Starting phenix.real_space_refine
on Fri May  9 20:22:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8a7t_15225/05_2025/8a7t_15225.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8a7t_15225/05_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_15225/05_2025/8a7t_15225.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8a7t_15225/05_2025/8a7t_15225.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8a7t_15225/05_2025/8a7t_15225.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8a7t_15225/05_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 2.50, per 1000 atoms: 0.68
  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: 0.74
  Conformation dependent library (CDL) restraints added in 395.7 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 18 sheets defined
      0.0% alpha, 45.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.52
  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: 0.89

  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:             1.090
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.610
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.360
-------------------------------------------------------------------------------
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  : 0.400 
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: 1.1581
  time to fit residues: 149.9983
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  : 0.459 
-------------------------------------------------------------------------------
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 = 0.4083 r_free = 0.4083 target = 0.143056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.121556 restraints weight = 4845.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3827 rms_B_bonded: 2.11
r_work: 0.3699 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3592 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.2804

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= 0.223
  Angle     :  0.582   4.524   5169  Z= 0.303
  Chirality :  0.045   0.142    534
  Planarity :  0.003   0.019    666
  Dihedral  :  4.393  12.120    486
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  :  9.29 %
    Favored  : 88.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.24 (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        0.04878 (   41)
  hydrogen bonds       : angle       6.12806 (  123)
  SS BOND              : bond        0.00483 (    6)
  SS BOND              : angle       0.40010 (   12)
  covalent geometry    : bond        0.00516 ( 3807)
  covalent geometry    : angle       0.58208 ( 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
  134 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 124
  time to evaluate  : 0.400 
Fit side-chains
REVERT: A   12 ARG cc_start: 0.7962 (ttt180) cc_final: 0.5765 (tpm-80)
REVERT: A   36 GLU cc_start: 0.8371 (tt0) cc_final: 0.7723 (mt-10)
REVERT: A   50 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8185 (mt-10)
REVERT: A   57 SER cc_start: 0.8725 (m) cc_final: 0.8466 (t)
REVERT: A   58 LYS cc_start: 0.8226 (mmtt) cc_final: 0.6253 (pmtt)
REVERT: C   16 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7893 (mt-10)
REVERT: C   36 GLU cc_start: 0.7992 (tt0) cc_final: 0.7218 (mt-10)
REVERT: C   48 LYS cc_start: 0.7664 (mttt) cc_final: 0.7407 (mmtp)
REVERT: C   50 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7916 (mt-10)
REVERT: C   51 HIS cc_start: 0.7736 (m90) cc_final: 0.7167 (m-70)
REVERT: D   36 GLU cc_start: 0.8238 (tt0) cc_final: 0.7824 (mt-10)
REVERT: D   47 GLU cc_start: 0.8218 (tp30) cc_final: 0.7866 (tp30)
REVERT: D   48 LYS cc_start: 0.8641 (mtmt) cc_final: 0.8337 (mtpp)
REVERT: D   74 GLU cc_start: 0.8070 (pm20) cc_final: 0.7840 (pm20)
REVERT: E    6 LYS cc_start: 0.6299 (mttt) cc_final: 0.5983 (mptt)
REVERT: E   36 GLU cc_start: 0.7992 (tt0) cc_final: 0.7249 (mt-10)
REVERT: E   50 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7893 (mt-10)
  outliers start: 10
  outliers final: 5
  residues processed: 128
  average time/residue: 1.3633
  time to fit residues: 178.7148
Evaluate side-chains
  116 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 111
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain F residue   61 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 38 optimal weight:    8.9990
   chunk 3 optimal weight:    9.9990
   chunk 32 optimal weight:   20.0000
   chunk 28 optimal weight:    6.9990
   chunk 36 optimal weight:    9.9990
   chunk 20 optimal weight:   20.0000
   chunk 13 optimal weight:   10.0000
   chunk 33 optimal weight:    7.9990
   chunk 30 optimal weight:    9.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    7.1990

