Starting phenix.real_space_refine
on Tue Mar  3 11:55:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8a7t_15225/03_2026/8a7t_15225.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8a7t_15225/03_2026/8a7t_15225.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8a7t_15225/03_2026/8a7t_15225.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8a7t_15225/03_2026/8a7t_15225.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8a7t_15225/03_2026/8a7t_15225.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8a7t_15225/03_2026/8a7t_15225.map"
  }
  resolution = 3.0
  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=   0.000 sd=   0.004
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      12      5.16       5
     C    2370      2.51       5
     N     600      2.21       5
     O     720      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3702
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 704
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 4, 'TRANS': 80}
    Chain: "B"
      Number of atoms: 530
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 530
          Classifications: {'peptide': 63}
          Link IDs: {'PTRANS': 2, 'TRANS': 60}
  Restraints were copied for chains:
    C, E, D, F
  Time building chain proxies: 0.64, per 1000 atoms: 0.17
  Number of scatterers: 3702
  At special positions: 0
  Unit cell: (104.58, 108.73, 34.86, 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      12     16.00
     O     720      8.00
     N     600      7.00
     C    2370      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  25 " - pdb=" SG  CYS A  80 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  25 " - pdb=" SG  CYS B  80 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  25 " - pdb=" SG  CYS C  80 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  25 " - pdb=" SG  CYS E  80 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  25 " - pdb=" SG  CYS D  80 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  25 " - pdb=" SG  CYS F  80 " 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: 0.18
  Conformation dependent library (CDL) restraints added in 136.7 milliseconds
  

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  858

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 18 sheets defined
      0.0% alpha, 45.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 12
      removed outlier: 6.813A  pdb=" N   GLN A   8 " --> pdb=" O   VAL C   9 " (cutoff:3.500A)
      removed outlier: 7.996A  pdb=" N   SER C  11 " --> pdb=" O   GLN A   8 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   TYR A  10 " --> pdb=" O   SER C  11 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   GLN C   8 " --> pdb=" O   VAL E   9 " (cutoff:3.500A)
      removed outlier: 7.872A  pdb=" N   SER E  11 " --> pdb=" O   GLN C   8 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   TYR C  10 " --> pdb=" O   SER E  11 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17
      removed outlier: 6.226A  pdb=" N   GLU A  16 " --> pdb=" O   ASN C  17 " (cutoff:3.500A)
      removed outlier: 6.063A  pdb=" N   GLU C  16 " --> pdb=" O   ASN E  17 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 23
      removed outlier: 6.648A  pdb=" N   SER A  20 " --> pdb=" O   ASN C  21 " (cutoff:3.500A)
      removed outlier: 8.412A  pdb=" N   LEU C  23 " --> pdb=" O   SER A  20 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   PHE A  22 " --> pdb=" O   LEU C  23 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   SER C  20 " --> pdb=" O   ASN E  21 " (cutoff:3.500A)
      removed outlier: 8.358A  pdb=" N   LEU E  23 " --> pdb=" O   SER C  20 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   PHE C  22 " --> pdb=" O   LEU E  23 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 39
      removed outlier: 6.985A  pdb=" N   ASP C  34 " --> pdb=" O   SER A  33 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   ASP E  34 " --> pdb=" O   SER C  33 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 42 through 44
      removed outlier: 6.767A  pdb=" N   GLY C  43 " --> pdb=" O   GLU E  44 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 48 through 55
      removed outlier: 7.243A  pdb=" N   VAL C  49 " --> pdb=" O   LYS A  48 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   GLU A  50 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   HIS C  51 " --> pdb=" O   GLU A  50 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   VAL E  49 " --> pdb=" O   LYS C  48 " (cutoff:3.500A)
      removed outlier: 7.278A  pdb=" N   GLU C  50 " --> pdb=" O   VAL E  49 " (cutoff:3.500A)
      removed outlier: 7.112A  pdb=" N   HIS E  51 " --> pdb=" O   GLU C  50 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 59 through 66
      removed outlier: 6.279A  pdb=" N   TRP A  60 " --> pdb=" O   SER C  61 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   TYR C  63 " --> pdb=" O   TRP A  60 " (cutoff:3.500A)
      removed outlier: 7.344A  pdb=" N   PHE A  62 " --> pdb=" O   TYR C  63 " (cutoff:3.500A)
      removed outlier: 9.764A  pdb=" N   LEU C  65 " --> pdb=" O   PHE A  62 " (cutoff:3.500A)
      removed outlier: 8.438A  pdb=" N   LEU A  64 " --> pdb=" O   LEU C  65 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   TRP C  60 " --> pdb=" O   SER E  61 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   TYR E  63 " --> pdb=" O   TRP C  60 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   PHE C  62 " --> pdb=" O   TYR E  63 " (cutoff:3.500A)
      removed outlier: 9.793A  pdb=" N   LEU E  65 " --> pdb=" O   PHE C  62 " (cutoff:3.500A)
      removed outlier: 8.482A  pdb=" N   LEU C  64 " --> pdb=" O   LEU E  65 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 69 through 70
      removed outlier: 6.440A  pdb=" N   GLU C  69 " --> pdb=" O   PHE A  70 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   GLU E  69 " --> pdb=" O   PHE C  70 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 73 through 74
      removed outlier: 3.529A  pdb=" N   GLU C  74 " --> pdb=" O   THR E  73 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'A' and resid 81 through 88
    Processing sheet with id=AB3, first strand: chain 'B' and resid 23 through 24
      removed outlier: 7.067A  pdb=" N   LEU B  23 " --> pdb=" O   ASN D  24 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   LEU D  23 " --> pdb=" O   ASN F  24 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'B' and resid 35 through 39
      removed outlier: 6.782A  pdb=" N   ILE B  35 " --> pdb=" O   GLU D  36 " (cutoff:3.500A)
      removed outlier: 8.051A  pdb=" N   ASP D  38 " --> pdb=" O   ILE B  35 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   VAL B  37 " --> pdb=" O   ASP D  38 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   ILE D  35 " --> pdb=" O   GLU F  36 " (cutoff:3.500A)
      removed outlier: 8.138A  pdb=" N   ASP F  38 " --> pdb=" O   ILE D  35 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   VAL D  37 " --> pdb=" O   ASP F  38 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'B' and resid 42 through 53
