Starting phenix.real_space_refine
on Tue Feb  3 13:54:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9oka_70557/02_2026/9oka_70557.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9oka_70557/02_2026/9oka_70557.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9oka_70557/02_2026/9oka_70557.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9oka_70557/02_2026/9oka_70557.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9oka_70557/02_2026/9oka_70557.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9oka_70557/02_2026/9oka_70557.map"
  }
  resolution = 2.92
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      15      5.16       5
     C    2045      2.51       5
     N     560      2.21       5
     O     715      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3335
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "E"
      Number of atoms: 667
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 87, 667
          Classifications: {'peptide': 87}
          Link IDs: {'PTRANS': 5, 'TRANS': 81}
          Chain breaks: 1
  Restraints were copied for chains:
    C, D, B, A
  Residues with excluded nonbonded symmetry interactions: 5
    residue:
      pdb=" N  ASER E  11 " occ=0.96
      ... (4 atoms not shown)
      pdb=" OG ASER E  11 " occ=0.96
    residue:
      pdb=" N  ASER C  11 " occ=0.96
      ... (4 atoms not shown)
      pdb=" OG ASER C  11 " occ=0.96
    residue:
      pdb=" N  ASER D  11 " occ=0.96
      ... (4 atoms not shown)
      pdb=" OG ASER D  11 " occ=0.96
    residue:
      pdb=" N  ASER B  11 " occ=0.96
      ... (4 atoms not shown)
      pdb=" OG ASER B  11 " occ=0.96
    residue:
      pdb=" N  ASER A  11 " occ=0.96
      ... (4 atoms not shown)
      pdb=" OG ASER A  11 " occ=0.96
  Time building chain proxies: 0.60, per 1000 atoms: 0.18
  Number of scatterers: 3335
  At special positions: 0
  Unit cell: (79.2, 74.7, 45, 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      15     16.00
     O     715      8.00
     N     560      7.00
     C    2045      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  91 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  91 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  91 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  91 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  91 " 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: 0.28
  Conformation dependent library (CDL) restraints added in 140.7 milliseconds
  

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  820

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 47.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 4
      removed outlier: 6.515A  pdb=" N   MET E   3 " --> pdb=" O   LEU D   4 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   MET C   3 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   MET B   3 " --> pdb=" O   LEU A   4 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 9 through 10
      removed outlier: 6.534A  pdb=" N   SER E   9 " --> pdb=" O   VAL D  10 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   SER C   9 " --> pdb=" O   VAL B  10 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   SER B   9 " --> pdb=" O   VAL A  10 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 19 through 21
      removed outlier: 6.343A  pdb=" N   ILE C  20 " --> pdb=" O   SER D  21 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   THR C  19 " --> pdb=" O   ILE B  20 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   THR B  19 " --> pdb=" O   ILE A  20 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 24 through 25
      removed outlier: 6.345A  pdb=" N   ARG E  24 " --> pdb=" O   SER D  25 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   ARG C  24 " --> pdb=" O   SER B  25 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   ARG B  24 " --> pdb=" O   SER A  25 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 28 through 39
      removed outlier: 6.516A  pdb=" N   SER E  28 " --> pdb=" O   ILE D  29 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   SER D  31 " --> pdb=" O   SER E  28 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ALA E  30 " --> pdb=" O   SER D  31 " (cutoff:3.500A)
      removed outlier: 7.626A  pdb=" N   TYR D  33 " --> pdb=" O   ALA E  30 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   ASN E  32 " --> pdb=" O   TYR D  33 " (cutoff:3.500A)
      removed outlier: 7.894A  pdb=" N   GLN D  35 " --> pdb=" O   ASN E  32 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   VAL E  34 " --> pdb=" O   GLN D  35 " (cutoff:3.500A)
      removed outlier: 7.713A  pdb=" N   TYR D  37 " --> pdb=" O   VAL E  34 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   TRP E  36 " --> pdb=" O   TYR D  37 " (cutoff:3.500A)
      removed outlier: 7.594A  pdb=" N   GLN D  39 " --> pdb=" O   TRP E  36 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   GLN E  38 " --> pdb=" O   GLN D  39 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 61 through 66
      removed outlier: 6.573A  pdb=" N   ASP C  61 " --> pdb=" O   ARG B  62 " (cutoff:3.500A)
      removed outlier: 7.965A  pdb=" N   SER B  64 " --> pdb=" O   ASP C  61 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   PHE C  63 " --> pdb=" O   SER B  64 " (cutoff:3.500A)
      removed outlier: 7.982A  pdb=" N   SER B  66 " --> pdb=" O   PHE C  63 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   GLY C  65 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   ASP B  61 " --> pdb=" O   ARG A  62 " (cutoff:3.500A)
      removed outlier: 8.001A  pdb=" N   SER A  64 " --> pdb=" O   ASP B  61 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   PHE B  63 " --> pdb=" O   SER A  64 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   SER A  66 " --> pdb=" O   PHE B  63 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   GLY B  65 " --> pdb=" O   SER A  66 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 70 through 78
      removed outlier: 6.830A  pdb=" N   SER E  70 " --> pdb=" O   SER D  71 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   SER D  73 " --> pdb=" O   SER E  70 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   ASN E  72 " --> pdb=" O   SER D  73 " (cutoff:3.500A)
      removed outlier: 8.018A  pdb=" N   SER D  75 " --> pdb=" O   ASN E  72 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   ALA E  74 " --> pdb=" O   SER D  75 " (cutoff:3.500A)