-------------------------------------------------------------------------------
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
** E  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  24 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.134204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.112208 restraints weight = 4823.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 2.14
r_work: 0.3629 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3515 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8674
moved from start:          0.4119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.039   3813  Z= 0.306
  Angle     :  0.662   4.715   5169  Z= 0.344
  Chirality :  0.048   0.148    534
  Planarity :  0.004   0.025    666
  Dihedral  :  4.945  14.231    486
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 13.33 %
    Favored  : 83.33 %
  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: -4.20 (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 E  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 C  12 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03187 (   41)
  hydrogen bonds       : angle       5.56620 (  123)
  SS BOND              : bond        0.00673 (    6)
  SS BOND              : angle       0.52939 (   12)
  covalent geometry    : bond        0.00700 ( 3807)
  covalent geometry    : angle       0.66251 ( 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
  129 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 ARG cc_start: 0.8066 (ttt180) cc_final: 0.5905 (tpm170)
REVERT: A   36 GLU cc_start: 0.8323 (tt0) cc_final: 0.7556 (mt-10)
REVERT: A   44 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7446 (mm-30)
REVERT: A   50 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8407 (mt-10)
REVERT: A   58 LYS cc_start: 0.8221 (mmtt) cc_final: 0.6288 (pmtt)
REVERT: B   36 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7496 (mp0)
REVERT: B   81 ARG cc_start: 0.7683 (mtt180) cc_final: 0.7120 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5865 (mptt) cc_final: 0.4903 (mtpp)
REVERT: C   16 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8266 (mt-10)
REVERT: C   36 GLU cc_start: 0.7848 (tt0) cc_final: 0.7127 (mt-10)
REVERT: C   50 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8080 (mt-10)
REVERT: D   36 GLU cc_start: 0.8208 (tt0) cc_final: 0.7890 (mp0)
REVERT: D   48 LYS cc_start: 0.8610 (mtmt) cc_final: 0.8349 (mtpp)
REVERT: D   69 GLU cc_start: 0.7695 (mp0) cc_final: 0.7402 (tt0)
REVERT: D   77 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8162 (tt0)
REVERT: E    6 LYS cc_start: 0.6621 (mttt) cc_final: 0.6324 (mptp)
REVERT: E   12 ARG cc_start: 0.8367 (ptm-80) cc_final: 0.8113 (ptm-80)
REVERT: E   36 GLU cc_start: 0.8000 (tt0) cc_final: 0.7199 (mt-10)
REVERT: E   48 LYS cc_start: 0.5025 (mmpt) cc_final: 0.4541 (mmtt)
REVERT: F   69 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7659 (tt0)
  outliers start: 14
  outliers final: 9
  residues processed: 121
  average time/residue: 1.4115
  time to fit residues: 174.9426
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  : 0.442 
-------------------------------------------------------------------------------
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 B residue   52 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   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:   20.0000
   chunk 19 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 36 optimal weight:    7.9990
   chunk 9 optimal weight:   10.0000
   chunk 24 optimal weight:    4.9990
   chunk 7 optimal weight:    7.9990
   chunk 39 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 37 optimal weight:    8.9990
   chunk 40 optimal weight:    6.9990
   overall best weight:    6.7990

-------------------------------------------------------------------------------
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**
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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.134194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.112646 restraints weight = 4846.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3766 rms_B_bonded: 2.14
r_work: 0.3649 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3541 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8666
moved from start:          0.4360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.039   3813  Z= 0.288
  Angle     :  0.643   4.694   5169  Z= 0.333
  Chirality :  0.048   0.141    534
  Planarity :  0.003   0.025    666
  Dihedral  :  4.956  14.962    486
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 13.81 %
