Starting phenix.real_space_refine
on Tue Feb 11 02:15:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8a7t_15225/02_2025/8a7t_15225.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8a7t_15225/02_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_15225/02_2025/8a7t_15225.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8a7t_15225/02_2025/8a7t_15225.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8a7t_15225/02_2025/8a7t_15225.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8a7t_15225/02_2025/8a7t_15225.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    2370      2.51       5
     N     600      2.21       5
     O     720      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 2.42, per 1000 atoms: 0.65
  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=2, 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

  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 396.4 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: 0.53
  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: 0.81

  Time building geometry restraints manager: 0.89 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: 2052
       10.61 -    21.21: 155
       21.21 -    31.82: 19
       31.82 -    42.42: 9
       42.42 -    53.03: 6
  Dihedral angle restraints: 2241
    sinusoidal: 912
      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 2238 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:
        2.03 -     2.60: 33
        2.60 -     3.18: 2833
        3.18 -     3.75: 5008
        3.75 -     4.33: 7229
        4.33 -     4.90: 11497
  Nonbonded interactions: 26600
  Sorted by model distance:
  nonbonded pdb=" SG  CYS E  25 "
            pdb=" SG  CYS E  80 "
     model   vdw
     2.026 3.760
  nonbonded pdb=" SG  CYS C  25 "
            pdb=" SG  CYS C  80 "
     model   vdw
     2.027 3.760
  nonbonded pdb=" SG  CYS F  25 "
            pdb=" SG  CYS F  80 "
     model   vdw
     2.028 3.760
  nonbonded pdb=" SG  CYS D  25 "
            pdb=" SG  CYS D  80 "
     model   vdw
     2.029 3.760
  nonbonded pdb=" OE2 GLU C  16 "
            pdb=" NH2 ARG C  81 "
     model   vdw
     2.302 3.120
  ... (remaining 26595 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:             0.690
  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:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     12.150
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3807  Z= 0.191
  Angle     :  0.465   3.534   5157  Z= 0.266
  Chirality :  0.042   0.127    534
  Planarity :  0.003   0.030    666
  Dihedral  :  8.475  53.030   1377
  Min Nonbonded Distance : 2.026

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 

*********************** 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  : 0.419 
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: 1.2512
  time to fit residues: 161.9088
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  : 0.507 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 31 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 10 optimal weight:    9.9990
   chunk 21 optimal weight:    1.9990
   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:    3.9990

-------------------------------------------------------------------------------
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**
C  31 HIS
** D  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  21 ASN
E  89 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.144774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.122913 restraints weight = 4731.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3845 rms_B_bonded: 2.17
r_work: 0.3718 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3608 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.2959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3807  Z= 0.283
  Angle     :  0.579   5.015   5157  Z= 0.301
  Chirality :  0.046   0.138    534
  Planarity :  0.003   0.021    666
  Dihedral  :  4.379  12.775    486
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  :  9.05 %
    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: -4.14 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.15 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP F  60 
 HIS   0.004   0.001   HIS C  13 
 PHE   0.012   0.002   PHE F  30 
 TYR   0.012   0.002   TYR A  63 
 ARG   0.001   0.000   ARG E  45 