      removed outlier: 6.912A  pdb=" N   GLY B  43 " --> pdb=" O   GLU D  44 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   ILE D  46 " --> pdb=" O   GLY B  43 " (cutoff:3.500A)
      removed outlier: 8.230A  pdb=" N   ARG B  45 " --> pdb=" O   ILE D  46 " (cutoff:3.500A)
      removed outlier: 9.850A  pdb=" N   LYS D  48 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   GLU B  47 " --> pdb=" O   LYS D  48 " (cutoff:3.500A)
      removed outlier: 8.124A  pdb=" N   GLU D  50 " --> pdb=" O   GLU B  47 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   VAL B  49 " --> pdb=" O   GLU D  50 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   SER D  52 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 7.857A  pdb=" N   HIS B  51 " --> pdb=" O   SER D  52 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   GLY D  43 " --> pdb=" O   GLU F  44 " (cutoff:3.500A)
      removed outlier: 7.267A  pdb=" N   ILE F  46 " --> pdb=" O   GLY D  43 " (cutoff:3.500A)
      removed outlier: 8.275A  pdb=" N   ARG D  45 " --> pdb=" O   ILE F  46 " (cutoff:3.500A)
      removed outlier: 9.853A  pdb=" N   LYS F  48 " --> pdb=" O   ARG D  45 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   GLU D  47 " --> pdb=" O   LYS F  48 " (cutoff:3.500A)
      removed outlier: 8.055A  pdb=" N   GLU F  50 " --> pdb=" O   GLU D  47 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   VAL D  49 " --> pdb=" O   GLU F  50 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   SER F  52 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
      removed outlier: 7.892A  pdb=" N   HIS D  51 " --> pdb=" O   SER F  52 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'B' and resid 59 through 66
      removed outlier: 9.790A  pdb=" N   ASP B  59 " --> pdb=" O   TRP D  60 " (cutoff:3.500A)
      removed outlier: 9.833A  pdb=" N   PHE D  62 " --> pdb=" O   ASP B  59 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   SER B  61 " --> pdb=" O   PHE D  62 " (cutoff:3.500A)
      removed outlier: 7.446A  pdb=" N   LEU D  64 " --> pdb=" O   SER B  61 " (cutoff:3.500A)
      removed outlier: 5.933A  pdb=" N   TYR B  63 " --> pdb=" O   LEU D  64 " (cutoff:3.500A)
      removed outlier: 7.213A  pdb=" N   TYR D  66 " --> pdb=" O   TYR B  63 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   LEU B  65 " --> pdb=" O   TYR D  66 " (cutoff:3.500A)
      removed outlier: 9.822A  pdb=" N   ASP D  59 " --> pdb=" O   TRP F  60 " (cutoff:3.500A)
      removed outlier: 9.840A  pdb=" N   PHE F  62 " --> pdb=" O   ASP D  59 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   SER D  61 " --> pdb=" O   PHE F  62 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   LEU F  64 " --> pdb=" O   SER D  61 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   TYR D  63 " --> pdb=" O   LEU F  64 " (cutoff:3.500A)
      removed outlier: 7.179A  pdb=" N   TYR F  66 " --> pdb=" O   TYR D  63 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   LEU D  65 " --> pdb=" O   TYR F  66 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'B' and resid 69 through 70
      removed outlier: 6.455A  pdb=" N   GLU D  69 " --> pdb=" O   PHE B  70 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   GLU F  69 " --> pdb=" O   PHE D  70 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'B' and resid 73 through 74
    Processing sheet with id=AB9, first strand: chain 'B' and resid 77 through 78

    41 hydrogen bonds defined for protein.
    123 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: 0.47

  Time building geometry restraints manager: 0.29 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1179
        1.34 -     1.46: 950
        1.46 -     1.58: 1666
        1.58 -     1.69: 0
        1.69 -     1.81: 12
  Bond restraints: 3807
  Sorted by residual:
  bond pdb=" C   ASN F  42 "
       pdb=" N   GLY F  43 "
    ideal  model  delta    sigma   weight residual
    1.333  1.324  0.010 1.22e-02 6.72e+03 6.72e-01
  bond pdb=" C   ASN D  42 "
       pdb=" N   GLY D  43 "
    ideal  model  delta    sigma   weight residual
    1.333  1.324  0.010 1.22e-02 6.72e+03 6.39e-01
  bond pdb=" N   GLY F  43 "
       pdb=" CA  GLY F  43 "
    ideal  model  delta    sigma   weight residual
    1.444  1.451 -0.008 1.02e-02 9.61e+03 5.60e-01
  bond pdb=" C   ASN B  42 "
       pdb=" N   GLY B  43 "
    ideal  model  delta    sigma   weight residual
    1.333  1.324  0.009 1.22e-02 6.72e+03 5.49e-01
  bond pdb=" N   GLY B  43 "
       pdb=" CA  GLY B  43 "
    ideal  model  delta    sigma   weight residual
    1.444  1.451 -0.007 1.02e-02 9.61e+03 4.66e-01
  ... (remaining 3802 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.71: 4654
        0.71 -     1.41: 421
        1.41 -     2.12: 52
        2.12 -     2.83: 13
        2.83 -     3.53: 17
  Bond angle restraints: 5157
  Sorted by residual:
  angle pdb=" NE  ARG A  12 "
        pdb=" CZ  ARG A  12 "
        pdb=" NH1 ARG A  12 "
      ideal   model   delta    sigma   weight residual
     121.50  119.96    1.54 1.00e+00 1.00e+00 2.38e+00
  angle pdb=" NE  ARG B  45 "
        pdb=" CZ  ARG B  45 "
        pdb=" NH1 ARG B  45 "
      ideal   model   delta    sigma   weight residual
     121.50  119.97    1.53 1.00e+00 1.00e+00 2.34e+00
  angle pdb=" NE  ARG C  12 "
        pdb=" CZ  ARG C  12 "
        pdb=" NH1 ARG C  12 "
      ideal   model   delta    sigma   weight residual
     121.50  120.00    1.50 1.00e+00 1.00e+00 2.26e+00
  angle pdb=" NE  ARG B  81 "
        pdb=" CZ  ARG B  81 "
        pdb=" NH1 ARG B  81 "
      ideal   model   delta    sigma   weight residual
     121.50  120.00    1.50 1.00e+00 1.00e+00 2.25e+00
  angle pdb=" NE  ARG A  45 "
        pdb=" CZ  ARG A  45 "
        pdb=" NH1 ARG A  45 "
      ideal   model   delta    sigma   weight residual
     121.50  120.01    1.49 1.00e+00 1.00e+00 2.22e+00
  ... (remaining 5152 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.61: 2056
       10.61 -    21.21: 161
       21.21 -    31.82: 21
       31.82 -    42.42: 9
       42.42 -    53.03: 6
  Dihedral angle restraints: 2253
    sinusoidal: 924
      harmonic: 1329
  Sorted by residual:
  dihedral pdb=" CA  LEU D  39 "
           pdb=" CB  LEU D  39 "
           pdb=" CG  LEU D  39 "
           pdb=" CD1 LEU D  39 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  141.26   38.74     3      1.50e+01 4.44e-03 6.83e+00
  dihedral pdb=" CA  LEU B  39 "
           pdb=" CB  LEU B  39 "
           pdb=" CG  LEU B  39 "
           pdb=" CD1 LEU B  39 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  141.27   38.73     3      1.50e+01 4.44e-03 6.83e+00
  dihedral pdb=" CA  LEU F  39 "
           pdb=" CB  LEU F  39 "
           pdb=" CG  LEU F  39 "
           pdb=" CD1 LEU F  39 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  141.27   38.73     3      1.50e+01 4.44e-03 6.83e+00
  ... (remaining 2250 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 262