      removed outlier: 7.945A  pdb=" N   THR D  77 " --> pdb=" O   ALA E  74 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   LEU E  76 " --> pdb=" O   THR D  77 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   SER C  70 " --> pdb=" O   SER B  71 " (cutoff:3.500A)
      removed outlier: 7.955A  pdb=" N   SER B  73 " --> pdb=" O   SER C  70 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   ASN C  72 " --> pdb=" O   SER B  73 " (cutoff:3.500A)
      removed outlier: 8.045A  pdb=" N   SER B  75 " --> pdb=" O   ASN C  72 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   ALA C  74 " --> pdb=" O   SER B  75 " (cutoff:3.500A)
      removed outlier: 7.955A  pdb=" N   THR B  77 " --> pdb=" O   ALA C  74 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   LEU C  76 " --> pdb=" O   THR B  77 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   SER B  70 " --> pdb=" O   SER A  71 " (cutoff:3.500A)
      removed outlier: 7.874A  pdb=" N   SER A  73 " --> pdb=" O   SER B  70 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ASN B  72 " --> pdb=" O   SER A  73 " (cutoff:3.500A)
      removed outlier: 7.964A  pdb=" N   SER A  75 " --> pdb=" O   ASN B  72 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   ALA B  74 " --> pdb=" O   SER A  75 " (cutoff:3.500A)
      removed outlier: 7.883A  pdb=" N   THR A  77 " --> pdb=" O   ALA B  74 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   LEU B  76 " --> pdb=" O   THR A  77 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 81 through 82
      removed outlier: 5.908A  pdb=" N   LEU C  81 " --> pdb=" O   GLN D  82 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 88 through 97
      removed outlier: 6.332A  pdb=" N   TYR E  89 " --> pdb=" O   TYR D  90 " (cutoff:3.500A)
      removed outlier: 7.153A  pdb=" N   GLN D  92 " --> pdb=" O   TYR E  89 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   CYS E  91 " --> pdb=" O   GLN D  92 " (cutoff:3.500A)
      removed outlier: 7.802A  pdb=" N   TYR D  94 " --> pdb=" O   CYS E  91 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   SER E  93 " --> pdb=" O   TYR D  94 " (cutoff:3.500A)
      removed outlier: 8.171A  pdb=" N   SER D  96 " --> pdb=" O   SER E  93 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   ASP E  95 " --> pdb=" O   SER D  96 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   TYR C  89 " --> pdb=" O   TYR B  90 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   GLN B  92 " --> pdb=" O   TYR C  89 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   CYS C  91 " --> pdb=" O   GLN B  92 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   TYR B  94 " --> pdb=" O   CYS C  91 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   SER C  93 " --> pdb=" O   TYR B  94 " (cutoff:3.500A)
      removed outlier: 8.143A  pdb=" N   SER B  96 " --> pdb=" O   SER C  93 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   ASP C  95 " --> pdb=" O   SER B  96 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 100 through 102
      removed outlier: 6.386A  pdb=" N   HIS C 100 " --> pdb=" O   VAL D 101 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   VAL C 101 " --> pdb=" O   VAL B 102 " (cutoff:3.500A)

    81 hydrogen bonds defined for protein.
    243 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.49

  Time building geometry restraints manager: 0.40 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1100
        1.35 -     1.46: 782
        1.46 -     1.58: 1508
        1.58 -     1.69: 0
        1.69 -     1.81: 20
  Bond restraints: 3410
  Sorted by residual:
  bond pdb=" C   VAL E  59 "
       pdb=" N   PRO E  60 "
    ideal  model  delta    sigma   weight residual
    1.334  1.357 -0.024 2.34e-02 1.83e+03 1.02e+00
  bond pdb=" C   VAL D  59 "
       pdb=" N   PRO D  60 "
    ideal  model  delta    sigma   weight residual
    1.334  1.357 -0.023 2.34e-02 1.83e+03 1.00e+00
  bond pdb=" C   VAL B  59 "
       pdb=" N   PRO B  60 "
    ideal  model  delta    sigma   weight residual
    1.334  1.357 -0.023 2.34e-02 1.83e+03 9.85e-01
  bond pdb=" C   VAL C  59 "
       pdb=" N   PRO C  60 "
    ideal  model  delta    sigma   weight residual
    1.334  1.357 -0.023 2.34e-02 1.83e+03 9.56e-01
  bond pdb=" C   VAL A  59 "
       pdb=" N   PRO A  60 "
    ideal  model  delta    sigma   weight residual
    1.334  1.357 -0.023 2.34e-02 1.83e+03 9.39e-01
  ... (remaining 3405 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.27: 4466
        1.27 -     2.54: 125
        2.54 -     3.81: 29
        3.81 -     5.08: 5
        5.08 -     6.35: 10
  Bond angle restraints: 4635
  Sorted by residual:
  angle pdb=" N   ILE B  67 "
        pdb=" CA  ILE B  67 "
        pdb=" C   ILE B  67 "
      ideal   model   delta    sigma   weight residual
     112.96  108.75    4.21 1.00e+00 1.00e+00 1.78e+01
  angle pdb=" N   ILE D  67 "
        pdb=" CA  ILE D  67 "
        pdb=" C   ILE D  67 "
      ideal   model   delta    sigma   weight residual
     112.96  108.75    4.21 1.00e+00 1.00e+00 1.77e+01
  angle pdb=" N   ILE C  67 "
        pdb=" CA  ILE C  67 "
        pdb=" C   ILE C  67 "
      ideal   model   delta    sigma   weight residual
     112.96  108.75    4.21 1.00e+00 1.00e+00 1.77e+01
  angle pdb=" N   ILE E  67 "
        pdb=" CA  ILE E  67 "
        pdb=" C   ILE E  67 "
      ideal   model   delta    sigma   weight residual
     112.96  108.76    4.20 1.00e+00 1.00e+00 1.77e+01
  angle pdb=" N   ILE A  67 "
        pdb=" CA  ILE A  67 "
        pdb=" C   ILE A  67 "
      ideal   model   delta    sigma   weight residual
     112.96  108.76    4.20 1.00e+00 1.00e+00 1.76e+01
  ... (remaining 4630 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     7.18: 1684
        7.18 -    14.36: 182
       14.36 -    21.55: 99
       21.55 -    28.73: 55
       28.73 -    35.91: 25
  Dihedral angle restraints: 2045
    sinusoidal: 775
      harmonic: 1270
  Sorted by residual:
  dihedral pdb=" CA  ASN B  32 "
           pdb=" C   ASN B  32 "
           pdb=" N   TYR B  33 "
           pdb=" CA  TYR B  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.02  -17.98     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  ASN A  32 "
           pdb=" C   ASN A  32 "
           pdb=" N   TYR A  33 "
           pdb=" CA  TYR A  33 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.05  -17.95     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  ASN C  32 "
           pdb=" C   ASN C  32 "
           pdb=" N   TYR C  33 "