*********************** 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
  138 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 127
  time to evaluate  : 0.446 
Fit side-chains
REVERT: A   12 ARG cc_start: 0.7968 (ttt180) cc_final: 0.5747 (tpm-80)
REVERT: A   36 GLU cc_start: 0.8337 (tt0) cc_final: 0.7653 (mt-10)
REVERT: A   38 ASP cc_start: 0.7948 (p0) cc_final: 0.7637 (p0)
REVERT: A   50 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8234 (mt-10)
REVERT: A   57 SER cc_start: 0.8647 (m) cc_final: 0.8407 (t)
REVERT: A   58 LYS cc_start: 0.8134 (mmtt) cc_final: 0.6190 (pmtt)
REVERT: B   58 LYS cc_start: 0.8570 (mmtm) cc_final: 0.6922 (mptt)
REVERT: C    6 LYS cc_start: 0.5797 (mptt) cc_final: 0.4909 (tttt)
REVERT: C   36 GLU cc_start: 0.7914 (tt0) cc_final: 0.7123 (mt-10)
REVERT: C   48 LYS cc_start: 0.7699 (mttt) cc_final: 0.7434 (mmtp)
REVERT: C   50 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7893 (mt-10)
REVERT: C   51 HIS cc_start: 0.7651 (m90) cc_final: 0.7085 (m-70)
REVERT: C   71 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8306 (p)
REVERT: D   36 GLU cc_start: 0.8212 (tt0) cc_final: 0.7798 (mt-10)
REVERT: D   47 GLU cc_start: 0.8194 (tp30) cc_final: 0.7809 (tp30)
REVERT: D   48 LYS cc_start: 0.8609 (mtmt) cc_final: 0.8364 (mtpp)
REVERT: D   69 GLU cc_start: 0.7781 (mp0) cc_final: 0.7519 (tt0)
REVERT: D   74 GLU cc_start: 0.8077 (pm20) cc_final: 0.7814 (pm20)
REVERT: E    6 LYS cc_start: 0.6263 (mttt) cc_final: 0.5945 (mptt)
REVERT: E   36 GLU cc_start: 0.7964 (tt0) cc_final: 0.7153 (mt-10)
REVERT: E   50 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7827 (mt-10)
REVERT: F   81 ARG cc_start: 0.5886 (OUTLIER) cc_final: 0.5231 (mmm160)
  outliers start: 11
  outliers final: 5
  residues processed: 131
  average time/residue: 1.3996
  time to fit residues: 187.9959
Evaluate side-chains
  120 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 113
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain F residue   61 SER
Chi-restraints excluded: chain F residue   81 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    8.9990
   chunk 38 optimal weight:   20.0000
   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:    7.9990
   chunk 13 optimal weight:    9.9990
   chunk 33 optimal weight:    7.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    9.9990
   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**
A  21 ASN
** D  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  21 ASN
F  24 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.140245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.119144 restraints weight = 4783.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3776 rms_B_bonded: 2.04
r_work: 0.3660 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3553 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.4094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.037   3807  Z= 0.440
  Angle     :  0.666   6.212   5157  Z= 0.347
  Chirality :  0.048   0.147    534
  Planarity :  0.004   0.027    666
  Dihedral  :  4.927  15.160    486
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 13.10 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.11 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.13 (0.23), 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   0.014   0.002   PHE F  30 
 TYR   0.016   0.002   TYR B  67 
 ARG   0.003   0.001   ARG A  45 

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

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 ARG cc_start: 0.8060 (ttt180) cc_final: 0.5909 (tpm170)
REVERT: A   36 GLU cc_start: 0.8346 (tt0) cc_final: 0.7584 (mt-10)
REVERT: A   50 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8426 (mt-10)
REVERT: A   58 LYS cc_start: 0.8251 (mmtt) cc_final: 0.6255 (pmtt)
REVERT: B   36 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7472 (mp0)
REVERT: B   58 LYS cc_start: 0.8733 (mmtm) cc_final: 0.7102 (mptt)
REVERT: B   81 ARG cc_start: 0.7681 (mtt180) cc_final: 0.7062 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5865 (mptt) cc_final: 0.4875 (mmmm)
REVERT: C   36 GLU cc_start: 0.7893 (tt0) cc_final: 0.7138 (mt-10)
REVERT: C   50 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8099 (mt-10)
REVERT: C   77 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8145 (mt-10)
REVERT: D   36 GLU cc_start: 0.8196 (tt0) cc_final: 0.7890 (mp0)
REVERT: D   48 LYS cc_start: 0.8632 (mtmt) cc_final: 0.8343 (mtpp)
REVERT: D   69 GLU cc_start: 0.7677 (mp0) cc_final: 0.7440 (tt0)
REVERT: D   77 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8218 (tt0)
REVERT: E    6 LYS cc_start: 0.6622 (mttt) cc_final: 0.6378 (mptp)
REVERT: E   36 GLU cc_start: 0.8042 (tt0) cc_final: 0.7218 (mt-10)
REVERT: E   48 LYS cc_start: 0.5094 (mmpt) cc_final: 0.4594 (mmtt)
REVERT: F   69 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7651 (tt0)
  outliers start: 16
  outliers final: 9
  residues processed: 121
  average time/residue: 1.4584
  time to fit residues: 180.6796
Evaluate side-chains
  124 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain B residue   36 GLU
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 F residue   61 SER
Chi-restraints excluded: chain F residue   69 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 28 optimal weight:    8.9990
   chunk 19 optimal weight:   10.0000
   chunk 16 optimal weight:    5.9990
   chunk 36 optimal weight:   10.0000
   chunk 9 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   chunk 7 optimal weight:    8.9990
   chunk 39 optimal weight:    9.9990
   chunk 4 optimal weight:    0.4980
   chunk 37 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    5.0988