       0.025 -    0.051: 203
       0.051 -    0.076: 24
       0.076 -    0.101: 9
       0.101 -    0.127: 36
  Chirality restraints: 534
  Sorted by residual:
  chirality pdb=" CA  VAL A  49 "
            pdb=" N   VAL A  49 "
            pdb=" C   VAL A  49 "
            pdb=" CB  VAL A  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.01e-01
  chirality pdb=" CA  VAL C  37 "
            pdb=" N   VAL C  37 "
            pdb=" C   VAL C  37 "
            pdb=" CB  VAL C  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.84e-01
  chirality pdb=" CA  VAL C  49 "
            pdb=" N   VAL C  49 "
            pdb=" C   VAL C  49 "
            pdb=" CB  VAL C  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.82e-01
  ... (remaining 531 not shown)

  Planarity restraints: 666
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR E  71 "   -0.020 5.00e-02 4.00e+02   2.98e-02 1.42e+00
        pdb=" N   PRO E  72 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO E  72 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO E  72 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  71 "   -0.020 5.00e-02 4.00e+02   2.98e-02 1.42e+00
        pdb=" N   PRO A  72 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO A  72 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A  72 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C  71 "   -0.020 5.00e-02 4.00e+02   2.95e-02 1.39e+00
        pdb=" N   PRO C  72 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO C  72 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C  72 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 663 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 994
        2.82 -     3.34: 2839
        3.34 -     3.86: 5703
        3.86 -     4.38: 6386
        4.38 -     4.90: 10666
  Nonbonded interactions: 26588
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU C  16 "
            pdb=" NH2 ARG C  81 "
     model   vdw
     2.302 3.120
  nonbonded pdb=" OE2 GLU A  16 "
            pdb=" NH2 ARG A  81 "
     model   vdw
     2.302 3.120
  nonbonded pdb=" OE2 GLU E  16 "
            pdb=" NH2 ARG E  81 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" O   LYS A  58 "
            pdb=" N   LYS C  58 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" O   LYS C  58 "
            pdb=" N   LYS E  58 "
     model   vdw
     2.392 3.120
  ... (remaining 26583 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.960
  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:7.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3813  Z= 0.149
  Angle     :  0.464   3.534   5169  Z= 0.266
  Chirality :  0.042   0.127    534
  Planarity :  0.003   0.030    666
  Dihedral  :  8.475  53.030   1377
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  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: -4.48 (0.28), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.40 (0.22), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  81 
 TYR   0.008   0.001   TYR F  63 
 PHE   0.007   0.001   PHE A  70 
 TRP   0.003   0.001   TRP D  60 
 HIS   0.002   0.001   HIS A  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 3807)
  covalent geometry    : angle       0.46453 ( 5157)
  SS BOND              : bond        0.00350 (    6)
  SS BOND              : angle       0.32229 (   12)
  hydrogen bonds       : bond        0.32032 (   41)
  hydrogen bonds       : angle       8.29141 (  123)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.5860 (mttt) cc_final: 0.5630 (mptt)
REVERT: A   12 ARG cc_start: 0.7894 (ttt180) cc_final: 0.5563 (tpm-80)
REVERT: A   50 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7834 (mt-10)
REVERT: C   36 GLU cc_start: 0.7582 (tt0) cc_final: 0.6991 (mt-10)
REVERT: C   38 ASP cc_start: 0.7971 (p0) cc_final: 0.7700 (p0)
REVERT: C   50 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7806 (mt-10)
REVERT: C   51 HIS cc_start: 0.7738 (m90) cc_final: 0.7146 (m-70)
REVERT: D   36 GLU cc_start: 0.7744 (tt0) cc_final: 0.7473 (mt-10)
REVERT: D   38 ASP cc_start: 0.8802 (p0) cc_final: 0.8448 (p0)
REVERT: D   45 ARG cc_start: 0.7976 (mtt-85) cc_final: 0.7753 (mtp85)
REVERT: E    6 LYS cc_start: 0.6277 (mttt) cc_final: 0.6077 (mptt)
REVERT: E   19 LYS cc_start: 0.8955 (pttt) cc_final: 0.8742 (pttm)
REVERT: E   36 GLU cc_start: 0.7577 (tt0) cc_final: 0.6903 (mt-10)
REVERT: E   48 LYS cc_start: 0.7635 (mttt) cc_final: 0.7405 (mmpt)
REVERT: E   50 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7524 (mp0)
REVERT: E   77 GLU cc_start: 0.8247 (mt-10) cc_final: 0.8046 (mt-10)
REVERT: F   34 ASP cc_start: 0.8311 (m-30) cc_final: 0.8060 (m-30)
REVERT: F   36 GLU cc_start: 0.7684 (tt0) cc_final: 0.7439 (tt0)
REVERT: F   38 ASP cc_start: 0.8341 (p0) cc_final: 0.8118 (p0)
REVERT: F   75 LYS cc_start: 0.8133 (mtmt) cc_final: 0.7868 (mtpp)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.5798
  time to fit residues: 74.8944
Evaluate side-chains
  117 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:   20.0000
   chunk 26 optimal weight:   10.0000
   chunk 2 optimal weight:   20.0000
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    9.9990
   chunk 31 optimal weight:    0.0670
   chunk 25 optimal weight:   20.0000
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:   20.0000
   chunk 37 optimal weight:    2.9990
   overall best weight:    3.1524

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

Flipped N/Q/H residues before XYZ refinement:
** A   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  31 HIS
** A  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  31 HIS
** D  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  21 ASN
E  89 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.141871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.119104 restraints weight = 4886.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3862 rms_B_bonded: 2.28
r_work: 0.3733 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3623 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.2779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3813  Z= 0.155
  Angle     :  0.546   4.494   5169  Z= 0.283
  Chirality :  0.045   0.137    534
  Planarity :  0.003   0.021    666
  Dihedral  :  4.244  12.801    486
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  :  9.29 %
    Favored  : 88.33 %
  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: -4.18 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.18 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  81 
 TYR   0.011   0.001   TYR A  63 
 PHE   0.011   0.002   PHE F  30 
 TRP   0.003   0.001   TRP F  60 
 HIS   0.003   0.001   HIS C  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 3807)
  covalent geometry    : angle       0.54591 ( 5157)
  SS BOND              : bond        0.00356 (    6)
  SS BOND              : angle       0.40440 (   12)
  hydrogen bonds       : bond        0.02384 (   41)