    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: -4.16 (0.29), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.16 (0.22), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  60 
 HIS   0.005   0.002   HIS A  31 
 PHE   0.014   0.002   PHE F  30 
 TYR   0.015   0.002   TYR B  67 
 ARG   0.002   0.000   ARG A  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02791 (   41)
  hydrogen bonds       : angle       5.36636 (  123)
  SS BOND              : bond        0.00716 (    6)
  SS BOND              : angle       0.55234 (   12)
  covalent geometry    : bond        0.00665 ( 3807)
  covalent geometry    : angle       0.64360 ( 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
  135 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.5920 (OUTLIER) cc_final: 0.5110 (mmmm)
REVERT: A   12 ARG cc_start: 0.8067 (ttt180) cc_final: 0.5960 (tpm170)
REVERT: A   36 GLU cc_start: 0.8302 (tt0) cc_final: 0.7505 (mt-10)
REVERT: A   44 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7480 (mm-30)
REVERT: A   50 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8371 (mt-10)
REVERT: A   58 LYS cc_start: 0.8189 (mmtt) cc_final: 0.6265 (pmtt)
REVERT: B   81 ARG cc_start: 0.7643 (mtt180) cc_final: 0.7096 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5752 (mptt) cc_final: 0.4906 (mmmm)
REVERT: C   12 ARG cc_start: 0.8276 (ptm-80) cc_final: 0.7961 (ptm-80)
REVERT: C   16 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7878 (mt-10)
REVERT: C   36 GLU cc_start: 0.7962 (tt0) cc_final: 0.7181 (mt-10)
REVERT: C   48 LYS cc_start: 0.7831 (tptm) cc_final: 0.7452 (tppp)
REVERT: C   50 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8049 (mt-10)
REVERT: D   36 GLU cc_start: 0.8181 (tt0) cc_final: 0.7847 (mp0)
REVERT: D   38 ASP cc_start: 0.8811 (p0) cc_final: 0.8594 (p0)
REVERT: D   69 GLU cc_start: 0.7779 (mp0) cc_final: 0.7445 (tt0)
REVERT: D   77 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8164 (tt0)
REVERT: E    6 LYS cc_start: 0.6608 (mttt) cc_final: 0.6206 (mptp)
REVERT: E   12 ARG cc_start: 0.8347 (ptm-80) cc_final: 0.8125 (ptm-80)
REVERT: E   36 GLU cc_start: 0.7986 (tt0) cc_final: 0.7206 (mt-10)
REVERT: E   48 LYS cc_start: 0.5100 (OUTLIER) cc_final: 0.4508 (tptt)
  outliers start: 21
  outliers final: 11
  residues processed: 123
  average time/residue: 1.3962
  time to fit residues: 176.0755
Evaluate side-chains
  125 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
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 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   chunk 25 optimal weight:   10.0000
   chunk 35 optimal weight:    9.9990
   chunk 41 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   chunk 32 optimal weight:    9.9990
   chunk 2 optimal weight:    7.9990
   chunk 21 optimal weight:    3.9990
   chunk 0 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    3.3988

-------------------------------------------------------------------------------
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**
** 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 = 0.4058 r_free = 0.4058 target = 0.136970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.115523 restraints weight = 4886.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3807 rms_B_bonded: 2.17
r_work: 0.3691 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3586 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.4395

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= 0.159
  Angle     :  0.566   8.836   5169  Z= 0.286
  Chirality :  0.045   0.137    534
  Planarity :  0.003   0.024    666
  Dihedral  :  4.662  15.392    486
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 13.81 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.98 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.03 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E  60 
 HIS   0.003   0.001   HIS C  13 
 PHE   0.010   0.002   PHE F  30 
 TYR   0.014   0.001   TYR B  67 
 ARG   0.001   0.000   ARG A  12 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02323 (   41)
  hydrogen bonds       : angle       5.08044 (  123)
  SS BOND              : bond        0.00426 (    6)
  SS BOND              : angle       0.38071 (   12)
  covalent geometry    : bond        0.00370 ( 3807)
  covalent geometry    : angle       0.56641 ( 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
  131 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.6092 (OUTLIER) cc_final: 0.5228 (mmmm)
REVERT: A   12 ARG cc_start: 0.8003 (ttt180) cc_final: 0.5937 (tpm170)
REVERT: A   36 GLU cc_start: 0.8296 (tt0) cc_final: 0.7493 (mt-10)