           pdb=" CA  TYR C  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.05  -17.95     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 2042 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 216
       0.024 -    0.048: 171
       0.048 -    0.071: 68
       0.071 -    0.095: 19
       0.095 -    0.119: 31
  Chirality restraints: 505
  Sorted by residual:
  chirality pdb=" CA  ILE A  29 "
            pdb=" N   ILE A  29 "
            pdb=" C   ILE A  29 "
            pdb=" CB  ILE A  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.54e-01
  chirality pdb=" CA  ILE C  78 "
            pdb=" N   ILE C  78 "
            pdb=" C   ILE C  78 "
            pdb=" CB  ILE C  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.42e-01
  chirality pdb=" CA  ILE E  29 "
            pdb=" N   ILE E  29 "
            pdb=" C   ILE E  29 "
            pdb=" CB  ILE E  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.42e-01
  ... (remaining 502 not shown)

  Planarity restraints: 610
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN D   6 "   -0.015 5.00e-02 4.00e+02   2.27e-02 8.21e-01
        pdb=" N   PRO D   7 "    0.039 5.00e-02 4.00e+02
        pdb=" CA  PRO D   7 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO D   7 "   -0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C   6 "   -0.015 5.00e-02 4.00e+02   2.26e-02 8.19e-01
        pdb=" N   PRO C   7 "    0.039 5.00e-02 4.00e+02
        pdb=" CA  PRO C   7 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO C   7 "   -0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A   6 "   -0.015 5.00e-02 4.00e+02   2.26e-02 8.15e-01
        pdb=" N   PRO A   7 "    0.039 5.00e-02 4.00e+02
        pdb=" CA  PRO A   7 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A   7 "   -0.013 5.00e-02 4.00e+02
  ... (remaining 607 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 832
        2.82 -     3.34: 2897
        3.34 -     3.86: 5784
        3.86 -     4.38: 6338
        4.38 -     4.90: 11856
  Nonbonded interactions: 27707
  Sorted by model distance:
  nonbonded pdb=" O   VAL E  59 "
            pdb=" N   VAL D  59 "
     model   vdw
     2.298 3.120
  nonbonded pdb=" OD1 ASP C  95 "
            pdb=" NZ  LYS D  16 "
     model   vdw
     2.330 3.120
  nonbonded pdb=" NZ  LYS E  16 "
            pdb=" OD1 ASP D  95 "
     model   vdw
     2.355 3.120
  nonbonded pdb=" O   VAL B  59 "
            pdb=" N   VAL A  59 "
     model   vdw
     2.362 3.120
  nonbonded pdb=" NZ  LYS B  16 "
            pdb=" OD1 ASP A  95 "
     model   vdw
     2.365 3.120
  ... (remaining 27702 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 'E'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'B'
  selection = chain 'A'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.96 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.400
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
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      :  0.002   0.024   3415  Z= 0.121
  Angle     :  0.602   6.350   4645  Z= 0.346
  Chirality :  0.045   0.119    505
  Planarity :  0.003   0.023    610
  Dihedral  :  9.734  35.909   1210
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.41 (0.31), residues: 415
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.35 (0.24), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  40 
 TYR   0.010   0.002   TYR C  33 
 PHE   0.005   0.001   PHE E  63 
 TRP   0.002   0.001   TRP B  36 
 HIS   0.001   0.000   HIS C   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 3410)
  covalent geometry    : angle       0.60225 ( 4635)
  SS BOND              : bond        0.00065 (    5)
  SS BOND              : angle       0.04618 (   10)
  hydrogen bonds       : bond        0.05941 (   81)
  hydrogen bonds       : angle       5.91895 (  243)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   16 LYS cc_start: 0.7476 (ttpt) cc_final: 0.6983 (tptt)
REVERT: E   36 TRP cc_start: 0.7935 (t60) cc_final: 0.7487 (t-100)
REVERT: C   38 GLN cc_start: 0.8108 (tt0) cc_final: 0.7679 (tt0)
REVERT: A    3 MET cc_start: 0.7668 (tpt) cc_final: 0.5335 (pmt)
REVERT: A   16 LYS cc_start: 0.7806 (ttpt) cc_final: 0.6533 (pmtt)
REVERT: A   98 ASN cc_start: 0.8641 (m-40) cc_final: 0.8282 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.4274
  time to fit residues: 56.7954
Evaluate side-chains
  56 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 26 optimal weight:    9.9990
   chunk 2 optimal weight:   20.0000
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:   10.0000
   chunk 25 optimal weight:    8.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:   40.0000
   chunk 22 optimal weight:   20.0000
   chunk 37 optimal weight:    9.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** E   1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  98 ASN
** C   1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 GLN
C  39 GLN
** D   1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  35 GLN
D  98 ASN
** B   1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  35 GLN
** A   1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  38 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4644 r_free = 0.4644 target = 0.129080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.104220 restraints weight = 6973.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.4393 rms_B_bonded: 4.76
r_work: 0.4328 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.4328
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4246
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4246 r_free = 0.4246    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4248 r_free = 0.4248    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4248
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7079
moved from start:          0.4435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.046   3415  Z= 0.329
  Angle     :  0.787   5.932   4645  Z= 0.416
  Chirality :  0.046   0.143    505
  Planarity :  0.004   0.022    610
  Dihedral  :  5.413  18.389    465
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.84 %
    Favored  : 89.16 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 14.68 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.67 (0.30), residues: 415
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.55 (0.23), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  40 
 TYR   0.027   0.004   TYR B  90 
 PHE   0.008   0.001   PHE E  63 
 TRP   0.039   0.004   TRP C  36 
 HIS   0.004   0.001   HIS E 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00722 ( 3410)