  hydrogen bonds       : angle       5.90929 (  123)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 125
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A   12 ARG cc_start: 0.7981 (ttt180) cc_final: 0.5697 (tpm-80)
REVERT: A   36 GLU cc_start: 0.8344 (tt0) cc_final: 0.7679 (mt-10)
REVERT: A   38 ASP cc_start: 0.7888 (p0) cc_final: 0.7621 (p0)
REVERT: A   50 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8210 (mt-10)
REVERT: A   57 SER cc_start: 0.8672 (m) cc_final: 0.8380 (t)
REVERT: A   58 LYS cc_start: 0.8106 (mmtt) cc_final: 0.6174 (pmtt)
REVERT: B   36 GLU cc_start: 0.8346 (tt0) cc_final: 0.8128 (mt-10)
REVERT: B   58 LYS cc_start: 0.8531 (mmtm) cc_final: 0.6893 (mptt)
REVERT: C   36 GLU cc_start: 0.7928 (tt0) cc_final: 0.7128 (mt-10)
REVERT: C   48 LYS cc_start: 0.7723 (mttt) cc_final: 0.7438 (mmtp)
REVERT: C   50 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7829 (mt-10)
REVERT: C   51 HIS cc_start: 0.7622 (m90) cc_final: 0.7055 (m-70)
REVERT: C   71 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8257 (p)
REVERT: D   36 GLU cc_start: 0.8281 (tt0) cc_final: 0.7827 (mt-10)
REVERT: D   47 GLU cc_start: 0.8116 (tp30) cc_final: 0.7772 (tp30)
REVERT: D   48 LYS cc_start: 0.8579 (mtmt) cc_final: 0.8339 (mtpp)
REVERT: D   69 GLU cc_start: 0.7782 (mp0) cc_final: 0.7499 (tt0)
REVERT: E    6 LYS cc_start: 0.6252 (mttt) cc_final: 0.6014 (mptt)
REVERT: E   36 GLU cc_start: 0.7944 (tt0) cc_final: 0.7167 (mt-10)
REVERT: E   50 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8081 (mt-10)
REVERT: F   36 GLU cc_start: 0.8186 (tt0) cc_final: 0.7777 (tt0)
REVERT: F   38 ASP cc_start: 0.9019 (p0) cc_final: 0.8733 (p0)
  outliers start: 10
  outliers final: 5
  residues processed: 129
  average time/residue: 0.6382
  time to fit residues: 84.1633
Evaluate side-chains
  116 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 110
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain F residue   61 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 37 optimal weight:    0.0170
   chunk 16 optimal weight:   10.0000
   chunk 35 optimal weight:    9.9990
   chunk 24 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 15 optimal weight:    9.9990
   chunk 40 optimal weight:    0.8980
   chunk 7 optimal weight:    9.9990
   chunk 33 optimal weight:    9.9990
   chunk 31 optimal weight:   10.0000
   chunk 41 optimal weight:    0.6980
   overall best weight:    4.3222

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

Flipped N/Q/H residues before XYZ refinement:
** A   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  31 HIS
** D  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  21 ASN
F  24 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.138039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.115120 restraints weight = 4826.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3804 rms_B_bonded: 2.26
r_work: 0.3684 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3573 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.3731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   3813  Z= 0.197
  Angle     :  0.589   7.150   5169  Z= 0.300
  Chirality :  0.045   0.136    534
  Planarity :  0.003   0.020    666
  Dihedral  :  4.509  14.754    486
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 10.95 %
    Favored  : 85.48 %
  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: -4.02 (0.31), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.05 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A  45 
 TYR   0.014   0.002   TYR B  67 
 PHE   0.012   0.002   PHE F  30 
 TRP   0.003   0.001   TRP B  60 
 HIS   0.005   0.001   HIS C  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 3807)
  covalent geometry    : angle       0.58953 ( 5157)
  SS BOND              : bond        0.00468 (    6)
  SS BOND              : angle       0.37774 (   12)
  hydrogen bonds       : bond        0.02813 (   41)
  hydrogen bonds       : angle       5.34379 (  123)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 ARG cc_start: 0.8024 (ttt180) cc_final: 0.5835 (tpm-80)
REVERT: A   36 GLU cc_start: 0.8361 (tt0) cc_final: 0.7597 (mt-10)
REVERT: A   44 GLU cc_start: 0.7762 (mp0) cc_final: 0.7090 (mm-30)
REVERT: A   50 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8313 (mt-10)
REVERT: A   58 LYS cc_start: 0.8116 (mmtt) cc_final: 0.6225 (pmtt)
REVERT: A   74 GLU cc_start: 0.8212 (pt0) cc_final: 0.7620 (pt0)
REVERT: B   36 GLU cc_start: 0.8405 (tt0) cc_final: 0.8077 (tt0)
REVERT: B   58 LYS cc_start: 0.8625 (mmtm) cc_final: 0.6958 (mptt)
REVERT: B   81 ARG cc_start: 0.7690 (mtt180) cc_final: 0.6948 (ptt-90)
REVERT: C   36 GLU cc_start: 0.7951 (tt0) cc_final: 0.7177 (mt-10)
REVERT: C   44 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6611 (mm-30)
REVERT: C   48 LYS cc_start: 0.7596 (mttt) cc_final: 0.7359 (mmtp)
REVERT: C   50 GLU cc_start: 0.8493 (mt-10) cc_final: 0.7910 (mt-10)
REVERT: C   77 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8155 (mt-10)
REVERT: D   36 GLU cc_start: 0.8249 (tt0) cc_final: 0.7799 (mt-10)
REVERT: D   38 ASP cc_start: 0.8875 (p0) cc_final: 0.8634 (p0)
REVERT: D   47 GLU cc_start: 0.8137 (tp30) cc_final: 0.7820 (tp30)
REVERT: D   48 LYS cc_start: 0.8620 (mtmt) cc_final: 0.8346 (mtpp)
REVERT: D   69 GLU cc_start: 0.7652 (mp0) cc_final: 0.7382 (tt0)
REVERT: E    6 LYS cc_start: 0.6569 (mttt) cc_final: 0.6178 (mptp)
REVERT: E   36 GLU cc_start: 0.8035 (tt0) cc_final: 0.7201 (mt-10)
REVERT: F   38 ASP cc_start: 0.9067 (p0) cc_final: 0.8858 (p0)
REVERT: F   69 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7603 (tt0)
  outliers start: 15
  outliers final: 11
  residues processed: 120
  average time/residue: 0.6385
  time to fit residues: 78.4277
Evaluate side-chains
  128 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue   77 GLU
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain F residue   61 SER
Chi-restraints excluded: chain F residue   69 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 32 optimal weight:    0.0570
   chunk 25 optimal weight:   20.0000
   chunk 35 optimal weight:    5.9990
   chunk 3 optimal weight:    9.9990
   chunk 16 optimal weight:    7.9990
   chunk 20 optimal weight:    7.9990
   chunk 21 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   chunk 9 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9990
   overall best weight:    3.8106

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

Flipped N/Q/H residues before XYZ refinement:
A   8 GLN
A  21 ASN
** B  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   8 GLN
** D  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  31 HIS
E  89 GLN
F  24 ASN
F  51 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.139070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.116795 restraints weight = 4806.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3826 rms_B_bonded: 2.24
r_work: 0.3706 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3596 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.4081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3813  Z= 0.172
