Starting phenix.real_space_refine
on Wed Jul 23 16:07:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8a7t_15225/07_2025/8a7t_15225.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8a7t_15225/07_2025/8a7t_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8a7t_15225/07_2025/8a7t_15225.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8a7t_15225/07_2025/8a7t_15225.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8a7t_15225/07_2025/8a7t_15225.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8a7t_15225/07_2025/8a7t_15225.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 2.33, per 1000 atoms: 0.63
  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: 0.73
  Conformation dependent library (CDL) restraints added in 380.1 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: 0.49
  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: 0.78

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 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: 0.02
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:             1.100
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.170
  Find NCS groups from input model:        0.060
  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:11.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.390
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.003   0.001   TRP D  60 
 HIS   0.002   0.001   HIS A  13 
 PHE   0.007   0.001   PHE A  70 
 TYR   0.008   0.001   TYR F  63 
 ARG   0.001   0.000   ARG E  81 

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

*********************** 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  : 0.389 
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: 1.2319
  time to fit residues: 159.4969
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  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 10 optimal weight:    9.9990
   chunk 21 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 12 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 11 optimal weight:    7.9990
   overall best weight:    4.9990

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.142896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.121427 restraints weight = 4847.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3825 rms_B_bonded: 2.11
r_work: 0.3698 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3591 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.2809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   3813  Z= 0.225
  Angle     :  0.583   4.300   5169  Z= 0.304
  Chirality :  0.045   0.141    534
  Planarity :  0.003   0.019    666
  Dihedral  :  4.396  12.267    486
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  :  8.81 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.23 (0.29), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.22 (0.22), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  60 
 HIS   0.004   0.001   HIS C  13 
 PHE   0.013   0.002   PHE F  30 
 TYR   0.011   0.002   TYR B  66 
 ARG   0.002   0.000   ARG E  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04738 (   41)
  hydrogen bonds       : angle       6.14393 (  123)
  SS BOND              : bond        0.00469 (    6)
  SS BOND              : angle       0.40554 (   12)
  covalent geometry    : bond        0.00515 ( 3807)
  covalent geometry    : angle       0.58296 ( 5157)

*********************** 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: 12
    poor density    : 123
  time to evaluate  : 0.440 
Fit side-chains
REVERT: A   12 ARG cc_start: 0.7958 (ttt180) cc_final: 0.5771 (tpm-80)
REVERT: A   36 GLU cc_start: 0.8374 (tt0) cc_final: 0.7726 (mt-10)
REVERT: A   50 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8180 (mt-10)
REVERT: A   57 SER cc_start: 0.8726 (m) cc_final: 0.8469 (t)
REVERT: A   58 LYS cc_start: 0.8229 (mmtt) cc_final: 0.6252 (pmtt)
REVERT: C   16 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7905 (mt-10)
REVERT: C   36 GLU cc_start: 0.7998 (tt0) cc_final: 0.7221 (mt-10)
REVERT: C   44 GLU cc_start: 0.6775 (mm-30) cc_final: 0.6569 (mm-30)
REVERT: C   48 LYS cc_start: 0.7666 (mttt) cc_final: 0.7426 (mmtp)
REVERT: C   50 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7901 (mt-10)
REVERT: D   36 GLU cc_start: 0.8244 (tt0) cc_final: 0.7840 (mt-10)
REVERT: D   47 GLU cc_start: 0.8212 (tp30) cc_final: 0.7857 (tp30)
REVERT: D   48 LYS cc_start: 0.8639 (mtmt) cc_final: 0.8347 (mtpp)
REVERT: D   74 GLU cc_start: 0.8063 (pm20) cc_final: 0.7830 (pm20)
REVERT: E    6 LYS cc_start: 0.6295 (mttt) cc_final: 0.5980 (mptt)
REVERT: E   36 GLU cc_start: 0.7973 (tt0) cc_final: 0.7252 (mt-10)
REVERT: E   50 GLU cc_start: 0.8412 (mt-10) cc_final: 0.7895 (mt-10)
REVERT: F   81 ARG cc_start: 0.6087 (OUTLIER) cc_final: 0.5440 (mtp180)
  outliers start: 12
  outliers final: 7
  residues processed: 127
  average time/residue: 1.4518
  time to fit residues: 188.7382
Evaluate side-chains
  119 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 SER
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   68 THR
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain F residue   61 SER
Chi-restraints excluded: chain F residue   81 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 38 optimal weight:   20.0000
   chunk 3 optimal weight:   10.0000
   chunk 32 optimal weight:   20.0000
   chunk 28 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 20 optimal weight:   20.0000
   chunk 13 optimal weight:    9.9990
   chunk 33 optimal weight:    6.9990
   chunk 30 optimal weight:    9.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    7.3990