  covalent geometry    : angle       0.78577 ( 4635)
  SS BOND              : bond        0.00609 (    5)
  SS BOND              : angle       1.27054 (   10)
  hydrogen bonds       : bond        0.02683 (   81)
  hydrogen bonds       : angle       4.87908 (  243)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.156 
Fit side-chains
REVERT: E    3 MET cc_start: 0.8153 (mmm) cc_final: 0.7942 (ttt)
REVERT: E   33 TYR cc_start: 0.7868 (t80) cc_final: 0.7614 (t80)
REVERT: E   39 GLN cc_start: 0.8828 (tt0) cc_final: 0.8447 (tt0)
REVERT: E   90 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.7016 (t80)
REVERT: C   13 SER cc_start: 0.9222 (t) cc_final: 0.9013 (m)
REVERT: C   33 TYR cc_start: 0.8378 (t80) cc_final: 0.8170 (t80)
REVERT: D   12 GLU cc_start: 0.8977 (pm20) cc_final: 0.7725 (mm-30)
REVERT: B    6 GLN cc_start: 0.8568 (pt0) cc_final: 0.8042 (pt0)
REVERT: B   39 GLN cc_start: 0.8542 (tt0) cc_final: 0.8162 (mt0)
REVERT: A    6 GLN cc_start: 0.7724 (pt0) cc_final: 0.7130 (tp40)
REVERT: A   12 GLU cc_start: 0.8871 (pm20) cc_final: 0.8533 (pm20)
REVERT: A   13 SER cc_start: 0.6100 (OUTLIER) cc_final: 0.5759 (t)
REVERT: A   16 LYS cc_start: 0.7301 (ttpt) cc_final: 0.6276 (pmtt)
  outliers start: 14
  outliers final: 5
  residues processed: 90
  average time/residue: 0.2493
  time to fit residues: 23.7739
Evaluate side-chains
  68 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   90 TYR
Chi-restraints excluded: chain D residue    9 SER
Chi-restraints excluded: chain B residue    9 SER
Chi-restraints excluded: chain B residue   13 SER
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain A residue   13 SER
Chi-restraints excluded: chain A residue   33 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 29 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9980
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    6.9990
   chunk 18 optimal weight:   10.0000
   chunk 31 optimal weight:    4.9990
   chunk 26 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
E   1 ASN
C   1 ASN
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   1 ASN
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  98 ASN
B   1 ASN
A   1 ASN
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4723 r_free = 0.4723 target = 0.135056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.109781 restraints weight = 6567.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.4468 rms_B_bonded: 4.57
r_work: 0.4447 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.4447
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4414
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4414 r_free = 0.4414    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4415 r_free = 0.4415    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4415
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6930
moved from start:          0.4633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3415  Z= 0.134
  Angle     :  0.703   7.394   4645  Z= 0.345
  Chirality :  0.045   0.132    505
  Planarity :  0.002   0.019    610
  Dihedral  :  4.755  18.580    465
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 20.25 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.52 (0.32), residues: 415
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.44 (0.24), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  62 
 TYR   0.014   0.002   TYR C  94 
 PHE   0.006   0.001   PHE D  63 
 TRP   0.010   0.001   TRP C  36 
 HIS   0.001   0.000   HIS E   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 3410)
  covalent geometry    : angle       0.70342 ( 4635)
  SS BOND              : bond        0.00163 (    5)
  SS BOND              : angle       0.35995 (   10)
  hydrogen bonds       : bond        0.01681 (   81)
  hydrogen bonds       : angle       4.41335 (  243)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.087 
Fit side-chains
REVERT: E   39 GLN cc_start: 0.8665 (tt0) cc_final: 0.8209 (tt0)
REVERT: D   12 GLU cc_start: 0.8838 (pm20) cc_final: 0.7732 (mm-30)
REVERT: B   39 GLN cc_start: 0.8430 (tt0) cc_final: 0.8049 (mt0)
REVERT: A    6 GLN cc_start: 0.7476 (pt0) cc_final: 0.7026 (tp-100)
REVERT: A   12 GLU cc_start: 0.8527 (pm20) cc_final: 0.8227 (pm20)
REVERT: A   13 SER cc_start: 0.5762 (OUTLIER) cc_final: 0.5552 (t)
REVERT: A   16 LYS cc_start: 0.7372 (ttpt) cc_final: 0.6271 (pmtt)
REVERT: A   86 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8100 (tm-30)
  outliers start: 13
  outliers final: 5
  residues processed: 79
  average time/residue: 0.3381
  time to fit residues: 27.9179
Evaluate side-chains
  69 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    9 SER
Chi-restraints excluded: chain B residue    9 SER
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain A residue   13 SER
Chi-restraints excluded: chain A residue   33 TYR
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   86 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 20 optimal weight:    9.9990
   chunk 13 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 25 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   chunk 17 optimal weight:    0.4980
   chunk 21 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 32 optimal weight:    0.2980
   chunk 15 optimal weight:   10.0000
   chunk 36 optimal weight:    0.0270
   overall best weight:    1.3642

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

Flipped N/Q/H residues before XYZ refinement:
E  98 ASN
D   6 GLN
D  98 ASN
A   6 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4708 r_free = 0.4708 target = 0.134641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.109341 restraints weight = 6547.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.4467 rms_B_bonded: 4.59
r_work: 0.4440 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.4440
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4401
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4401 r_free = 0.4401    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4402 r_free = 0.4402    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4402
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6932
moved from start:          0.4888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3415  Z= 0.143
  Angle     :  0.700   7.556   4645  Z= 0.342
  Chirality :  0.045   0.133    505
  Planarity :  0.003   0.019    610
  Dihedral  :  4.628  17.111    465
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.84 %
    Favored  : 89.16 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 23.29 %