REVERT: A   44 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7403 (mm-30)
REVERT: A   50 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8410 (mt-10)
REVERT: A   58 LYS cc_start: 0.8108 (mmtt) cc_final: 0.6216 (pmtt)
REVERT: A   71 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8588 (p)
REVERT: B   45 ARG cc_start: 0.8255 (mtp85) cc_final: 0.8043 (mtp85)
REVERT: B   81 ARG cc_start: 0.7591 (mtt180) cc_final: 0.7049 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5788 (mptt) cc_final: 0.4836 (mmmm)
REVERT: C   36 GLU cc_start: 0.7941 (tt0) cc_final: 0.7170 (mt-10)
REVERT: C   48 LYS cc_start: 0.7788 (tptm) cc_final: 0.7435 (tppp)
REVERT: C   50 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8092 (mt-10)
REVERT: C   71 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8361 (p)
REVERT: C   77 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8129 (mt-10)
REVERT: D   36 GLU cc_start: 0.8147 (tt0) cc_final: 0.7814 (mp0)
REVERT: D   38 ASP cc_start: 0.8789 (p0) cc_final: 0.8570 (p0)
REVERT: D   44 GLU cc_start: 0.7842 (tt0) cc_final: 0.7151 (mm-30)
REVERT: D   48 LYS cc_start: 0.8597 (mtmt) cc_final: 0.8320 (mtpp)
REVERT: D   69 GLU cc_start: 0.7705 (mp0) cc_final: 0.7398 (tt0)
REVERT: D   77 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8140 (tt0)
REVERT: E    6 LYS cc_start: 0.6509 (mttt) cc_final: 0.6144 (mptp)
REVERT: E   36 GLU cc_start: 0.7954 (tt0) cc_final: 0.7187 (mt-10)
REVERT: E   48 LYS cc_start: 0.5154 (OUTLIER) cc_final: 0.4642 (tptt)
REVERT: F   74 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8103 (pm20)
  outliers start: 19
  outliers final: 8
  residues processed: 119
  average time/residue: 1.3034
  time to fit residues: 159.0233
Evaluate side-chains
  124 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
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 C residue   77 GLU
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain E residue   48 LYS
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   61 SER
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:    7.9990
   chunk 13 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   chunk 40 optimal weight:    4.9990
   chunk 2 optimal weight:    8.9990
   chunk 21 optimal weight:    6.9990
   chunk 5 optimal weight:    0.5980
   chunk 20 optimal weight:    6.9990
   chunk 25 optimal weight:    7.9990
   overall best weight:    2.6984

-------------------------------------------------------------------------------
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**
** 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 = 0.4105 r_free = 0.4105 target = 0.143189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.121666 restraints weight = 4704.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3823 rms_B_bonded: 2.11
r_work: 0.3712 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3606 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.4474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3813  Z= 0.134
  Angle     :  0.545   8.332   5169  Z= 0.275
  Chirality :  0.044   0.137    534
  Planarity :  0.003   0.021    666
  Dihedral  :  4.502  15.127    486
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 15.48 %
    Favored  : 80.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 A  60 
 HIS   0.003   0.001   HIS C  13 
 PHE   0.011   0.001   PHE E  70 
 TYR   0.015   0.001   TYR B  67 
 ARG   0.001   0.000   ARG A  12 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01982 (   41)
  hydrogen bonds       : angle       4.91782 (  123)
  SS BOND              : bond        0.00364 (    6)
  SS BOND              : angle       0.34261 (   12)
  covalent geometry    : bond        0.00315 ( 3807)
  covalent geometry    : angle       0.54577 ( 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
  127 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.6084 (OUTLIER) cc_final: 0.5100 (mmmm)
REVERT: A   12 ARG cc_start: 0.8001 (ttt180) cc_final: 0.5885 (tpm170)
REVERT: A   16 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8025 (pt0)
REVERT: A   36 GLU cc_start: 0.8258 (tt0) cc_final: 0.7457 (mt-10)
REVERT: A   44 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7428 (mm-30)
REVERT: A   50 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8415 (mt-10)
REVERT: A   58 LYS cc_start: 0.8020 (mmtt) cc_final: 0.6187 (pmtt)
REVERT: A   71 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8550 (p)
REVERT: A   74 GLU cc_start: 0.8195 (pt0) cc_final: 0.7756 (pt0)
REVERT: B   45 ARG cc_start: 0.8259 (mtp85) cc_final: 0.8034 (mtp85)
REVERT: B   81 ARG cc_start: 0.7560 (mtt180) cc_final: 0.7051 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5839 (mptt) cc_final: 0.4843 (mmmm)