-------------------------------------------------------------------------------
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  51 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.137191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.115594 restraints weight = 4785.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3808 rms_B_bonded: 2.17
r_work: 0.3689 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3582 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.4308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   3807  Z= 0.336
  Angle     :  0.602   4.477   5157  Z= 0.310
  Chirality :  0.046   0.137    534
  Planarity :  0.003   0.022    666
  Dihedral  :  4.807  15.629    486
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 14.76 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.08 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.10 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E  60 
 HIS   0.005   0.001   HIS C  31 
 PHE   0.012   0.002   PHE F  30 
 TYR   0.015   0.002   TYR B  67 
 ARG   0.003   0.000   ARG A  81 

*********************** 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: 20
    poor density    : 115
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.5925 (OUTLIER) cc_final: 0.5036 (mmmm)
REVERT: A   12 ARG cc_start: 0.8050 (ttt180) cc_final: 0.5919 (tpm170)
REVERT: A   36 GLU cc_start: 0.8270 (tt0) cc_final: 0.7468 (mt-10)
REVERT: A   44 GLU cc_start: 0.7761 (mp0) cc_final: 0.7027 (mm-30)
REVERT: A   50 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8371 (mt-10)
REVERT: A   58 LYS cc_start: 0.8213 (mmtt) cc_final: 0.6274 (pmtt)
REVERT: A   71 THR cc_start: 0.8847 (OUTLIER) cc_final: 0.8592 (p)
REVERT: B   45 ARG cc_start: 0.8282 (mtp85) cc_final: 0.8030 (mtp85)
REVERT: B   58 LYS cc_start: 0.8677 (mmtm) cc_final: 0.7031 (mptt)
REVERT: B   81 ARG cc_start: 0.7656 (mtt180) cc_final: 0.6991 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5728 (mptt) cc_final: 0.4822 (mmmm)
REVERT: C   36 GLU cc_start: 0.7889 (tt0) cc_final: 0.7115 (mt-10)
REVERT: C   44 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6737 (mm-30)
REVERT: C   48 LYS cc_start: 0.7826 (tptm) cc_final: 0.7463 (tppp)
REVERT: C   50 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8082 (mt-10)
REVERT: C   77 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8165 (mt-10)
REVERT: D   36 GLU cc_start: 0.8179 (tt0) cc_final: 0.7841 (mp0)
REVERT: D   38 ASP cc_start: 0.8836 (p0) cc_final: 0.8617 (p0)
REVERT: D   48 LYS cc_start: 0.8559 (mtmt) cc_final: 0.8288 (mtpp)
REVERT: D   69 GLU cc_start: 0.7707 (mp0) cc_final: 0.7469 (tt0)
REVERT: D   77 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8195 (tt0)
REVERT: E    6 LYS cc_start: 0.6644 (mttt) cc_final: 0.6241 (mptp)
REVERT: E   12 ARG cc_start: 0.8351 (ptm-80) cc_final: 0.8124 (ptm-80)
REVERT: E   36 GLU cc_start: 0.7955 (tt0) cc_final: 0.7133 (mt-10)
REVERT: E   48 LYS cc_start: 0.4983 (mmpt) cc_final: 0.4328 (tptt)
  outliers start: 20
  outliers final: 10
  residues processed: 123
  average time/residue: 1.4066
  time to fit residues: 177.2219
Evaluate side-chains
  126 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
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 F residue   50 GLU
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   61 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:   20.0000
   chunk 4 optimal weight:    6.9990
   chunk 25 optimal weight:   20.0000
   chunk 35 optimal weight:   10.0000
   chunk 41 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 32 optimal weight:   20.0000
   chunk 2 optimal weight:    0.0770
   chunk 21 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    2.6146