  Angle     :  0.546   5.436   5169  Z= 0.280
  Chirality :  0.045   0.135    534
  Planarity :  0.003   0.019    666
  Dihedral  :  4.493  15.120    486
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 12.86 %
    Favored  : 82.38 %
  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: -4.01 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.05 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  81 
 TYR   0.016   0.001   TYR B  67 
 PHE   0.011   0.002   PHE F  30 
 TRP   0.002   0.001   TRP E  60 
 HIS   0.004   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 3807)
  covalent geometry    : angle       0.54658 ( 5157)
  SS BOND              : bond        0.00445 (    6)
  SS BOND              : angle       0.34541 (   12)
  hydrogen bonds       : bond        0.02222 (   41)
  hydrogen bonds       : angle       5.03766 (  123)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.094 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.6031 (OUTLIER) cc_final: 0.5079 (mmmm)
REVERT: A   12 ARG cc_start: 0.8066 (ttt180) cc_final: 0.5856 (tpm170)
REVERT: A   36 GLU cc_start: 0.8319 (tt0) cc_final: 0.7520 (mt-10)
REVERT: A   44 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7106 (mm-30)
REVERT: A   50 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8305 (mt-10)
REVERT: A   58 LYS cc_start: 0.8087 (mmtt) cc_final: 0.6222 (pmtt)
REVERT: A   71 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8544 (p)
REVERT: A   74 GLU cc_start: 0.8194 (pt0) cc_final: 0.7683 (pt0)
REVERT: B   36 GLU cc_start: 0.8411 (tt0) cc_final: 0.8051 (tt0)
REVERT: B   38 ASP cc_start: 0.8857 (p0) cc_final: 0.8574 (p0)
REVERT: B   45 ARG cc_start: 0.8222 (mtp85) cc_final: 0.7977 (mtp85)
REVERT: B   58 LYS cc_start: 0.8600 (mmtm) cc_final: 0.6920 (mptt)
REVERT: B   81 ARG cc_start: 0.7611 (mtt180) cc_final: 0.6900 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5968 (mptp) cc_final: 0.5004 (tttt)
REVERT: C   36 GLU cc_start: 0.7885 (tt0) cc_final: 0.7123 (mt-10)
REVERT: C   44 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6749 (mm-30)
REVERT: C   50 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7930 (mt-10)
REVERT: D   36 GLU cc_start: 0.8221 (tt0) cc_final: 0.7807 (mp0)
REVERT: D   38 ASP cc_start: 0.8897 (p0) cc_final: 0.8662 (p0)
REVERT: D   47 GLU cc_start: 0.8208 (tp30) cc_final: 0.7863 (tp30)
REVERT: D   48 LYS cc_start: 0.8574 (mtmt) cc_final: 0.8287 (mtpp)
REVERT: D   69 GLU cc_start: 0.7711 (mp0) cc_final: 0.7405 (tt0)
REVERT: D   77 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8155 (tt0)
REVERT: E    6 LYS cc_start: 0.6573 (mttt) cc_final: 0.6161 (mptp)
REVERT: E   36 GLU cc_start: 0.8027 (tt0) cc_final: 0.7172 (mt-10)
REVERT: E   50 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7471 (mt-10)
REVERT: F   36 GLU cc_start: 0.8196 (tt0) cc_final: 0.7862 (mt-10)
REVERT: F   38 ASP cc_start: 0.9059 (p0) cc_final: 0.8731 (p0)
REVERT: F   69 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7566 (tt0)
  outliers start: 20
  outliers final: 10
  residues processed: 118
  average time/residue: 0.6608
  time to fit residues: 79.8452
Evaluate side-chains
  123 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LYS
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue   44 GLU
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain F residue   50 GLU
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   61 SER
Chi-restraints excluded: chain F residue   69 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 5 optimal weight:    9.9990
   chunk 41 optimal weight:    0.9980
   chunk 26 optimal weight:    9.9990
   chunk 20 optimal weight:    8.9990
   chunk 18 optimal weight:    6.9990
   chunk 36 optimal weight:    8.9990
   chunk 35 optimal weight:    8.9990
   chunk 7 optimal weight:    9.9990
   chunk 15 optimal weight:    6.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    4.9988

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.136564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.114423 restraints weight = 4821.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3788 rms_B_bonded: 2.20
r_work: 0.3674 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3568 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.4372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   3813  Z= 0.220
  Angle     :  0.589   8.435   5169  Z= 0.299
  Chirality :  0.046   0.137    534
  Planarity :  0.003   0.019    666
  Dihedral  :  4.710  15.348    486
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 14.52 %
    Favored  : 81.19 %
  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: -3.99 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.04 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  81 
 TYR   0.017   0.002   TYR B  67 
 PHE   0.013   0.002   PHE F  30 
 TRP   0.003   0.001   TRP A  60 
 HIS   0.004   0.001   HIS C  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 ( 3807)
  covalent geometry    : angle       0.58923 ( 5157)
  SS BOND              : bond        0.00541 (    6)
  SS BOND              : angle       0.47954 (   12)
  hydrogen bonds       : bond        0.02393 (   41)
  hydrogen bonds       : angle       4.96259 (  123)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.6137 (mptp) cc_final: 0.5195 (mmmm)
REVERT: A   12 ARG cc_start: 0.8050 (ttt180) cc_final: 0.5871 (tpm170)
REVERT: A   36 GLU cc_start: 0.8285 (tt0) cc_final: 0.7477 (mt-10)
REVERT: A   44 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7308 (mp0)
REVERT: A   50 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8345 (mt-10)
REVERT: A   58 LYS cc_start: 0.8161 (mmtt) cc_final: 0.6258 (pmtt)
REVERT: A   71 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8576 (p)
REVERT: A   74 GLU cc_start: 0.8192 (pt0) cc_final: 0.7740 (pt0)
REVERT: B   58 LYS cc_start: 0.8721 (mmtm) cc_final: 0.7034 (mptt)
REVERT: B   81 ARG cc_start: 0.7574 (mtt180) cc_final: 0.7024 (pmt-80)
REVERT: C   21 ASN cc_start: 0.8757 (t0) cc_final: 0.8490 (m-40)
REVERT: C   36 GLU cc_start: 0.7935 (tt0) cc_final: 0.7168 (mt-10)
REVERT: C   48 LYS cc_start: 0.7814 (tptm) cc_final: 0.7420 (tppp)
REVERT: C   50 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7995 (mt-10)
REVERT: D   36 GLU cc_start: 0.8161 (tt0) cc_final: 0.7798 (mp0)
REVERT: D   38 ASP cc_start: 0.8890 (p0) cc_final: 0.8632 (p0)
REVERT: D   48 LYS cc_start: 0.8612 (mtmt) cc_final: 0.8317 (mtpp)
REVERT: D   69 GLU cc_start: 0.7675 (mp0) cc_final: 0.7430 (tt0)
REVERT: D   74 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7825 (mp0)
REVERT: D   77 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8195 (tt0)
REVERT: E    6 LYS cc_start: 0.6445 (mttt) cc_final: 0.6043 (mptp)
REVERT: E   36 GLU cc_start: 0.8083 (tt0) cc_final: 0.7226 (mt-10)
REVERT: E   48 LYS cc_start: 0.5082 (OUTLIER) cc_final: 0.4513 (tptt)
REVERT: F   38 ASP cc_start: 0.9066 (p0) cc_final: 0.8825 (p0)
REVERT: F   45 ARG cc_start: 0.8162 (mtp85) cc_final: 0.7552 (mtt-85)