-------------------------------------------------------------------------------
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  21 ASN
C  31 HIS
C  83 ASN
** D  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  21 ASN
F  24 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.137928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.116585 restraints weight = 4673.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 2.02
r_work: 0.3627 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3518 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8659
moved from start:          0.4099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.040   3813  Z= 0.314
  Angle     :  0.665   4.774   5169  Z= 0.347
  Chirality :  0.048   0.148    534
  Planarity :  0.004   0.026    666
  Dihedral  :  4.958  15.173    486
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 13.57 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.19 (0.29), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.19 (0.22), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  60 
 HIS   0.006   0.002   HIS C  13 
 PHE   0.015   0.002   PHE F  30 
 TYR   0.014   0.002   TYR B  67 
 ARG   0.003   0.001   ARG A  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03339 (   41)
  hydrogen bonds       : angle       5.58152 (  123)
  SS BOND              : bond        0.00708 (    6)
  SS BOND              : angle       0.54463 (   12)
  covalent geometry    : bond        0.00722 ( 3807)
  covalent geometry    : angle       0.66569 ( 5157)

*********************** 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
  131 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 ARG cc_start: 0.8044 (ttt180) cc_final: 0.5871 (tpm170)
REVERT: A   36 GLU cc_start: 0.8311 (tt0) cc_final: 0.7541 (mt-10)
REVERT: A   44 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7293 (mm-30)
REVERT: A   50 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8366 (mt-10)
REVERT: A   58 LYS cc_start: 0.8215 (mmtt) cc_final: 0.6283 (pmtt)
REVERT: B   36 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7476 (mp0)
REVERT: B   81 ARG cc_start: 0.7667 (mtt180) cc_final: 0.7094 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5797 (mptt) cc_final: 0.4858 (mtpp)
REVERT: C   16 GLU cc_start: 0.8431 (mt-10) cc_final: 0.7769 (mt-10)
REVERT: C   36 GLU cc_start: 0.7844 (tt0) cc_final: 0.7114 (mt-10)
REVERT: C   50 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8055 (mt-10)
REVERT: D   36 GLU cc_start: 0.8184 (tt0) cc_final: 0.7857 (mp0)
REVERT: D   38 ASP cc_start: 0.8791 (p0) cc_final: 0.8586 (p0)
REVERT: D   69 GLU cc_start: 0.7722 (mp0) cc_final: 0.7381 (tt0)
REVERT: D   77 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8163 (tt0)
REVERT: E    6 LYS cc_start: 0.6580 (mttt) cc_final: 0.6290 (mptp)
REVERT: E   36 GLU cc_start: 0.7980 (tt0) cc_final: 0.7178 (mt-10)
REVERT: E   48 LYS cc_start: 0.5103 (mmpt) cc_final: 0.4595 (mmtt)
REVERT: F   69 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7573 (tt0)
  outliers start: 15
  outliers final: 8
  residues processed: 122
  average time/residue: 1.4397
  time to fit residues: 179.8624
Evaluate side-chains
  124 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
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 B residue   36 GLU
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   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 28 optimal weight:    8.9990
   chunk 19 optimal weight:   10.0000
   chunk 16 optimal weight:    2.9990
   chunk 36 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 24 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   chunk 4 optimal weight:   10.0000
   chunk 37 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   overall best weight:    3.9988

-------------------------------------------------------------------------------
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  21 ASN
** B  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  31 HIS
** D  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  24 ASN
F  51 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.138046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.116419 restraints weight = 4748.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.3807 rms_B_bonded: 2.13
r_work: 0.3695 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3588 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8628
moved from start:          0.4207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3813  Z= 0.182
  Angle     :  0.569   4.537   5169  Z= 0.293
  Chirality :  0.045   0.135    534
  Planarity :  0.003   0.020    666
  Dihedral  :  4.653  15.469    486
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 14.52 %
    Favored  : 81.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.07 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.09 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E  60 
 HIS   0.004   0.001   HIS C  13 
 PHE   0.011   0.002   PHE F  30 
 TYR   0.014   0.001   TYR B  67 
 ARG   0.002   0.000   ARG E  12 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02511 (   41)
  hydrogen bonds       : angle       5.20200 (  123)
  SS BOND              : bond        0.00489 (    6)
  SS BOND              : angle       0.39657 (   12)
  covalent geometry    : bond        0.00420 ( 3807)
  covalent geometry    : angle       0.56978 ( 5157)