    Favored  : 74.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.43 (0.32), residues: 415
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.37 (0.25), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  62 
 TYR   0.013   0.002   TYR C  94 
 PHE   0.005   0.001   PHE D  63 
 TRP   0.007   0.001   TRP C  36 
 HIS   0.001   0.000   HIS D   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 3410)
  covalent geometry    : angle       0.70109 ( 4635)
  SS BOND              : bond        0.00211 (    5)
  SS BOND              : angle       0.32348 (   10)
  hydrogen bonds       : bond        0.01646 (   81)
  hydrogen bonds       : angle       4.24284 (  243)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.137 
Fit side-chains
REVERT: E   39 GLN cc_start: 0.8636 (tt0) cc_final: 0.8228 (tt0)
REVERT: E   85 ASP cc_start: 0.6782 (OUTLIER) cc_final: 0.5598 (p0)
REVERT: C    6 GLN cc_start: 0.8517 (pt0) cc_final: 0.7807 (pm20)
REVERT: D   12 GLU cc_start: 0.8823 (pm20) cc_final: 0.7767 (mm-30)
REVERT: B    6 GLN cc_start: 0.8374 (pt0) cc_final: 0.7225 (pm20)
REVERT: B   39 GLN cc_start: 0.8443 (tt0) cc_final: 0.8041 (mt0)
REVERT: A    6 GLN cc_start: 0.7390 (pt0) cc_final: 0.6968 (tp40)
REVERT: A   12 GLU cc_start: 0.8692 (pm20) cc_final: 0.8388 (pm20)
REVERT: A   13 SER cc_start: 0.5841 (OUTLIER) cc_final: 0.5581 (t)
REVERT: A   16 LYS cc_start: 0.7419 (ttpt) cc_final: 0.6272 (pmtt)
REVERT: A   86 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8190 (tm-30)
  outliers start: 9
  outliers final: 4
  residues processed: 74
  average time/residue: 0.3443
  time to fit residues: 26.7152
Evaluate side-chains
  67 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   67 ILE
Chi-restraints excluded: chain E residue   85 ASP
Chi-restraints excluded: chain B residue    9 SER
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain A residue   13 SER
Chi-restraints excluded: chain A residue   33 TYR
Chi-restraints excluded: chain A residue   86 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 19 optimal weight:    8.9990
   chunk 24 optimal weight:    6.9990
   chunk 12 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 14 optimal weight:   30.0000
   chunk 0 optimal weight:    9.9990
   chunk 18 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
D  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4620 r_free = 0.4620 target = 0.127870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.102985 restraints weight = 6777.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.4369 rms_B_bonded: 4.59
r_work: 0.4341 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.4341
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4253
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4253 r_free = 0.4253    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4253 r_free = 0.4253    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4253
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6996
moved from start:          0.5419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   3415  Z= 0.240
  Angle     :  0.738   6.713   4645  Z= 0.372
  Chirality :  0.045   0.138    505
  Planarity :  0.003   0.025    610
  Dihedral  :  4.968  17.445    465
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.05 %
    Favored  : 87.95 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 23.04 %
    Favored  : 73.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.52 (0.31), residues: 415
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.44 (0.24), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG C  24 
 TYR   0.017   0.003   TYR A  90 
 PHE   0.007   0.001   PHE C   2 
 TRP   0.009   0.002   TRP C  36 
 HIS   0.003   0.001   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 ( 3410)
  covalent geometry    : angle       0.73779 ( 4635)
  SS BOND              : bond        0.00434 (    5)
  SS BOND              : angle       0.97027 (   10)
  hydrogen bonds       : bond        0.02257 (   81)
  hydrogen bonds       : angle       4.57571 (  243)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.092 
Fit side-chains
REVERT: E   39 GLN cc_start: 0.8665 (tt0) cc_final: 0.8212 (tt0)
REVERT: C   12 GLU cc_start: 0.8929 (pm20) cc_final: 0.8675 (pm20)
REVERT: C   29 ILE cc_start: 0.9104 (mm) cc_final: 0.8895 (mp)
REVERT: C   68 ASP cc_start: 0.7933 (t70) cc_final: 0.7445 (m-30)
REVERT: D   12 GLU cc_start: 0.8958 (pm20) cc_final: 0.8556 (pm20)
REVERT: D   68 ASP cc_start: 0.8062 (t70) cc_final: 0.7414 (m-30)
REVERT: B   68 ASP cc_start: 0.8163 (t70) cc_final: 0.7527 (m-30)
REVERT: A    3 MET cc_start: 0.8938 (mmm) cc_final: 0.6607 (pmt)
REVERT: A    6 GLN cc_start: 0.7332 (pt0) cc_final: 0.6896 (tp40)
REVERT: A   12 GLU cc_start: 0.8867 (pm20) cc_final: 0.8518 (pm20)
REVERT: A   13 SER cc_start: 0.5764 (OUTLIER) cc_final: 0.5535 (t)
REVERT: A   16 LYS cc_start: 0.7123 (ttpt) cc_final: 0.6101 (pmtt)
REVERT: A   86 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8096 (tm-30)
  outliers start: 13
  outliers final: 8
  residues processed: 72
  average time/residue: 0.3061
  time to fit residues: 23.1458
Evaluate side-chains
  68 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue   67 ILE
Chi-restraints excluded: chain D residue    9 SER
Chi-restraints excluded: chain B residue    9 SER
Chi-restraints excluded: chain B residue   13 SER
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain A residue   13 SER
Chi-restraints excluded: chain A residue   33 TYR
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   86 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 13 optimal weight:   10.0000
   chunk 38 optimal weight:    6.9990
   chunk 33 optimal weight:    0.0050
   chunk 4 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0370
   chunk 10 optimal weight:    9.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.8078

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

Flipped N/Q/H residues before XYZ refinement:
D  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4696 r_free = 0.4696 target = 0.134542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.109374 restraints weight = 6581.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.4451 rms_B_bonded: 4.65
r_work: 0.4432 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.4432
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4388
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4388 r_free = 0.4388    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4388 r_free = 0.4388    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4388