REVERT: F   69 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7660 (tt0)
  outliers start: 18
  outliers final: 10
  residues processed: 120
  average time/residue: 0.6464
  time to fit residues: 79.4261
Evaluate side-chains
  126 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue   44 GLU
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain D residue   74 GLU
Chi-restraints excluded: chain E residue   48 LYS
Chi-restraints excluded: chain F residue   50 GLU
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   61 SER
Chi-restraints excluded: chain F residue   69 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 3 optimal weight:   10.0000
   chunk 2 optimal weight:    9.9990
   chunk 25 optimal weight:    9.9990
   chunk 5 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 32 optimal weight:    9.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  24 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.135086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.113006 restraints weight = 4946.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3774 rms_B_bonded: 2.21
r_work: 0.3657 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3548 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8659
moved from start:          0.4512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035   3813  Z= 0.257
  Angle     :  0.615   8.175   5169  Z= 0.314
  Chirality :  0.046   0.143    534
  Planarity :  0.003   0.022    666
  Dihedral  :  4.844  14.881    486
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 15.24 %
    Favored  : 80.95 %
  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: -4.03 (0.29), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.06 (0.22), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  81 
 TYR   0.018   0.002   TYR B  67 
 PHE   0.014   0.002   PHE F  30 
 TRP   0.004   0.001   TRP C  60 
 HIS   0.004   0.002   HIS A  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00594 ( 3807)
  covalent geometry    : angle       0.61556 ( 5157)
  SS BOND              : bond        0.00624 (    6)
  SS BOND              : angle       0.53114 (   12)
  hydrogen bonds       : bond        0.02428 (   41)
  hydrogen bonds       : angle       4.98793 (  123)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.6027 (mptp) cc_final: 0.5149 (mmmm)
REVERT: A   12 ARG cc_start: 0.8057 (ttt180) cc_final: 0.5934 (tpm170)
REVERT: A   36 GLU cc_start: 0.8291 (tt0) cc_final: 0.7472 (mt-10)
REVERT: A   44 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7302 (mp0)
REVERT: A   58 LYS cc_start: 0.8191 (mmtt) cc_final: 0.6261 (pmtt)
REVERT: A   74 GLU cc_start: 0.8219 (pt0) cc_final: 0.7782 (pt0)
REVERT: B   38 ASP cc_start: 0.8881 (p0) cc_final: 0.8519 (p0)
REVERT: B   45 ARG cc_start: 0.8343 (mtp85) cc_final: 0.8113 (mtp85)
REVERT: B   58 LYS cc_start: 0.8713 (mmtm) cc_final: 0.7064 (mptt)
REVERT: B   81 ARG cc_start: 0.7638 (mtt180) cc_final: 0.7038 (pmt-80)
REVERT: C   36 GLU cc_start: 0.7921 (tt0) cc_final: 0.7184 (mt-10)
REVERT: C   48 LYS cc_start: 0.7825 (tptm) cc_final: 0.7455 (tppp)
REVERT: C   50 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8115 (mt-10)
REVERT: D   36 GLU cc_start: 0.8131 (tt0) cc_final: 0.7818 (mp0)
REVERT: D   38 ASP cc_start: 0.8889 (p0) cc_final: 0.8633 (p0)
REVERT: D   74 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7830 (mp0)
REVERT: D   77 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8188 (tt0)
REVERT: E    6 LYS cc_start: 0.6457 (mttt) cc_final: 0.6058 (mptp)
REVERT: E   36 GLU cc_start: 0.8084 (tt0) cc_final: 0.7279 (mt-10)
REVERT: E   48 LYS cc_start: 0.5205 (OUTLIER) cc_final: 0.4675 (tptt)
REVERT: F   38 ASP cc_start: 0.9039 (p0) cc_final: 0.8833 (p0)
REVERT: F   45 ARG cc_start: 0.8163 (mtp85) cc_final: 0.7522 (mtt-85)
  outliers start: 16
  outliers final: 10
  residues processed: 118
  average time/residue: 0.6525
  time to fit residues: 78.7729
Evaluate side-chains
  123 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue   44 GLU
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain D residue   74 GLU
Chi-restraints excluded: chain E residue   48 LYS
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   61 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 40 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 39 optimal weight:    8.9990
   chunk 11 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   chunk 41 optimal weight:    7.9990
   chunk 8 optimal weight:    8.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.137567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.115595 restraints weight = 4897.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3795 rms_B_bonded: 2.22
r_work: 0.3680 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3571 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.4531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3813  Z= 0.162
  Angle     :  0.558   8.035   5169  Z= 0.282
  Chirality :  0.044   0.139    534
  Planarity :  0.003   0.023    666
  Dihedral  :  4.574  14.416    486
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 15.95 %
    Favored  : 80.24 %
  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: -3.95 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.00 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  12 
 TYR   0.016   0.001   TYR B  67 
 PHE   0.010   0.001   PHE F  30 
 TRP   0.002   0.001   TRP E  60 
 HIS   0.003   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 3807)
  covalent geometry    : angle       0.55828 ( 5157)
  SS BOND              : bond        0.00426 (    6)
  SS BOND              : angle       0.39010 (   12)
  hydrogen bonds       : bond        0.02031 (   41)
  hydrogen bonds       : angle       4.79429 (  123)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.6001 (OUTLIER) cc_final: 0.5085 (mmmm)
REVERT: A   12 ARG cc_start: 0.8054 (ttt180) cc_final: 0.5881 (tpm170)
REVERT: A   16 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8007 (pt0)
REVERT: A   36 GLU cc_start: 0.8258 (tt0) cc_final: 0.7472 (mt-10)
REVERT: A   44 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7374 (mp0)
REVERT: A   58 LYS cc_start: 0.8145 (mmtt) cc_final: 0.6237 (pmtt)
REVERT: A   71 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8563 (p)
REVERT: A   74 GLU cc_start: 0.8198 (pt0) cc_final: 0.7809 (pt0)
REVERT: B   58 LYS cc_start: 0.8659 (mmtm) cc_final: 0.6956 (mptt)
REVERT: B   81 ARG cc_start: 0.7615 (mtt180) cc_final: 0.7036 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5901 (mptp) cc_final: 0.4999 (mtpp)
REVERT: C   36 GLU cc_start: 0.7895 (tt0) cc_final: 0.7178 (mt-10)
REVERT: C   48 LYS cc_start: 0.7816 (tptm) cc_final: 0.7455 (tppp)
REVERT: C   50 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8107 (mt-10)
REVERT: C   71 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8335 (p)
REVERT: C   77 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8175 (mt-10)
REVERT: D   36 GLU cc_start: 0.8127 (tt0) cc_final: 0.7784 (mp0)