*********************** 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
  127 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.6106 (OUTLIER) cc_final: 0.5200 (mmmm)
REVERT: A   12 ARG cc_start: 0.8027 (ttt180) cc_final: 0.5915 (tpm170)
REVERT: A   36 GLU cc_start: 0.8313 (tt0) cc_final: 0.7526 (mt-10)
REVERT: A   44 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7462 (mm-30)
REVERT: A   50 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8345 (mt-10)
REVERT: A   58 LYS cc_start: 0.8135 (mmtt) cc_final: 0.6208 (pmtt)
REVERT: A   71 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8585 (p)
REVERT: B   45 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7992 (mtp85)
REVERT: B   81 ARG cc_start: 0.7554 (mtt180) cc_final: 0.7051 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5709 (mptt) cc_final: 0.4792 (mmmm)
REVERT: C   36 GLU cc_start: 0.7911 (tt0) cc_final: 0.7147 (mt-10)
REVERT: C   44 GLU cc_start: 0.6979 (mm-30) cc_final: 0.6672 (mm-30)
REVERT: C   48 LYS cc_start: 0.7819 (tptm) cc_final: 0.7450 (tppp)
REVERT: C   50 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8054 (mt-10)
REVERT: D   36 GLU cc_start: 0.8162 (tt0) cc_final: 0.7828 (mp0)
REVERT: D   38 ASP cc_start: 0.8837 (p0) cc_final: 0.8619 (p0)
REVERT: D   69 GLU cc_start: 0.7705 (mp0) cc_final: 0.7402 (tt0)
REVERT: D   77 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8181 (tt0)
REVERT: E    6 LYS cc_start: 0.6642 (mttt) cc_final: 0.6270 (mptp)
REVERT: E   36 GLU cc_start: 0.7951 (tt0) cc_final: 0.7154 (mt-10)
REVERT: E   48 LYS cc_start: 0.5006 (mmpt) cc_final: 0.4373 (tptt)
  outliers start: 17
  outliers final: 10
  residues processed: 115
  average time/residue: 1.4191
  time to fit residues: 167.3140
Evaluate side-chains
  119 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:   20.0000
   chunk 4 optimal weight:   20.0000
   chunk 25 optimal weight:   20.0000
   chunk 35 optimal weight:   10.0000
   chunk 41 optimal weight:    0.2980
   chunk 6 optimal weight:    5.9990
   chunk 32 optimal weight:   20.0000
   chunk 2 optimal weight:   20.0000
   chunk 21 optimal weight:    6.9990
   chunk 0 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    3.2588

-------------------------------------------------------------------------------
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**
** B  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  83 ASN
** D  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.138807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.117075 restraints weight = 4860.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.3821 rms_B_bonded: 2.18
r_work: 0.3703 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3598 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.4252

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= 0.155
  Angle     :  0.533   3.859   5169  Z= 0.275
  Chirality :  0.044   0.136    534
  Planarity :  0.003   0.018    666
  Dihedral  :  4.508  15.186    486
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 13.57 %
    Favored  : 81.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.94 (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
 TRP   0.002   0.001   TRP A  60 
 HIS   0.004   0.001   HIS C  13 
 PHE   0.010   0.001   PHE F  30 
 TYR   0.015   0.001   TYR B  67 
 ARG   0.001   0.000   ARG E  12 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02151 (   41)
  hydrogen bonds       : angle       4.90346 (  123)
  SS BOND              : bond        0.00419 (    6)
  SS BOND              : angle       0.36837 (   12)
  covalent geometry    : bond        0.00360 ( 3807)
  covalent geometry    : angle       0.53375 ( 5157)