-------------------------------------------------------------------------------
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**
** E  89 GLN ** 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 = 0.4119 r_free = 0.4119 target = 0.145057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.124204 restraints weight = 4725.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3854 rms_B_bonded: 2.10
r_work: 0.3741 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3637 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
moved from start:          0.4326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3807  Z= 0.198
  Angle     :  0.546   8.760   5157  Z= 0.276
  Chirality :  0.044   0.136    534
  Planarity :  0.003   0.019    666
  Dihedral  :  4.530  15.586    486
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 15.24 %
    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: -3.96 (0.31), 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   0.000   TRP E  60 
 HIS   0.003   0.001   HIS C  13 
 PHE   0.009   0.001   PHE F  30 
 TYR   0.013   0.001   TYR B  67 
 ARG   0.002   0.000   ARG A  81 

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

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.6129 (OUTLIER) cc_final: 0.5127 (mmmm)
REVERT: A   12 ARG cc_start: 0.8037 (ttt180) cc_final: 0.5915 (tpm170)
REVERT: A   16 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8041 (pt0)
REVERT: A   36 GLU cc_start: 0.8201 (tt0) cc_final: 0.7429 (mt-10)
REVERT: A   44 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7063 (mm-30)
REVERT: A   50 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8395 (mt-10)
REVERT: A   58 LYS cc_start: 0.8137 (mmtt) cc_final: 0.6206 (pmtt)
REVERT: A   71 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8541 (p)
REVERT: A   74 GLU cc_start: 0.8188 (pt0) cc_final: 0.7809 (pt0)
REVERT: B   45 ARG cc_start: 0.8287 (mtp85) cc_final: 0.8008 (mtp85)
REVERT: B   58 LYS cc_start: 0.8669 (mmtm) cc_final: 0.6982 (mptt)
REVERT: B   81 ARG cc_start: 0.7549 (mtt180) cc_final: 0.6924 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5787 (mptt) cc_final: 0.4876 (mmmm)
REVERT: C   36 GLU cc_start: 0.7868 (tt0) cc_final: 0.7126 (mt-10)
REVERT: C   44 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6890 (mm-30)
REVERT: C   48 LYS cc_start: 0.7837 (tptm) cc_final: 0.7473 (tppp)
REVERT: C   50 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8065 (mt-10)
REVERT: C   71 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8365 (p)
REVERT: C   77 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8163 (mt-10)
REVERT: D   36 GLU cc_start: 0.8170 (tt0) cc_final: 0.7839 (mp0)
REVERT: D   38 ASP cc_start: 0.8802 (p0) cc_final: 0.8586 (p0)
REVERT: D   44 GLU cc_start: 0.7775 (tt0) cc_final: 0.7239 (mm-30)
REVERT: D   48 LYS cc_start: 0.8593 (mtmt) cc_final: 0.8319 (mtpp)
REVERT: D   69 GLU cc_start: 0.7664 (mp0) cc_final: 0.7410 (tt0)
REVERT: E    6 LYS cc_start: 0.6658 (mttt) cc_final: 0.6261 (mptp)
REVERT: E   36 GLU cc_start: 0.7956 (tt0) cc_final: 0.7136 (mt-10)
REVERT: E   48 LYS cc_start: 0.5183 (OUTLIER) cc_final: 0.4640 (tptt)
REVERT: F   69 GLU cc_start: 0.7841 (mp0) cc_final: 0.7635 (tt0)
  outliers start: 19
  outliers final: 9
  residues processed: 118
  average time/residue: 1.3532
  time to fit residues: 163.7350
Evaluate side-chains
  121 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LYS
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue   44 GLU
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue   77 GLU
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain E residue   48 LYS
Chi-restraints excluded: chain F residue   50 GLU
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   61 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:   20.0000
   chunk 34 optimal weight:    5.9990
   chunk 13 optimal weight:    9.9990
   chunk 11 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 40 optimal weight:    9.9990
   chunk 2 optimal weight:    7.9990
   chunk 21 optimal weight:   10.0000
   chunk 5 optimal weight:    7.9990
   chunk 20 optimal weight:   10.0000
   chunk 25 optimal weight:    9.9990
   overall best weight:    4.9188