REVERT: C   36 GLU cc_start: 0.7859 (tt0) cc_final: 0.7124 (mt-10)
REVERT: C   48 LYS cc_start: 0.7812 (tptm) cc_final: 0.7439 (tppp)
REVERT: C   50 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8004 (mt-10)
REVERT: C   71 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8334 (p)
REVERT: C   77 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8107 (mt-10)
REVERT: D   36 GLU cc_start: 0.8134 (tt0) cc_final: 0.7801 (mp0)
REVERT: D   38 ASP cc_start: 0.8841 (p0) cc_final: 0.8639 (p0)
REVERT: D   44 GLU cc_start: 0.7796 (tt0) cc_final: 0.7145 (mm-30)
REVERT: D   48 LYS cc_start: 0.8601 (mtmt) cc_final: 0.8323 (mtpp)
REVERT: D   69 GLU cc_start: 0.7698 (mp0) cc_final: 0.7392 (tt0)
REVERT: D   77 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8120 (tt0)
REVERT: E    6 LYS cc_start: 0.6518 (mttt) cc_final: 0.6129 (mptp)
REVERT: E   36 GLU cc_start: 0.7970 (tt0) cc_final: 0.7207 (mt-10)
REVERT: E   48 LYS cc_start: 0.4895 (OUTLIER) cc_final: 0.4333 (tptt)
REVERT: F   74 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8090 (pm20)
  outliers start: 18
  outliers final: 9
  residues processed: 115
  average time/residue: 1.3921
  time to fit residues: 163.9836
Evaluate side-chains
  123 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
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   57 SER
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue   77 GLU
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain E residue   48 LYS
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   61 SER
Chi-restraints excluded: chain F residue   74 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   chunk 4 optimal weight:   20.0000
   chunk 5 optimal weight:    3.9990
   chunk 36 optimal weight:    9.9990
   chunk 33 optimal weight:    9.9990
   chunk 8 optimal weight:   10.0000
   chunk 17 optimal weight:    8.9990
   chunk 29 optimal weight:   10.0000
   chunk 1 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   overall best weight:    4.7588

-------------------------------------------------------------------------------
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**
** 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 = 0.4051 r_free = 0.4051 target = 0.136056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.114202 restraints weight = 4826.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3792 rms_B_bonded: 2.17
r_work: 0.3677 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3568 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.4689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   3813  Z= 0.211
  Angle     :  0.603   8.089   5169  Z= 0.303
  Chirality :  0.046   0.144    534
  Planarity :  0.003   0.024    666
  Dihedral  :  4.688  14.726    486
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 16.43 %
    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: -3.95 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.01 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  60 
 HIS   0.003   0.001   HIS A  31 
 PHE   0.012   0.002   PHE F  30 
 TYR   0.018   0.002   TYR B  67 
 ARG   0.002   0.000   ARG E  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02174 (   41)
  hydrogen bonds       : angle       4.93563 (  123)
  SS BOND              : bond        0.00520 (    6)
  SS BOND              : angle       0.43159 (   12)
  covalent geometry    : bond        0.00495 ( 3807)
  covalent geometry    : angle       0.60308 ( 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
  133 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.6083 (mptp) cc_final: 0.5139 (mmmm)
REVERT: A   12 ARG cc_start: 0.8005 (ttt180) cc_final: 0.5905 (tpm170)
REVERT: A   16 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8048 (pt0)
REVERT: A   36 GLU cc_start: 0.8269 (tt0) cc_final: 0.7458 (mt-10)
REVERT: A   44 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7457 (mm-30)
REVERT: A   58 LYS cc_start: 0.8096 (mmtt) cc_final: 0.6232 (pmtt)
REVERT: A   74 GLU cc_start: 0.8193 (pt0) cc_final: 0.7791 (pt0)
REVERT: B   45 ARG cc_start: 0.8347 (mtp85) cc_final: 0.8098 (mtp85)
REVERT: B   81 ARG cc_start: 0.7647 (mtt180) cc_final: 0.7067 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5812 (mptt) cc_final: 0.4831 (mmmm)
REVERT: C   36 GLU cc_start: 0.7911 (tt0) cc_final: 0.7152 (mt-10)
REVERT: C   48 LYS cc_start: 0.7799 (tptm) cc_final: 0.7422 (tppp)
REVERT: C   50 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8094 (mt-10)
REVERT: D   36 GLU cc_start: 0.8141 (tt0) cc_final: 0.7828 (mp0)
REVERT: D   38 ASP cc_start: 0.8785 (p0) cc_final: 0.8572 (p0)