*********************** 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: 19
    poor density    : 111
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.6083 (OUTLIER) cc_final: 0.5162 (mmmm)
REVERT: A   12 ARG cc_start: 0.8042 (ttt180) cc_final: 0.5903 (tpm170)
REVERT: A   16 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8034 (pt0)
REVERT: A   36 GLU cc_start: 0.8271 (tt0) cc_final: 0.7474 (mt-10)
REVERT: A   50 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8400 (mt-10)
REVERT: A   58 LYS cc_start: 0.8082 (mmtt) cc_final: 0.6224 (pmtt)
REVERT: A   71 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8547 (p)
REVERT: A   74 GLU cc_start: 0.8148 (pt0) cc_final: 0.7700 (pt0)
REVERT: B   45 ARG cc_start: 0.8268 (mtp85) cc_final: 0.8002 (mtp85)
REVERT: B   81 ARG cc_start: 0.7513 (mtt180) cc_final: 0.7047 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5722 (mptt) cc_final: 0.4824 (mmmm)
REVERT: C   16 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8109 (mt-10)
REVERT: C   36 GLU cc_start: 0.7890 (tt0) cc_final: 0.7169 (mt-10)
REVERT: C   48 LYS cc_start: 0.7817 (tptm) cc_final: 0.7427 (tppp)
REVERT: C   50 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8089 (mt-10)
REVERT: C   71 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8350 (p)
REVERT: D   36 GLU cc_start: 0.8168 (tt0) cc_final: 0.7817 (mp0)
REVERT: D   38 ASP cc_start: 0.8809 (p0) cc_final: 0.8602 (p0)
REVERT: D   69 GLU cc_start: 0.7714 (mp0) cc_final: 0.7393 (tt0)
REVERT: D   77 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8127 (tt0)
REVERT: E    6 LYS cc_start: 0.6518 (mttt) cc_final: 0.6192 (mptp)
REVERT: E   36 GLU cc_start: 0.7986 (tt0) cc_final: 0.7173 (mt-10)
REVERT: E   48 LYS cc_start: 0.5207 (OUTLIER) cc_final: 0.4615 (tptt)
REVERT: F   74 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8139 (pm20)
  outliers start: 19
  outliers final: 9
  residues processed: 120
  average time/residue: 1.3580
  time to fit residues: 166.9896
Evaluate side-chains
  122 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
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   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   57 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
Chi-restraints excluded: chain F residue   74 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:   20.0000
   chunk 34 optimal weight:    6.9990
   chunk 13 optimal weight:   10.0000
   chunk 11 optimal weight:   10.0000
   chunk 9 optimal weight:    8.9990
   chunk 40 optimal weight:    0.0370
   chunk 2 optimal weight:   10.0000
   chunk 21 optimal weight:   20.0000
   chunk 5 optimal weight:    7.9990
   chunk 20 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   overall best weight:    5.4066

-------------------------------------------------------------------------------
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**
** B  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  89 GLN ** 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 = 0.4042 r_free = 0.4042 target = 0.135705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.113761 restraints weight = 4884.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3777 rms_B_bonded: 2.17
r_work: 0.3663 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3555 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8651
moved from start:          0.4444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   3813  Z= 0.234
  Angle     :  0.604   8.487   5169  Z= 0.307
  Chirality :  0.046   0.145    534
  Planarity :  0.003   0.022    666
  Dihedral  :  4.781  15.068    486
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 14.76 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.00 (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
 TRP   0.003   0.001   TRP C  60 
 HIS   0.004   0.001   HIS C  13 
 PHE   0.013   0.002   PHE F  30 
 TYR   0.018   0.002   TYR B  67 
 ARG   0.002   0.000   ARG A  12 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02526 (   41)
  hydrogen bonds       : angle       4.93026 (  123)
  SS BOND              : bond        0.00588 (    6)
  SS BOND              : angle       0.52443 (   12)
  covalent geometry    : bond        0.00544 ( 3807)
  covalent geometry    : angle       0.60379 ( 5157)