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6946
moved from start:          0.5425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3415  Z= 0.130
  Angle     :  0.706   7.907   4645  Z= 0.344
  Chirality :  0.045   0.129    505
  Planarity :  0.003   0.022    610
  Dihedral  :  4.586  16.164    465
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.57 %
    Favored  : 88.43 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 24.56 %
    Favored  : 72.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -4.36 (0.32), residues: 415
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.32 (0.25), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  62 
 TYR   0.011   0.001   TYR C  94 
 PHE   0.005   0.001   PHE C   2 
 TRP   0.003   0.001   TRP C  36 
 HIS   0.002   0.000   HIS E   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 3410)
  covalent geometry    : angle       0.70664 ( 4635)
  SS BOND              : bond        0.00134 (    5)
  SS BOND              : angle       0.33080 (   10)
  hydrogen bonds       : bond        0.01376 (   81)
  hydrogen bonds       : angle       4.26040 (  243)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.146 
Fit side-chains
REVERT: E   39 GLN cc_start: 0.8620 (tt0) cc_final: 0.8252 (tt0)
REVERT: C   68 ASP cc_start: 0.7953 (t70) cc_final: 0.7460 (m-30)
REVERT: D   12 GLU cc_start: 0.8934 (pm20) cc_final: 0.7607 (mm-30)
REVERT: D   68 ASP cc_start: 0.8193 (t70) cc_final: 0.7661 (m-30)
REVERT: B    6 GLN cc_start: 0.8557 (pt0) cc_final: 0.7930 (pt0)
REVERT: B   16 LYS cc_start: 0.7141 (ttpp) cc_final: 0.6785 (tttp)
REVERT: B   39 GLN cc_start: 0.8379 (tt0) cc_final: 0.7989 (mt0)
REVERT: A    3 MET cc_start: 0.8871 (mmm) cc_final: 0.6388 (pmt)
REVERT: A    6 GLN cc_start: 0.7328 (pt0) cc_final: 0.6958 (tp40)
REVERT: A   12 GLU cc_start: 0.8835 (pm20) cc_final: 0.8612 (pm20)
REVERT: A   13 SER cc_start: 0.5906 (OUTLIER) cc_final: 0.5668 (t)
REVERT: A   16 LYS cc_start: 0.7336 (ttpt) cc_final: 0.6191 (pmtt)
REVERT: A   84 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7808 (tp30)
  outliers start: 10
  outliers final: 7
  residues processed: 73
  average time/residue: 0.3086
  time to fit residues: 23.6756
Evaluate side-chains
  67 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue   67 ILE
Chi-restraints excluded: chain D residue    9 SER
Chi-restraints excluded: chain B residue    9 SER
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain A residue   13 SER
Chi-restraints excluded: chain A residue   33 TYR
Chi-restraints excluded: chain A residue   70 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 6 optimal weight:   20.0000
   chunk 13 optimal weight:    9.9990
   chunk 39 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 19 optimal weight:    8.9990
   chunk 3 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0060
   chunk 38 optimal weight:    0.3980
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.8800

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

Flipped N/Q/H residues before XYZ refinement:
D  98 ASN
A   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4724 r_free = 0.4724 target = 0.122995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.099811 restraints weight = 6961.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.4488 rms_B_bonded: 4.69
r_work: 0.4431 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.4431
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4392
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4392 r_free = 0.4392    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4391 r_free = 0.4391    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4391
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6951
moved from start:          0.5479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3415  Z= 0.134
  Angle     :  0.727   7.883   4645  Z= 0.355
  Chirality :  0.046   0.129    505
  Planarity :  0.003   0.021    610
  Dihedral  :  4.679  31.185    465
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.33 %
    Favored  : 88.67 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 24.05 %
    Favored  : 73.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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: -4.28 (0.33), residues: 415
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.26 (0.25), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  62 
 TYR   0.010   0.001   TYR C  94 
 PHE   0.005   0.001   PHE D  63 
 TRP   0.003   0.001   TRP C  36 
 HIS   0.001   0.001   HIS D   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 3410)
  covalent geometry    : angle       0.72779 ( 4635)
  SS BOND              : bond        0.00134 (    5)
  SS BOND              : angle       0.25324 (   10)
  hydrogen bonds       : bond        0.01395 (   81)
  hydrogen bonds       : angle       4.21044 (  243)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.088 
Fit side-chains
REVERT: E   39 GLN cc_start: 0.8632 (tt0) cc_final: 0.8255 (tt0)
REVERT: C   29 ILE cc_start: 0.9139 (mm) cc_final: 0.8896 (mp)
REVERT: C   68 ASP cc_start: 0.7987 (t70) cc_final: 0.7546 (m-30)
REVERT: C   86 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7702 (tm-30)
REVERT: D   12 GLU cc_start: 0.8923 (pm20) cc_final: 0.7520 (mm-30)
REVERT: D   33 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.8207 (t80)
REVERT: D   68 ASP cc_start: 0.8221 (t70) cc_final: 0.7736 (m-30)
REVERT: B    3 MET cc_start: 0.8276 (mmm) cc_final: 0.7982 (tpt)
REVERT: B    6 GLN cc_start: 0.8594 (pt0) cc_final: 0.8019 (pt0)
REVERT: B   16 LYS cc_start: 0.7354 (ttpp) cc_final: 0.6958 (tttp)
REVERT: B   33 TYR cc_start: 0.7918 (OUTLIER) cc_final: 0.7710 (t80)
REVERT: B   39 GLN cc_start: 0.8365 (tt0) cc_final: 0.7967 (mt0)
REVERT: A    3 MET cc_start: 0.8853 (mmm) cc_final: 0.6317 (pmt)
REVERT: A    6 GLN cc_start: 0.7675 (pt0) cc_final: 0.7007 (tp40)
REVERT: A   12 GLU cc_start: 0.8794 (pm20) cc_final: 0.8554 (pm20)
REVERT: A   13 SER cc_start: 0.5823 (OUTLIER) cc_final: 0.5572 (t)
REVERT: A   16 LYS cc_start: 0.7436 (ttpt) cc_final: 0.6268 (pmtt)
  outliers start: 11
  outliers final: 7
  residues processed: 71
  average time/residue: 0.2513
  time to fit residues: 18.7545
Evaluate side-chains
  68 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue   33 TYR
Chi-restraints excluded: chain E residue   67 ILE
Chi-restraints excluded: chain E residue   81 LEU
Chi-restraints excluded: chain D residue   33 TYR
Chi-restraints excluded: chain B residue   13 SER