REVERT: D   48 LYS cc_start: 0.8628 (mtmt) cc_final: 0.8362 (mtpp)
REVERT: D   69 GLU cc_start: 0.7713 (mp0) cc_final: 0.7407 (tt0)
REVERT: D   77 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8180 (tt0)
REVERT: E    6 LYS cc_start: 0.6455 (mttt) cc_final: 0.6090 (mptp)
REVERT: E   36 GLU cc_start: 0.8029 (tt0) cc_final: 0.7261 (mt-10)
REVERT: E   48 LYS cc_start: 0.4957 (OUTLIER) cc_final: 0.4676 (tptt)
REVERT: F   45 ARG cc_start: 0.8165 (mtp85) cc_final: 0.7578 (mtt-85)
  outliers start: 18
  outliers final: 10
  residues processed: 121
  average time/residue: 1.3694
  time to fit residues: 169.7771
Evaluate side-chains
  128 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
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   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:   10.0000
   chunk 9 optimal weight:    8.9990
   chunk 6 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 12 optimal weight:    8.9990
   chunk 17 optimal weight:    2.9990
   chunk 34 optimal weight:   10.0000
   chunk 2 optimal weight:    5.9990
   chunk 35 optimal weight:    6.9990
   chunk 19 optimal weight:   10.0000
   overall best weight:    6.7990

-------------------------------------------------------------------------------
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**
** 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 = 0.4045 r_free = 0.4045 target = 0.139420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.118909 restraints weight = 4742.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3768 rms_B_bonded: 2.00
r_work: 0.3650 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3546 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8674
moved from start:          0.4819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.039   3813  Z= 0.289
  Angle     :  0.669   7.992   5169  Z= 0.340
  Chirality :  0.048   0.151    534
  Planarity :  0.003   0.028    666
  Dihedral  :  4.962  14.163    486
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 17.62 %
    Favored  : 78.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.02 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.06 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  60 
 HIS   0.005   0.002   HIS A  31 
 PHE   0.015   0.002   PHE F  30 
 TYR   0.020   0.002   TYR B  67 
 ARG   0.002   0.000   ARG E  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02510 (   41)
  hydrogen bonds       : angle       5.06508 (  123)
  SS BOND              : bond        0.00692 (    6)
  SS BOND              : angle       0.56269 (   12)
  covalent geometry    : bond        0.00672 ( 3807)
  covalent geometry    : angle       0.66938 ( 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: 15
    poor density    : 115
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.6026 (mptp) cc_final: 0.5176 (mmmm)
REVERT: A   12 ARG cc_start: 0.7999 (ttt180) cc_final: 0.5859 (tpm170)
REVERT: A   36 GLU cc_start: 0.8221 (tt0) cc_final: 0.7478 (mt-10)
REVERT: A   44 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7438 (mm-30)
REVERT: A   58 LYS cc_start: 0.8176 (mmtt) cc_final: 0.6268 (pmtt)
REVERT: A   74 GLU cc_start: 0.8217 (pt0) cc_final: 0.7810 (pt0)
REVERT: B   23 LEU cc_start: 0.8633 (tt) cc_final: 0.8348 (pp)
REVERT: B   81 ARG cc_start: 0.7734 (mtt180) cc_final: 0.7069 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5835 (mptt) cc_final: 0.4925 (mmmm)
REVERT: C   36 GLU cc_start: 0.7909 (tt0) cc_final: 0.7174 (mt-10)
REVERT: C   48 LYS cc_start: 0.7796 (tptm) cc_final: 0.7581 (tppt)
REVERT: C   50 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8245 (mt-10)
REVERT: D   36 GLU cc_start: 0.8121 (tt0) cc_final: 0.7867 (mp0)
REVERT: D   38 ASP cc_start: 0.8815 (p0) cc_final: 0.8596 (p0)
REVERT: D   69 GLU cc_start: 0.7739 (mp0) cc_final: 0.7472 (tt0)
REVERT: D   77 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8218 (tt0)
REVERT: E    6 LYS cc_start: 0.6428 (mttt) cc_final: 0.6144 (mptp)
REVERT: E   36 GLU cc_start: 0.8137 (tt0) cc_final: 0.7373 (mt-10)
REVERT: E   48 LYS cc_start: 0.4854 (OUTLIER) cc_final: 0.4371 (tptt)
REVERT: F   45 ARG cc_start: 0.8152 (mtp85) cc_final: 0.7540 (mtt-85)
  outliers start: 15
  outliers final: 9
  residues processed: 120
  average time/residue: 1.4054
  time to fit residues: 172.7787
Evaluate side-chains
  126 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 115
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
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   88 SER
Chi-restraints excluded: chain C residue   55 SER
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:    9.9990
   chunk 37 optimal weight:    4.9990