*********************** 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
  128 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.6004 (mptp) cc_final: 0.5135 (mmmm)
REVERT: A   12 ARG cc_start: 0.8002 (ttt180) cc_final: 0.5920 (tpm170)
REVERT: A   36 GLU cc_start: 0.8284 (tt0) cc_final: 0.7481 (mt-10)
REVERT: A   44 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7460 (mm-30)
REVERT: A   50 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8427 (mt-10)
REVERT: A   58 LYS cc_start: 0.8124 (mmtt) cc_final: 0.6222 (pmtt)
REVERT: A   71 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8567 (p)
REVERT: A   74 GLU cc_start: 0.8201 (pt0) cc_final: 0.7697 (pt0)
REVERT: B   81 ARG cc_start: 0.7586 (mtt180) cc_final: 0.7054 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5646 (mptt) cc_final: 0.4790 (mmmm)
REVERT: C   16 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8023 (mt-10)
REVERT: C   36 GLU cc_start: 0.7923 (tt0) cc_final: 0.7201 (mt-10)
REVERT: C   48 LYS cc_start: 0.7812 (tptm) cc_final: 0.7431 (tppp)
REVERT: C   50 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8124 (mt-10)
REVERT: D   36 GLU cc_start: 0.8146 (tt0) cc_final: 0.7830 (mp0)
REVERT: D   38 ASP cc_start: 0.8845 (p0) cc_final: 0.8621 (p0)
REVERT: D   44 GLU cc_start: 0.7877 (tt0) cc_final: 0.7221 (mm-30)
REVERT: D   69 GLU cc_start: 0.7736 (mp0) cc_final: 0.7414 (tt0)
REVERT: D   77 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8189 (tt0)
REVERT: E    6 LYS cc_start: 0.6486 (mttt) cc_final: 0.6096 (mptp)
REVERT: E   12 ARG cc_start: 0.8360 (ptm-80) cc_final: 0.8157 (ptm-80)
REVERT: E   36 GLU cc_start: 0.8020 (tt0) cc_final: 0.7254 (mt-10)
REVERT: E   48 LYS cc_start: 0.5026 (OUTLIER) cc_final: 0.4672 (tptt)
  outliers start: 17
  outliers final: 9
  residues processed: 118
  average time/residue: 1.4043
  time to fit residues: 169.7082
Evaluate side-chains
  122 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
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 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 2 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    7.9990
   chunk 5 optimal weight:    6.9990
   chunk 36 optimal weight:    8.9990
   chunk 33 optimal weight:    6.9990
   chunk 8 optimal weight:    8.9990
   chunk 17 optimal weight:    9.9990
   chunk 29 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    5.3990

-------------------------------------------------------------------------------
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**
** B  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  89 GLN ** 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 = 0.4042 r_free = 0.4042 target = 0.135785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.113889 restraints weight = 4817.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.3770 rms_B_bonded: 2.17
r_work: 0.3657 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3548 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.4557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   3813  Z= 0.234
  Angle     :  0.612   8.391   5169  Z= 0.310
  Chirality :  0.046   0.145    534
  Planarity :  0.003   0.025    666
  Dihedral  :  4.819  14.755    486
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 15.71 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.003   0.001   TRP C  60 
 HIS   0.004   0.001   HIS A  31 
 PHE   0.013   0.002   PHE F  30 
 TYR   0.017   0.002   TYR B  67 
 ARG   0.002   0.000   ARG E  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02359 (   41)
  hydrogen bonds       : angle       4.89219 (  123)
  SS BOND              : bond        0.00591 (    6)
  SS BOND              : angle       0.50136 (   12)
  covalent geometry    : bond        0.00543 ( 3807)
  covalent geometry    : angle       0.61232 ( 5157)

