: 0.8548 (mtt90) cc_final: 0.8279 (ttm110)
REVERT: E   58 THR cc_start: 0.9198 (p) cc_final: 0.8989 (t)
REVERT: E   59 ASP cc_start: 0.8546 (t0) cc_final: 0.8054 (t0)
REVERT: E   65 LYS cc_start: 0.9424 (mmmm) cc_final: 0.9167 (mmmm)
REVERT: E  110 GLN cc_start: 0.8497 (mp10) cc_final: 0.7774 (pp30)
REVERT: F   79 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8831 (mm)
REVERT: G   59 ASP cc_start: 0.8936 (t0) cc_final: 0.8297 (t0)
  outliers start: 16
  outliers final: 10
  residues processed: 76
  average time/residue: 0.0899
  time to fit residues: 10.0400
Evaluate side-chains
  76 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 GLN
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue   97 MET
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain E residue  114 VAL
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue   79 LEU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 100 optimal weight:    7.9990
   chunk 21 optimal weight:    4.9990
   chunk 75 optimal weight:    4.9990
   chunk 89 optimal weight:    7.9990
   chunk 77 optimal weight:    3.9990
   chunk 91 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 43 optimal weight:    4.9990
   chunk 101 optimal weight:    0.0050
   chunk 57 optimal weight:    0.3980
   chunk 64 optimal weight:    1.9990
   overall best weight:    1.0398

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.062198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.045225 restraints weight = 41737.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.046683 restraints weight = 20008.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.047679 restraints weight = 13203.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.048275 restraints weight = 10325.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.048648 restraints weight = 8914.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.2210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9166  Z= 0.129
  Angle     :  0.650  13.847  12442  Z= 0.332
  Chirality :  0.043   0.233   1330
  Planarity :  0.003   0.035   1578
  Dihedral  :  4.615  38.259   1233
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.49 %
    Favored  : 92.51 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 15.91 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 1.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.13 (0.26), residues: 1122
  helix:  0.71 (0.62), residues: 72
  sheet: -0.48 (0.30), residues: 342
  loop : -1.05 (0.25), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  18 
 TYR   0.015   0.001   TYR A  32 
 PHE   0.015   0.001   PHE A  34 
 TRP   0.015   0.001   TRP A  68 
 HIS   0.003   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 9150)
  covalent geometry    : angle       0.65065 (12410)
  SS BOND              : bond        0.00169 (   16)
  SS BOND              : angle       0.48683 (   32)
  hydrogen bonds       : bond        0.03281 (  219)
  hydrogen bonds       : angle       5.22312 (  564)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8673 (pm20)
REVERT: A  184 MET cc_start: 0.8482 (tpp) cc_final: 0.8198 (ttt)
REVERT: B  123 MET cc_start: 0.8743 (tpp) cc_final: 0.8518 (tpt)
REVERT: B  272 ARG cc_start: 0.8500 (mtt90) cc_final: 0.8234 (ttm110)
REVERT: E   59 ASP cc_start: 0.8460 (t0) cc_final: 0.8032 (t0)
REVERT: E   65 LYS cc_start: 0.9425 (mmmm) cc_final: 0.9168 (mmmm)
REVERT: E  110 GLN cc_start: 0.8456 (mp10) cc_final: 0.7752 (pp30)
REVERT: F   79 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8746 (mm)
REVERT: G   59 ASP cc_start: 0.8913 (t0) cc_final: 0.8281 (t0)
  outliers start: 12
  outliers final: 8
  residues processed: 73
  average time/residue: 0.0958
  time to fit residues: 9.9847
Evaluate side-chains
  74 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 GLN
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain B residue   97 MET
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue   79 LEU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 61 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 91 optimal weight:    0.8980
   chunk 100 optimal weight:    0.8980
   chunk 18 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 93 optimal weight:    0.4980
   chunk 70 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 GLN
** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.062018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.045061 restraints weight = 41693.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.046544 restraints weight = 19943.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.047532 restraints weight = 13145.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.048082 restraints weight = 10245.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.048482 restraints weight = 8911.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9166  Z= 0.144
  Angle     :  0.668  16.241  12442  Z= 0.340
  Chirality :  0.044   0.233   1330
  Planarity :  0.003   0.037   1578
  Dihedral  :  4.459  30.449   1230
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 16.22 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 1.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.26), residues: 1122
  helix:  1.05 (0.64), residues: 68
  sheet: -0.43 (0.30), residues: 338
  loop : -0.99 (0.25), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 174 
 TYR   0.018   0.001   TYR A  32 
 PHE   0.029   0.001   PHE B  20 
 TRP   0.015   0.001   TRP A  68 
 HIS   0.003   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 9150)
  covalent geometry    : angle       0.66789 (12410)
  SS BOND              : bond        0.00180 (   16)
  SS BOND              : angle       0.49606 (   32)
  hydrogen bonds       : bond        0.03356 (  219)
  hydrogen bonds       : angle       5.22608 (  564)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8678 (pm20)
REVERT: B  123 MET cc_start: 0.8836 (tpp) cc_final: 0.8629 (tpt)
REVERT: B  174 ARG cc_start: 0.8719 (ptt-90) cc_final: 0.7977 (pmt-80)
REVERT: E   59 ASP cc_start: 0.8494 (t0) cc_final: 0.8045 (t0)
REVERT: E   65 LYS cc_start: 0.9420 (mmmm) cc_final: 0.9159 (mmmm)
REVERT: E  110 GLN cc_start: 0.8459 (mp10) cc_final: 0.7783 (pp30)
REVERT: F   79 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8840 (mm)
REVERT: G   59 ASP cc_start: 0.8939 (t0) cc_final: 0.8646 (t0)
  outliers start: 12
  outliers final: 9
  residues processed: 74
  average time/residue: 0.0980
  time to fit residues: 10.1508
Evaluate side-chains
  75 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 GLN
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain B residue   97 MET
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain E residue  114 VAL
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue   79 LEU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 77 optimal weight:    7.9990
   chunk 69 optimal weight:   10.0000
   chunk 35 optimal weight:   20.0000
   chunk 104 optimal weight:    0.9990
   chunk 14 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 45 optimal weight:    9.9990
   chunk 32 optimal weight:    5.9990
   chunk 2 optimal weight:    8.9990
   chunk 70 optimal weight:    6.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 GLN
** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.061116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.043058 restraints weight = 41920.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.044500 restraints weight = 21158.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.045463 restraints weight = 14425.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.046011 restraints weight = 11527.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.046375 restraints weight = 10123.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.2687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.068   9166  Z= 0.359
  Angle     :  0.811  19.032  12442  Z= 0.413
  Chirality :  0.046   0.237   1330
  Planarity :  0.004   0.041   1578
  Dihedral  :  5.229  32.164   1230
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 16.32 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 1.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.19 (0.26), residues: 1122
  helix:  1.08 (0.64), residues: 68
  sheet: -0.42 (0.30), residues: 320
  loop : -1.18 (0.24), residues: 734

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 272 
 TYR   0.021   0.002   TYR H  87 
 PHE   0.025   0.002   PHE A  34 
 TRP   0.019   0.002   TRP B 168 
 HIS   0.007   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00797 ( 9150)
  covalent geometry    : angle       0.81178 (12410)
  SS BOND              : bond        0.00386 (   16)
  SS BOND              : angle       0.67491 (   32)
  hydrogen bonds       : bond        0.04153 (  219)
  hydrogen bonds       : angle       5.56291 (  564)

===============================================================================
Job complete
usr+sys time: 1563.79 seconds
wall clock time: 27 minutes 48.35 seconds (1668.35 seconds total)