   chunk 41 optimal weight:    7.9990
   chunk 21 optimal weight:    6.9990
   chunk 4 optimal weight:    7.9990
   chunk 23 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 36 optimal weight:    8.9990
   chunk 2 optimal weight:    5.9990
   chunk 35 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    3.9588

-------------------------------------------------------------------------------
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 = 0.4065 r_free = 0.4065 target = 0.141049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.119814 restraints weight = 4703.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3790 rms_B_bonded: 2.10
r_work: 0.3676 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3567 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8639
moved from start:          0.4834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3813  Z= 0.185
  Angle     :  0.621   8.024   5169  Z= 0.309
  Chirality :  0.045   0.145    534
  Planarity :  0.003   0.031    666
  Dihedral  :  4.726  14.498    486
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 19.29 %
    Favored  : 77.86 %
  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: -3.98 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.02 (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 C  13 
 PHE   0.010   0.002   PHE F  30 
 TYR   0.017   0.002   TYR B  67 
 ARG   0.005   0.000   ARG D  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02053 (   41)
  hydrogen bonds       : angle       4.96628 (  123)
  SS BOND              : bond        0.00476 (    6)
  SS BOND              : angle       0.41281 (   12)
  covalent geometry    : bond        0.00435 ( 3807)
  covalent geometry    : angle       0.62141 ( 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
  130 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 118
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.5980 (mptp) cc_final: 0.5053 (mmmm)
REVERT: A   12 ARG cc_start: 0.7998 (ttt180) cc_final: 0.5874 (tpm170)
REVERT: A   16 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8054 (pt0)
REVERT: A   36 GLU cc_start: 0.8208 (tt0) cc_final: 0.7460 (mt-10)
REVERT: A   44 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7329 (mm-30)
REVERT: A   58 LYS cc_start: 0.8106 (mmtt) cc_final: 0.6225 (pmtt)
REVERT: A   74 GLU cc_start: 0.8204 (pt0) cc_final: 0.7850 (pt0)
REVERT: B   81 ARG cc_start: 0.7713 (mtt180) cc_final: 0.6947 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5807 (mptt) cc_final: 0.4842 (mmmm)
REVERT: C   36 GLU cc_start: 0.7880 (tt0) cc_final: 0.7133 (mt-10)
REVERT: C   48 LYS cc_start: 0.7758 (tptm) cc_final: 0.7459 (tppp)
REVERT: C   50 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8152 (mt-10)
REVERT: C   77 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8181 (mt-10)
REVERT: D   36 GLU cc_start: 0.8131 (tt0) cc_final: 0.7831 (mp0)
REVERT: D   38 ASP cc_start: 0.8797 (p0) cc_final: 0.8563 (p0)
REVERT: D   48 LYS cc_start: 0.8642 (mtmt) cc_final: 0.8376 (mtpp)
REVERT: D   69 GLU cc_start: 0.7662 (mp0) cc_final: 0.7360 (tt0)
REVERT: D   77 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8142 (tt0)
REVERT: E    6 LYS cc_start: 0.6469 (mttt) cc_final: 0.6141 (mptp)
REVERT: E   36 GLU cc_start: 0.8126 (tt0) cc_final: 0.7365 (mt-10)
REVERT: E   48 LYS cc_start: 0.4768 (OUTLIER) cc_final: 0.4346 (tptt)
REVERT: F   45 ARG cc_start: 0.8108 (mtp85) cc_final: 0.7677 (mtt-85)
  outliers start: 12
  outliers final: 9
  residues processed: 122
  average time/residue: 1.4335
  time to fit residues: 179.1143
Evaluate side-chains
  129 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
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   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 17 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9990
   chunk 16 optimal weight:    8.9990
   chunk 23 optimal weight:    9.9990
   chunk 35 optimal weight:    8.9990
   chunk 8 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 14 optimal weight:    8.9990
   chunk 39 optimal weight:    7.9990
   chunk 38 optimal weight:    7.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    3.7788

-------------------------------------------------------------------------------
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**
** 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 = 0.4058 r_free = 0.4058 target = 0.137341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.115401 restraints weight = 4785.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3798 rms_B_bonded: 2.20
r_work: 0.3680 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3570 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.4889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3813  Z= 0.178