*********************** 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
  126 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.5995 (mptp) cc_final: 0.5111 (mmmm)
REVERT: A   12 ARG cc_start: 0.7977 (ttt180) cc_final: 0.5877 (tpm170)
REVERT: A   16 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8055 (pt0)
REVERT: A   36 GLU cc_start: 0.8265 (tt0) cc_final: 0.7470 (mt-10)
REVERT: A   44 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7380 (mm-30)
REVERT: A   50 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8582 (mt-10)
REVERT: A   58 LYS cc_start: 0.8160 (mmtt) cc_final: 0.6243 (pmtt)
REVERT: A   71 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8644 (p)
REVERT: A   74 GLU cc_start: 0.8181 (pt0) cc_final: 0.7724 (pt0)
REVERT: B   81 ARG cc_start: 0.7627 (mtt180) cc_final: 0.7083 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5668 (mptt) cc_final: 0.4828 (mmmm)
REVERT: C   36 GLU cc_start: 0.7926 (tt0) cc_final: 0.7202 (mt-10)
REVERT: C   48 LYS cc_start: 0.7811 (tptm) cc_final: 0.7466 (tppp)
REVERT: C   50 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8235 (mt-10)
REVERT: D   36 GLU cc_start: 0.8124 (tt0) cc_final: 0.7830 (mp0)
REVERT: D   38 ASP cc_start: 0.8766 (p0) cc_final: 0.8548 (p0)
REVERT: D   69 GLU cc_start: 0.7725 (mp0) cc_final: 0.7420 (tt0)
REVERT: D   77 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8171 (tt0)
REVERT: E    6 LYS cc_start: 0.6432 (mttt) cc_final: 0.6088 (mptp)
REVERT: E   36 GLU cc_start: 0.8032 (tt0) cc_final: 0.7287 (mt-10)
REVERT: E   48 LYS cc_start: 0.4800 (OUTLIER) cc_final: 0.4347 (tptt)
REVERT: F   45 ARG cc_start: 0.8186 (mtp85) cc_final: 0.7591 (mtt-85)
  outliers start: 14
  outliers final: 10
  residues processed: 118
  average time/residue: 1.3505
  time to fit residues: 163.1968
Evaluate side-chains
  121 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
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 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 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 9 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   chunk 12 optimal weight:    7.9990
   chunk 17 optimal weight:    6.9990
   chunk 34 optimal weight:    7.9990
   chunk 2 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 19 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:
** A   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  89 GLN ** 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 = 0.4029 r_free = 0.4029 target = 0.134479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.112609 restraints weight = 4882.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3764 rms_B_bonded: 2.18
r_work: 0.3649 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3540 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.4678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   3813  Z= 0.259
  Angle     :  0.648   8.260   5169  Z= 0.326
  Chirality :  0.047   0.150    534
  Planarity :  0.003   0.026    666
  Dihedral  :  4.898  14.775    486
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 16.19 %
    Favored  : 79.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.003   0.001   TRP C  60 
 HIS   0.004   0.002   HIS A  31 
 PHE   0.014   0.002   PHE F  30 
 TYR   0.019   0.002   TYR B  67 
 ARG   0.002   0.000   ARG E  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02429 (   41)
  hydrogen bonds       : angle       4.91924 (  123)
  SS BOND              : bond        0.00645 (    6)
  SS BOND              : angle       0.55382 (   12)
  covalent geometry    : bond        0.00602 ( 3807)
  covalent geometry    : angle       0.64844 ( 5157)

*********************** 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
  130 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.6023 (OUTLIER) cc_final: 0.5142 (mmmm)
REVERT: A   12 ARG cc_start: 0.7991 (ttt180) cc_final: 0.5893 (tpm170)
REVERT: A   16 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8049 (pt0)
REVERT: A   36 GLU cc_start: 0.8242 (tt0) cc_final: 0.7483 (mt-10)
REVERT: A   44 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7419 (mm-30)
REVERT: A   58 LYS cc_start: 0.8195 (mmtt) cc_final: 0.6266 (pmtt)
REVERT: A   74 GLU cc_start: 0.8221 (pt0) cc_final: 0.7782 (pt0)
REVERT: B   23 LEU cc_start: 0.8614 (tt) cc_final: 0.8296 (pp)
REVERT: B   38 ASP cc_start: 0.8786 (p0) cc_final: 0.8300 (p0)
REVERT: B   81 ARG cc_start: 0.7676 (mtt180) cc_final: 0.7090 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5667 (mptt) cc_final: 0.4833 (mmmm)
REVERT: C   36 GLU cc_start: 0.7941 (tt0) cc_final: 0.7257 (mt-10)
REVERT: C   48 LYS cc_start: 0.7792 (tptm) cc_final: 0.7583 (tppt)
REVERT: C   50 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8256 (mt-10)
REVERT: C   77 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8228 (mt-10)
REVERT: D   36 GLU cc_start: 0.8123 (tt0) cc_final: 0.7834 (mp0)
REVERT: D   38 ASP cc_start: 0.8848 (p0) cc_final: 0.8609 (p0)
REVERT: D   69 GLU cc_start: 0.7723 (mp0) cc_final: 0.7423 (tt0)
REVERT: D   77 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8197 (tt0)
REVERT: E    6 LYS cc_start: 0.6486 (mttt) cc_final: 0.6153 (mptp)
REVERT: E   36 GLU cc_start: 0.8054 (tt0) cc_final: 0.7323 (mt-10)
REVERT: E   48 LYS cc_start: 0.4678 (OUTLIER) cc_final: 0.4254 (tptt)
REVERT: F   45 ARG cc_start: 0.8140 (mtp85) cc_final: 0.7578 (mtt-85)
  outliers start: 17
  outliers final: 11
  residues processed: 120
  average time/residue: 1.3459
  time to fit residues: 165.4722
Evaluate side-chains
  127 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
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   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 30 optimal weight:   10.0000
   chunk 37 optimal weight:    7.9990
   chunk 41 optimal weight:    3.9990
   chunk 21 optimal weight:    9.9990
   chunk 4 optimal weight:   20.0000
   chunk 23 optimal weight:    3.9990
   chunk 9 optimal weight:    8.9990
   chunk 36 optimal weight:    6.9990
   chunk 2 optimal weight:    7.9990
   chunk 35 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    5.3990