REVERT: D   38 ASP cc_start: 0.8905 (p0) cc_final: 0.8642 (p0)
REVERT: D   48 LYS cc_start: 0.8591 (mtmt) cc_final: 0.8328 (mtpp)
REVERT: D   77 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8172 (tt0)
REVERT: E    6 LYS cc_start: 0.6554 (mttt) cc_final: 0.6107 (mptp)
REVERT: E   36 GLU cc_start: 0.8089 (tt0) cc_final: 0.7274 (mt-10)
REVERT: E   48 LYS cc_start: 0.5165 (OUTLIER) cc_final: 0.4691 (tptt)
REVERT: F   38 ASP cc_start: 0.9003 (p0) cc_final: 0.8776 (p0)
REVERT: F   45 ARG cc_start: 0.8124 (mtp85) cc_final: 0.7446 (mtt-85)
  outliers start: 16
  outliers final: 8
  residues processed: 119
  average time/residue: 0.6656
  time to fit residues: 81.0518
Evaluate side-chains
  123 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LYS
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue   44 GLU
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue   77 GLU
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain E residue   48 LYS
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   61 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 33 optimal weight:    8.9990
   chunk 17 optimal weight:   10.0000
   chunk 20 optimal weight:   20.0000
   chunk 41 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 30 optimal weight:    7.9990
   chunk 34 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 16 optimal weight:    8.9990
   chunk 22 optimal weight:    7.9990
   chunk 3 optimal weight:    6.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  24 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.136142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.113965 restraints weight = 4890.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3783 rms_B_bonded: 2.21
r_work: 0.3666 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3557 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.4693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   3813  Z= 0.221
  Angle     :  0.605   7.847   5169  Z= 0.306
  Chirality :  0.046   0.146    534
  Planarity :  0.003   0.021    666
  Dihedral  :  4.714  14.350    486
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 15.24 %
    Favored  : 80.48 %
  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: -3.99 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.03 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  45 
 TYR   0.018   0.002   TYR B  67 
 PHE   0.013   0.002   PHE F  30 
 TRP   0.003   0.001   TRP A  60 
 HIS   0.004   0.001   HIS A  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00516 ( 3807)
  covalent geometry    : angle       0.60509 ( 5157)
  SS BOND              : bond        0.00533 (    6)
  SS BOND              : angle       0.50436 (   12)
  hydrogen bonds       : bond        0.02233 (   41)
  hydrogen bonds       : angle       4.86768 (  123)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.6013 (OUTLIER) cc_final: 0.5097 (mmmm)
REVERT: A   12 ARG cc_start: 0.8060 (ttt180) cc_final: 0.5939 (tpm170)
REVERT: A   16 GLU cc_start: 0.8560 (mt-10) cc_final: 0.7989 (pt0)
REVERT: A   36 GLU cc_start: 0.8274 (tt0) cc_final: 0.7478 (mt-10)
REVERT: A   44 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7182 (mm-30)
REVERT: A   58 LYS cc_start: 0.8191 (mmtt) cc_final: 0.6250 (pmtt)
REVERT: A   74 GLU cc_start: 0.8215 (pt0) cc_final: 0.7846 (pt0)
REVERT: B   58 LYS cc_start: 0.8740 (mmtm) cc_final: 0.7060 (mptt)
REVERT: B   81 ARG cc_start: 0.7694 (mtt180) cc_final: 0.7044 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5916 (mptp) cc_final: 0.5025 (mtpp)
REVERT: C   12 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7857 (ptm-80)
REVERT: C   36 GLU cc_start: 0.7931 (tt0) cc_final: 0.7211 (mt-10)
REVERT: C   48 LYS cc_start: 0.7818 (tptm) cc_final: 0.7472 (tppp)
REVERT: C   50 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8136 (mt-10)
REVERT: D   36 GLU cc_start: 0.8116 (tt0) cc_final: 0.7807 (mp0)
REVERT: D   48 LYS cc_start: 0.8606 (mtmt) cc_final: 0.8353 (mtpp)
REVERT: D   74 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7817 (mp0)
REVERT: D   77 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8196 (tt0)
REVERT: E    6 LYS cc_start: 0.6521 (mttt) cc_final: 0.6110 (mptp)
REVERT: E   36 GLU cc_start: 0.8113 (tt0) cc_final: 0.7299 (mt-10)
REVERT: E   48 LYS cc_start: 0.5151 (OUTLIER) cc_final: 0.4738 (tptt)
REVERT: F   45 ARG cc_start: 0.8120 (mtp85) cc_final: 0.7429 (mtt-85)
  outliers start: 18
  outliers final: 11
  residues processed: 119
  average time/residue: 0.7150
  time to fit residues: 86.9953
Evaluate side-chains
  127 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LYS
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue   44 GLU
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain C residue   12 ARG
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain D residue   74 GLU
Chi-restraints excluded: chain E residue   48 LYS
Chi-restraints excluded: chain F residue   50 GLU
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   61 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0870
   chunk 40 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0020
   chunk 17 optimal weight:    5.9990
   chunk 37 optimal weight:    0.8980
   chunk 18 optimal weight:    8.9990
   chunk 34 optimal weight:    9.9990
   chunk 33 optimal weight:    0.7980
   chunk 7 optimal weight:   10.0000
   chunk 21 optimal weight:    5.9990
   overall best weight:    0.5566

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

Flipped N/Q/H residues before XYZ refinement:
B  31 HIS
D  76 ASN
F  31 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.151947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.130528 restraints weight = 4565.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.3920 rms_B_bonded: 2.16
r_work: 0.3802 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3691 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.4613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3813  Z= 0.087
  Angle     :  0.528   7.818   5169  Z= 0.264
  Chirality :  0.043   0.133    534
  Planarity :  0.002   0.023    666
  Dihedral  :  4.206  14.043    486
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 17.14 %
    Favored  : 80.24 %
  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: -3.83 (0.31), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.91 (0.24), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  45 
 TYR   0.013   0.001   TYR B  67 
 PHE   0.010   0.001   PHE E  70 
 TRP   0.004   0.001   TRP C  60 
 HIS   0.003   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 3807)
  covalent geometry    : angle       0.52901 ( 5157)
  SS BOND              : bond        0.00178 (    6)
  SS BOND              : angle       0.20982 (   12)
  hydrogen bonds       : bond        0.01650 (   41)
  hydrogen bonds       : angle       4.51954 (  123)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 115
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.5973 (OUTLIER) cc_final: 0.4868 (mmmm)
REVERT: A   12 ARG cc_start: 0.7977 (ttt180) cc_final: 0.5880 (tpm170)