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain A residue   13 SER
Chi-restraints excluded: chain A residue   33 TYR
Chi-restraints excluded: chain A residue   70 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 20 optimal weight:    8.9990
   chunk 30 optimal weight:    6.9990
   chunk 37 optimal weight:   10.0000
   chunk 1 optimal weight:    0.0970
   chunk 9 optimal weight:    0.7980
   chunk 10 optimal weight:    8.9990
   chunk 31 optimal weight:    5.9990
   chunk 7 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 34 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   overall best weight:    3.3784

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

Flipped N/Q/H residues before XYZ refinement:
D  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4661 r_free = 0.4661 target = 0.130488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.105372 restraints weight = 6937.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.4405 rms_B_bonded: 4.65
r_work: 0.4366 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.4366
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4327
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4327 r_free = 0.4327    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4327 r_free = 0.4327    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4327
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6994
moved from start:          0.5823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   3415  Z= 0.223
  Angle     :  0.752   7.511   4645  Z= 0.372
  Chirality :  0.046   0.134    505
  Planarity :  0.003   0.025    610
  Dihedral  :  4.805  20.164    465
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.81 %
    Favored  : 88.19 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 26.08 %
    Favored  : 71.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -4.37 (0.32), residues: 415
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.32 (0.24), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  24 
 TYR   0.014   0.002   TYR C  90 
 PHE   0.006   0.001   PHE C   2 
 TRP   0.005   0.001   TRP A  36 
 HIS   0.002   0.001   HIS E 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 ( 3410)
  covalent geometry    : angle       0.75236 ( 4635)
  SS BOND              : bond        0.00385 (    5)
  SS BOND              : angle       0.75507 (   10)
  hydrogen bonds       : bond        0.02049 (   81)
  hydrogen bonds       : angle       4.48630 (  243)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.139 
Fit side-chains
REVERT: E   39 GLN cc_start: 0.8631 (tt0) cc_final: 0.8277 (tt0)
REVERT: C   29 ILE cc_start: 0.9128 (mm) cc_final: 0.8890 (mp)
REVERT: C   68 ASP cc_start: 0.8021 (t70) cc_final: 0.7608 (m-30)
REVERT: D   68 ASP cc_start: 0.8262 (t70) cc_final: 0.7780 (m-30)
REVERT: B    3 MET cc_start: 0.8276 (mmm) cc_final: 0.8069 (tpt)
REVERT: B    6 GLN cc_start: 0.8586 (pt0) cc_final: 0.8025 (pt0)
REVERT: B   68 ASP cc_start: 0.8144 (t70) cc_final: 0.7637 (m-30)
REVERT: A    3 MET cc_start: 0.8911 (mmm) cc_final: 0.6670 (pmt)
REVERT: A    6 GLN cc_start: 0.7808 (pt0) cc_final: 0.7093 (tp40)
REVERT: A   13 SER cc_start: 0.5884 (OUTLIER) cc_final: 0.5638 (t)
REVERT: A   16 LYS cc_start: 0.7141 (ttpt) cc_final: 0.6089 (pmtt)
  outliers start: 10
  outliers final: 7
  residues processed: 64
  average time/residue: 0.2541
  time to fit residues: 17.3014
Evaluate side-chains
  63 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue   67 ILE
Chi-restraints excluded: chain D residue    9 SER
Chi-restraints excluded: chain B residue    9 SER
Chi-restraints excluded: chain B residue   13 SER
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain A residue   13 SER
Chi-restraints excluded: chain A residue   70 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 29 optimal weight:   20.0000
   chunk 10 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 22 optimal weight:   30.0000
   chunk 8 optimal weight:    7.9990
   chunk 23 optimal weight:    5.9990
   chunk 2 optimal weight:   20.0000
   chunk 15 optimal weight:    3.9990
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
D  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4647 r_free = 0.4647 target = 0.128287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.103798 restraints weight = 7019.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.4318 rms_B_bonded: 4.74
r_work: 0.4224 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.4224
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4225
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4225 r_free = 0.4225    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4223 r_free = 0.4223    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4223
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7012
moved from start:          0.6169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   3415  Z= 0.270
  Angle     :  0.808   8.268   4645  Z= 0.405
  Chirality :  0.047   0.136    505
  Planarity :  0.004   0.025    610
  Dihedral  :  5.066  17.252    465
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.57 %
    Favored  : 88.43 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 26.84 %
    Favored  : 70.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.50 (0.30), residues: 415
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.43 (0.23), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG C  24 
 TYR   0.018   0.003   TYR C  90 
 PHE   0.006   0.001   PHE B  63 
 TRP   0.007   0.002   TRP C  36 
 HIS   0.003   0.001   HIS C 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00593 ( 3410)
  covalent geometry    : angle       0.80803 ( 4635)
  SS BOND              : bond        0.00469 (    5)
  SS BOND              : angle       0.96420 (   10)
  hydrogen bonds       : bond        0.02388 (   81)
  hydrogen bonds       : angle       4.74789 (  243)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.144 
Fit side-chains
REVERT: E   39 GLN cc_start: 0.8569 (tt0) cc_final: 0.8154 (tt0)
REVERT: C   12 GLU cc_start: 0.9162 (pm20) cc_final: 0.8836 (pm20)
REVERT: C   29 ILE cc_start: 0.9119 (mm) cc_final: 0.8893 (mp)
REVERT: C   68 ASP cc_start: 0.8078 (t70) cc_final: 0.7679 (m-30)
REVERT: D   68 ASP cc_start: 0.8160 (t70) cc_final: 0.7604 (m-30)
REVERT: B   68 ASP cc_start: 0.8213 (t70) cc_final: 0.7820 (m-30)
REVERT: B   88 ASP cc_start: 0.6020 (t0) cc_final: 0.5721 (m-30)
REVERT: A    3 MET cc_start: 0.8906 (mmm) cc_final: 0.6865 (pmt)