-------------------------------------------------------------------------------
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**
** B  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  89 GLN ** 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 = 0.4039 r_free = 0.4039 target = 0.135386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.113498 restraints weight = 4820.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.3770 rms_B_bonded: 2.17
r_work: 0.3654 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3545 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8660
moved from start:          0.4740

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= 0.237
  Angle     :  0.645   8.208   5169  Z= 0.323
  Chirality :  0.046   0.149    534
  Planarity :  0.003   0.025    666
  Dihedral  :  4.850  14.315    486
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 17.14 %
    Favored  : 79.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.003   0.001   TRP A  60 
 HIS   0.004   0.001   HIS A  31 
 PHE   0.013   0.002   PHE F  30 
 TYR   0.019   0.002   TYR B  67 
 ARG   0.002   0.000   ARG A  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02346 (   41)
  hydrogen bonds       : angle       4.86809 (  123)
  SS BOND              : bond        0.00587 (    6)
  SS BOND              : angle       0.49580 (   12)
  covalent geometry    : bond        0.00555 ( 3807)
  covalent geometry    : angle       0.64572 ( 5157)

*********************** 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
  129 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.617 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.6010 (OUTLIER) cc_final: 0.5079 (mmmm)
REVERT: A   12 ARG cc_start: 0.7964 (ttt180) cc_final: 0.5822 (tpm170)
REVERT: A   16 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8046 (pt0)
REVERT: A   36 GLU cc_start: 0.8239 (tt0) cc_final: 0.7486 (mt-10)
REVERT: A   44 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7404 (mm-30)
REVERT: A   58 LYS cc_start: 0.8186 (mmtt) cc_final: 0.6264 (pmtt)
REVERT: A   74 GLU cc_start: 0.8203 (pt0) cc_final: 0.7780 (pt0)
REVERT: B   23 LEU cc_start: 0.8569 (tt) cc_final: 0.8369 (pp)
REVERT: B   81 ARG cc_start: 0.7721 (mtt180) cc_final: 0.7061 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5691 (mptt) cc_final: 0.4834 (mmmm)
REVERT: C   36 GLU cc_start: 0.7925 (tt0) cc_final: 0.7200 (mt-10)
REVERT: C   48 LYS cc_start: 0.7796 (tptm) cc_final: 0.7584 (tppt)
REVERT: C   50 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8226 (mt-10)
REVERT: C   71 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8428 (p)
REVERT: C   77 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8247 (mt-10)
REVERT: D   36 GLU cc_start: 0.8131 (tt0) cc_final: 0.7817 (mp0)
REVERT: D   69 GLU cc_start: 0.7699 (mp0) cc_final: 0.7402 (tt0)
REVERT: D   77 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8172 (tt0)
REVERT: E    6 LYS cc_start: 0.6542 (mttt) cc_final: 0.6202 (mptp)
REVERT: E   36 GLU cc_start: 0.8099 (tt0) cc_final: 0.7339 (mt-10)
REVERT: E   48 LYS cc_start: 0.4789 (OUTLIER) cc_final: 0.4391 (tptt)
REVERT: F   45 ARG cc_start: 0.8106 (mtp85) cc_final: 0.7557 (mtt-85)
  outliers start: 15
  outliers final: 10
  residues processed: 120
  average time/residue: 1.8103
  time to fit residues: 222.2378
Evaluate side-chains
  127 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
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   50 GLU
Chi-restraints excluded: chain F residue   52 SER
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 17 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 35 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 32 optimal weight:    7.9990
   chunk 14 optimal weight:    6.9990
   chunk 39 optimal weight:    8.9990
   chunk 38 optimal weight:    8.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    3.1788