  Angle     :  0.628   7.774   5169  Z= 0.311
  Chirality :  0.045   0.146    534
  Planarity :  0.003   0.030    666
  Dihedral  :  4.640  14.480    486
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 19.29 %
    Favored  : 77.62 %
  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: -3.98 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.03 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 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   0.018   0.002   TYR B  67 
 ARG   0.004   0.000   ARG D  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02009 (   41)
  hydrogen bonds       : angle       4.90360 (  123)
  SS BOND              : bond        0.00443 (    6)
  SS BOND              : angle       0.42913 (   12)
  covalent geometry    : bond        0.00419 ( 3807)
  covalent geometry    : angle       0.62876 ( 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
  131 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.5923 (mptp) cc_final: 0.5029 (mmmm)
REVERT: A   12 ARG cc_start: 0.8003 (ttt180) cc_final: 0.5868 (tpm170)
REVERT: A   16 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8058 (pt0)
REVERT: A   36 GLU cc_start: 0.8217 (tt0) cc_final: 0.7461 (mt-10)
REVERT: A   44 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6810 (mm-30)
REVERT: A   58 LYS cc_start: 0.8082 (mmtt) cc_final: 0.6211 (pmtt)
REVERT: A   74 GLU cc_start: 0.8206 (pt0) cc_final: 0.7869 (pt0)
REVERT: B   81 ARG cc_start: 0.7744 (mtt180) cc_final: 0.7043 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5689 (mptt) cc_final: 0.4730 (mmmm)
REVERT: C   36 GLU cc_start: 0.7903 (tt0) cc_final: 0.7149 (mt-10)
REVERT: C   48 LYS cc_start: 0.7795 (tptm) cc_final: 0.7500 (tppp)
REVERT: C   50 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8149 (mt-10)
REVERT: D   36 GLU cc_start: 0.8150 (tt0) cc_final: 0.7836 (mp0)
REVERT: D   38 ASP cc_start: 0.8870 (p0) cc_final: 0.8638 (p0)
REVERT: D   48 LYS cc_start: 0.8643 (mtmt) cc_final: 0.8382 (mtpp)
REVERT: D   69 GLU cc_start: 0.7687 (mp0) cc_final: 0.7378 (tt0)
REVERT: D   77 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8171 (tt0)
REVERT: E    6 LYS cc_start: 0.6486 (mttt) cc_final: 0.6135 (mptp)
REVERT: E   36 GLU cc_start: 0.8140 (tt0) cc_final: 0.7376 (mt-10)
REVERT: E   48 LYS cc_start: 0.4679 (OUTLIER) cc_final: 0.4287 (tptt)
REVERT: F   45 ARG cc_start: 0.8066 (mtp85) cc_final: 0.7654 (mtt-85)
  outliers start: 13
  outliers final: 10
  residues processed: 122
  average time/residue: 1.3814
  time to fit residues: 172.5409
Evaluate side-chains
  127 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
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   88 SER
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain C residue   55 SER
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:    9.9990
   chunk 22 optimal weight:    4.9990
   chunk 13 optimal weight:    9.9990
   chunk 14 optimal weight:    7.9990
   chunk 9 optimal weight:   10.0000
   chunk 21 optimal weight:   20.0000
   chunk 32 optimal weight:    8.9990
   chunk 8 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    3.7990

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.137536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.115440 restraints weight = 4800.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.3790 rms_B_bonded: 2.23
r_work: 0.3677 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3564 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.4933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3813  Z= 0.179
  Angle     :  0.633   7.790   5169  Z= 0.313
  Chirality :  0.045   0.146    534
  Planarity :  0.003   0.028    666
  Dihedral  :  4.612  14.296    486
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 19.76 %
    Favored  : 76.90 %
  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: -3.95 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.01 (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 C  13 
 PHE   0.011   0.002   PHE F  30 
 TYR   0.018   0.002   TYR B  67 
 ARG   0.004   0.000   ARG D  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01973 (   41)
  hydrogen bonds       : angle       4.88128 (  123)
  SS BOND              : bond        0.00434 (    6)
  SS BOND              : angle       0.40645 (   12)
  covalent geometry    : bond        0.00422 ( 3807)
  covalent geometry    : angle       0.63363 ( 5157)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3820.58 seconds
wall clock time: 66 minutes 29.29 seconds (3989.29 seconds total)