REVERT: A    6 GLN cc_start: 0.7758 (pt0) cc_final: 0.7106 (tp40)
REVERT: A   13 SER cc_start: 0.5835 (OUTLIER) cc_final: 0.5618 (t)
REVERT: A   16 LYS cc_start: 0.7112 (ttpt) cc_final: 0.6122 (pmtt)
  outliers start: 10
  outliers final: 8
  residues processed: 66
  average time/residue: 0.2626
  time to fit residues: 18.4047
Evaluate side-chains
  65 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue   67 ILE
Chi-restraints excluded: chain E residue   81 LEU
Chi-restraints excluded: chain B residue    9 SER
Chi-restraints excluded: chain B residue   13 SER
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain A residue   13 SER
Chi-restraints excluded: chain A residue   33 TYR
Chi-restraints excluded: chain A residue   70 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 31 optimal weight:    9.9990
   chunk 6 optimal weight:   20.0000
   chunk 21 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 1 optimal weight:    0.1980
   chunk 25 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 37 optimal weight:    6.9990
   chunk 33 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
D  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4662 r_free = 0.4662 target = 0.132067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.106960 restraints weight = 6707.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.4421 rms_B_bonded: 4.57
r_work: 0.4376 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.4376
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4338
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4338 r_free = 0.4338    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4338 r_free = 0.4338    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4338
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
moved from start:          0.6279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3415  Z= 0.193
  Angle     :  0.797   8.268   4645  Z= 0.393
  Chirality :  0.047   0.133    505
  Planarity :  0.003   0.027    610
  Dihedral  :  4.820  16.515    465
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.57 %
    Favored  : 88.43 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 27.59 %
    Favored  : 69.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.44 (0.31), residues: 415
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.37 (0.24), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  24 
 TYR   0.011   0.002   TYR C  90 
 PHE   0.006   0.001   PHE C  63 
 TRP   0.006   0.001   TRP C  36 
 HIS   0.001   0.001   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 3410)
  covalent geometry    : angle       0.79754 ( 4635)
  SS BOND              : bond        0.00291 (    5)
  SS BOND              : angle       0.51001 (   10)
  hydrogen bonds       : bond        0.01987 (   81)
  hydrogen bonds       : angle       4.59736 (  243)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.135 
Fit side-chains
REVERT: E   39 GLN cc_start: 0.8672 (tt0) cc_final: 0.8361 (tt0)
REVERT: C   12 GLU cc_start: 0.9041 (pm20) cc_final: 0.8714 (pm20)
REVERT: C   29 ILE cc_start: 0.9165 (mm) cc_final: 0.8920 (mp)
REVERT: C   68 ASP cc_start: 0.8110 (t70) cc_final: 0.7704 (m-30)
REVERT: D   68 ASP cc_start: 0.8134 (t70) cc_final: 0.7606 (m-30)
REVERT: B   39 GLN cc_start: 0.8282 (tt0) cc_final: 0.7910 (mt0)
REVERT: B   68 ASP cc_start: 0.8242 (t70) cc_final: 0.7838 (m-30)
REVERT: B   88 ASP cc_start: 0.5900 (t0) cc_final: 0.5642 (m-30)
REVERT: A    3 MET cc_start: 0.8966 (mmm) cc_final: 0.6696 (pmt)
REVERT: A    6 GLN cc_start: 0.7905 (pt0) cc_final: 0.7205 (tp40)
REVERT: A   13 SER cc_start: 0.5624 (OUTLIER) cc_final: 0.5405 (t)
REVERT: A   16 LYS cc_start: 0.7271 (ttpt) cc_final: 0.6170 (pmtt)
  outliers start: 10
  outliers final: 8
  residues processed: 67
  average time/residue: 0.2556
  time to fit residues: 18.1733
Evaluate side-chains
  67 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue   67 ILE
Chi-restraints excluded: chain E residue   81 LEU
Chi-restraints excluded: chain D residue   33 TYR
Chi-restraints excluded: chain B residue    9 SER
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain A residue   13 SER
Chi-restraints excluded: chain A residue   33 TYR
Chi-restraints excluded: chain A residue   70 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:   30.0000
   chunk 25 optimal weight:    6.9990
   chunk 17 optimal weight:    9.9990
   chunk 19 optimal weight:    8.9990
   chunk 4 optimal weight:    4.9990
   chunk 6 optimal weight:   10.0000
   chunk 13 optimal weight:    9.9990
   chunk 37 optimal weight:   20.0000
   chunk 16 optimal weight:    7.9990
   chunk 22 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
D  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4623 r_free = 0.4623 target = 0.113187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.091264 restraints weight = 7347.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.4294 rms_B_bonded: 4.41
r_work: 0.4191 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.4191
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4189
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4189 r_free = 0.4189    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4188 r_free = 0.4188    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4188
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7243
moved from start:          0.6515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042   3415  Z= 0.341
  Angle     :  0.846   8.340   4645  Z= 0.428
  Chirality :  0.048   0.140    505
  Planarity :  0.004   0.030    610
  Dihedral  :  5.212  16.792    465
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.25 %
    Favored  : 86.75 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 28.35 %
    Favored  : 69.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.61 (0.30), residues: 415
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.51 (0.23), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG C  24 
 TYR   0.021   0.004   TYR B  90 
 PHE   0.008   0.002   PHE C  63 
 TRP   0.009   0.002   TRP C  36 
 HIS   0.003   0.001   HIS E 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00744 ( 3410)
  covalent geometry    : angle       0.84574 ( 4635)
  SS BOND              : bond        0.00563 (    5)
  SS BOND              : angle       1.13001 (   10)
  hydrogen bonds       : bond        0.02665 (   81)
  hydrogen bonds       : angle       4.88114 (  243)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1260.77 seconds
wall clock time: 22 minutes 30.44 seconds (1350.44 seconds total)