-------------------------------------------------------------------------------
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**
** C  89 GLN ** 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 = 0.4077 r_free = 0.4077 target = 0.138456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.116513 restraints weight = 4762.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3814 rms_B_bonded: 2.18
r_work: 0.3699 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3592 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          0.4744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3813  Z= 0.157
  Angle     :  0.615   8.036   5169  Z= 0.303
  Chirality :  0.045   0.163    534
  Planarity :  0.003   0.023    666
  Dihedral  :  4.637  14.126    486
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 17.86 %
    Favored  : 78.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.002   0.001   TRP E  60 
 HIS   0.003   0.001   HIS C  13 
 PHE   0.010   0.001   PHE E  70 
 TYR   0.017   0.001   TYR B  67 
 ARG   0.001   0.000   ARG A  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02001 (   41)
  hydrogen bonds       : angle       4.69612 (  123)
  SS BOND              : bond        0.00406 (    6)
  SS BOND              : angle       0.36654 (   12)
  covalent geometry    : bond        0.00373 ( 3807)
  covalent geometry    : angle       0.61512 ( 5157)

********************** 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
  129 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.5897 (OUTLIER) cc_final: 0.4966 (mmmm)
REVERT: A   12 ARG cc_start: 0.7962 (ttt180) cc_final: 0.5903 (tpm170)
REVERT: A   16 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8064 (pt0)
REVERT: A   36 GLU cc_start: 0.8232 (tt0) cc_final: 0.7485 (mt-10)
REVERT: A   44 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7433 (mm-30)
REVERT: A   58 LYS cc_start: 0.8144 (mmtt) cc_final: 0.6265 (pmtt)
REVERT: A   71 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8657 (p)
REVERT: A   74 GLU cc_start: 0.8168 (pt0) cc_final: 0.7837 (pt0)
REVERT: B   81 ARG cc_start: 0.7558 (mtt180) cc_final: 0.6851 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5693 (mptt) cc_final: 0.4876 (mmmm)
REVERT: C   36 GLU cc_start: 0.7900 (tt0) cc_final: 0.7147 (mt-10)
REVERT: C   48 LYS cc_start: 0.7847 (tptm) cc_final: 0.7647 (tppt)
REVERT: C   50 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8241 (mt-10)
REVERT: C   77 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8196 (mt-10)
REVERT: D   36 GLU cc_start: 0.8142 (tt0) cc_final: 0.7823 (mp0)
REVERT: D   69 GLU cc_start: 0.7627 (mp0) cc_final: 0.7309 (tt0)
REVERT: D   77 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8109 (tt0)
REVERT: E    6 LYS cc_start: 0.6569 (mttt) cc_final: 0.6244 (mptp)
REVERT: E   36 GLU cc_start: 0.8181 (tt0) cc_final: 0.7368 (mt-10)
REVERT: E   48 LYS cc_start: 0.4678 (OUTLIER) cc_final: 0.4278 (tptt)
REVERT: F   45 ARG cc_start: 0.8125 (mtp85) cc_final: 0.7458 (mtt-85)
  outliers start: 16
  outliers final: 9
  residues processed: 119
  average time/residue: 2.6195
  time to fit residues: 317.9655
Evaluate side-chains
  126 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
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   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   50 GLU
Chi-restraints excluded: chain F residue   52 SER
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 41 optimal weight:    7.9990
   chunk 22 optimal weight:    8.9990
   chunk 13 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 9 optimal weight:    0.0980
   chunk 21 optimal weight:   20.0000
   chunk 32 optimal weight:    9.9990
   chunk 8 optimal weight:    6.9990
   chunk 4 optimal weight:    8.9990
   chunk 0 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    3.8188

-------------------------------------------------------------------------------
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**
** 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 = 0.4055 r_free = 0.4055 target = 0.136668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.114732 restraints weight = 4831.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3792 rms_B_bonded: 2.20
r_work: 0.3678 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3569 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8640
moved from start:          0.4841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3813  Z= 0.181
  Angle     :  0.634   7.958   5169  Z= 0.314
  Chirality :  0.046   0.170    534
  Planarity :  0.003   0.024    666
  Dihedral  :  4.645  13.790    486
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 18.57 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.94 (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
 TRP   0.002   0.001   TRP A  60 
 HIS   0.003   0.001   HIS D  31 
 PHE   0.011   0.002   PHE F  30 
 TYR   0.017   0.002   TYR B  67 
 ARG   0.001   0.000   ARG B  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02057 (   41)
  hydrogen bonds       : angle       4.71315 (  123)
  SS BOND              : bond        0.00452 (    6)
  SS BOND              : angle       0.41493 (   12)
  covalent geometry    : bond        0.00429 ( 3807)
  covalent geometry    : angle       0.63402 ( 5157)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4196.13 seconds
wall clock time: 74 minutes 29.86 seconds (4469.86 seconds total)