REVERT: A   16 GLU cc_start: 0.8441 (mt-10) cc_final: 0.7929 (pt0)
REVERT: A   36 GLU cc_start: 0.8145 (tt0) cc_final: 0.7376 (mt-10)
REVERT: A   44 GLU cc_start: 0.7765 (mp0) cc_final: 0.7368 (mp0)
REVERT: A   58 LYS cc_start: 0.8033 (mmtt) cc_final: 0.6230 (pmtt)
REVERT: A   71 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8592 (p)
REVERT: A   74 GLU cc_start: 0.8109 (pt0) cc_final: 0.7829 (pt0)
REVERT: B   58 LYS cc_start: 0.8661 (mmtm) cc_final: 0.6945 (mptt)
REVERT: B   81 ARG cc_start: 0.7572 (mtt180) cc_final: 0.6903 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5969 (mptp) cc_final: 0.4994 (mmmm)
REVERT: C   36 GLU cc_start: 0.7825 (tt0) cc_final: 0.7043 (mt-10)
REVERT: C   48 LYS cc_start: 0.7813 (tptm) cc_final: 0.7502 (tppp)
REVERT: C   50 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8160 (mt-10)
REVERT: C   81 ARG cc_start: 0.8344 (ttm-80) cc_final: 0.8096 (ttm-80)
REVERT: D   36 GLU cc_start: 0.8191 (tt0) cc_final: 0.7836 (mp0)
REVERT: D   38 ASP cc_start: 0.8840 (p0) cc_final: 0.8633 (p0)
REVERT: D   44 GLU cc_start: 0.7833 (tt0) cc_final: 0.7236 (mm-30)
REVERT: E    6 LYS cc_start: 0.6518 (mttt) cc_final: 0.6260 (mptp)
REVERT: E   36 GLU cc_start: 0.8100 (tt0) cc_final: 0.7271 (mt-10)
REVERT: E   48 LYS cc_start: 0.5068 (OUTLIER) cc_final: 0.4550 (tptt)
REVERT: E   74 GLU cc_start: 0.8299 (pt0) cc_final: 0.8000 (pt0)
  outliers start: 11
  outliers final: 6
  residues processed: 119
  average time/residue: 0.6838
  time to fit residues: 83.1296
Evaluate side-chains
  117 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LYS
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain E residue   48 LYS
Chi-restraints excluded: chain F residue   50 GLU
Chi-restraints excluded: chain F residue   61 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 18 optimal weight:   20.0000
   chunk 35 optimal weight:    9.9990
   chunk 22 optimal weight:    3.9990
   chunk 27 optimal weight:    8.9990
   chunk 32 optimal weight:    5.9990
   chunk 23 optimal weight:   10.0000
   chunk 25 optimal weight:    1.9990
   chunk 14 optimal weight:    8.9990
   chunk 29 optimal weight:    7.9990
   chunk 19 optimal weight:   10.0000
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.135974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.113439 restraints weight = 4934.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3777 rms_B_bonded: 2.22
r_work: 0.3663 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3552 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.4852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   3813  Z= 0.252
  Angle     :  0.642   7.768   5169  Z= 0.323
  Chirality :  0.046   0.147    534
  Planarity :  0.003   0.022    666
  Dihedral  :  4.664  13.902    486
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 18.10 %
    Favored  : 78.81 %
  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: -3.93 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.99 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  12 
 TYR   0.020   0.002   TYR B  67 
 PHE   0.015   0.002   PHE F  30 
 TRP   0.004   0.001   TRP C  60 
 HIS   0.005   0.002   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00585 ( 3807)
  covalent geometry    : angle       0.64209 ( 5157)
  SS BOND              : bond        0.00572 (    6)
  SS BOND              : angle       0.49600 (   12)
  hydrogen bonds       : bond        0.02288 (   41)
  hydrogen bonds       : angle       4.81433 (  123)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.6015 (OUTLIER) cc_final: 0.5125 (mmmm)
REVERT: A   12 ARG cc_start: 0.8020 (ttt180) cc_final: 0.5865 (tpm170)
REVERT: A   36 GLU cc_start: 0.8249 (tt0) cc_final: 0.7468 (mt-10)
REVERT: A   44 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7366 (mp0)
REVERT: A   58 LYS cc_start: 0.8217 (mmtt) cc_final: 0.6289 (pmtt)
REVERT: A   74 GLU cc_start: 0.8189 (pt0) cc_final: 0.7919 (pt0)
REVERT: B   48 LYS cc_start: 0.8802 (mtpt) cc_final: 0.8568 (mtpp)
REVERT: B   58 LYS cc_start: 0.8773 (mmtm) cc_final: 0.7044 (mptt)
REVERT: B   81 ARG cc_start: 0.7687 (mtt180) cc_final: 0.7073 (pmt-80)
REVERT: C   36 GLU cc_start: 0.7956 (tt0) cc_final: 0.7191 (mt-10)
REVERT: C   48 LYS cc_start: 0.7812 (tptm) cc_final: 0.7486 (tppp)
REVERT: C   50 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8129 (mt-10)
REVERT: D   36 GLU cc_start: 0.8136 (tt0) cc_final: 0.7799 (mp0)
REVERT: D   38 ASP cc_start: 0.8894 (p0) cc_final: 0.8688 (p0)
REVERT: D   77 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8177 (tt0)
REVERT: E    6 LYS cc_start: 0.6525 (mttt) cc_final: 0.6131 (mptp)
REVERT: E   36 GLU cc_start: 0.8163 (tt0) cc_final: 0.7331 (mt-10)
REVERT: E   48 LYS cc_start: 0.4959 (OUTLIER) cc_final: 0.4528 (tptt)
REVERT: F   45 ARG cc_start: 0.8109 (mtp85) cc_final: 0.7475 (mtt-85)
  outliers start: 13
  outliers final: 7
  residues processed: 119
  average time/residue: 0.7203
  time to fit residues: 87.6714
Evaluate side-chains
  125 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LYS
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue   44 GLU
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain E residue   48 LYS
Chi-restraints excluded: chain F residue   50 GLU
Chi-restraints excluded: chain F residue   61 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 6 optimal weight:   10.0000
   chunk 29 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 24 optimal weight:   20.0000
   chunk 35 optimal weight:    9.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
F  24 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.140822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.118508 restraints weight = 4725.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3837 rms_B_bonded: 2.23
r_work: 0.3719 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3612 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.4779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3813  Z= 0.131
  Angle     :  0.603   7.892   5169  Z= 0.296
  Chirality :  0.044   0.139    534
  Planarity :  0.002   0.019    666
  Dihedral  :  4.409  13.947    486
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 18.81 %
    Favored  : 78.57 %
  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: -3.86 (0.31), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.94 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  45 
 TYR   0.019   0.001   TYR E  10 
 PHE   0.010   0.001   PHE C  70 
 TRP   0.002   0.001   TRP D  60 
 HIS   0.003   0.001   HIS C  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 3807)
  covalent geometry    : angle       0.60370 ( 5157)
  SS BOND              : bond        0.00330 (    6)
  SS BOND              : angle       0.30662 (   12)
  hydrogen bonds       : bond        0.01911 (   41)
  hydrogen bonds       : angle       4.62715 (  123)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1933.87 seconds
wall clock time: 33 minutes 28.74 seconds (2008.74 seconds total)