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.137127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.115251 restraints weight = 4887.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3803 rms_B_bonded: 2.21
r_work: 0.3686 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3577 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8639
moved from start:          0.4571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   3807  Z= 0.328
  Angle     :  0.617   8.371   5157  Z= 0.310
  Chirality :  0.046   0.142    534
  Planarity :  0.003   0.023    666
  Dihedral  :  4.783  15.014    486
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 16.90 %
    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: -3.98 (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 A  60 
 HIS   0.004   0.001   HIS C  13 
 PHE   0.013   0.002   PHE F  30 
 TYR   0.017   0.002   TYR B  67 
 ARG   0.002   0.000   ARG A  81 

*********************** 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
  129 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.6073 (mptp) cc_final: 0.5127 (mmmm)
REVERT: A   12 ARG cc_start: 0.8032 (ttt180) cc_final: 0.5945 (tpm170)
REVERT: A   36 GLU cc_start: 0.8257 (tt0) cc_final: 0.7451 (mt-10)
REVERT: A   44 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7319 (mp0)
REVERT: A   50 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8422 (mt-10)
REVERT: A   58 LYS cc_start: 0.8203 (mmtt) cc_final: 0.6287 (pmtt)
REVERT: A   71 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8600 (p)
REVERT: A   74 GLU cc_start: 0.8236 (pt0) cc_final: 0.7801 (pt0)
REVERT: B   38 ASP cc_start: 0.8729 (p0) cc_final: 0.8175 (p0)
REVERT: B   58 LYS cc_start: 0.8752 (mmtm) cc_final: 0.7072 (mptt)
REVERT: B   81 ARG cc_start: 0.7681 (mtt180) cc_final: 0.6991 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5785 (mptt) cc_final: 0.4833 (mmmm)
REVERT: C   36 GLU cc_start: 0.7938 (tt0) cc_final: 0.7162 (mt-10)
REVERT: C   48 LYS cc_start: 0.7800 (tptm) cc_final: 0.7431 (tppp)
REVERT: C   50 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8146 (mt-10)
REVERT: C   77 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8166 (mt-10)
REVERT: D   36 GLU cc_start: 0.8160 (tt0) cc_final: 0.7841 (mp0)
REVERT: D   38 ASP cc_start: 0.8852 (p0) cc_final: 0.8619 (p0)
REVERT: D   44 GLU cc_start: 0.7806 (tt0) cc_final: 0.7189 (mm-30)
REVERT: D   48 LYS cc_start: 0.8608 (mtmt) cc_final: 0.8335 (mtpp)
REVERT: D   77 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8232 (tt0)
REVERT: E    6 LYS cc_start: 0.6575 (mttt) cc_final: 0.6131 (mptp)
REVERT: E   36 GLU cc_start: 0.8028 (tt0) cc_final: 0.7195 (mt-10)
REVERT: E   48 LYS cc_start: 0.5244 (OUTLIER) cc_final: 0.4634 (tptt)
  outliers start: 16
  outliers final: 10
  residues processed: 119
  average time/residue: 1.3938
  time to fit residues: 169.9393
Evaluate side-chains
  126 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
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   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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    0.4980
   chunk 5 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 33 optimal weight:   10.0000
   chunk 8 optimal weight:    7.9990
   chunk 17 optimal weight:    6.9990
   chunk 29 optimal weight:    7.9990
   chunk 1 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    3.0988

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.140013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.118378 restraints weight = 4750.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3839 rms_B_bonded: 2.20
r_work: 0.3722 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3612 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.4561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3807  Z= 0.229
  Angle     :  0.575   8.135   5157  Z= 0.286
  Chirality :  0.044   0.139    534
  Planarity :  0.003   0.023    666
  Dihedral  :  4.577  14.735    486
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 18.33 %
    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: -3.89 (0.31), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.96 (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  31 
 PHE   0.010   0.001   PHE E  70 
 TYR   0.015   0.001   TYR B  67 
 ARG   0.002   0.000   ARG D  45 

*********************** 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
  130 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.5989 (OUTLIER) cc_final: 0.5040 (mmmm)
REVERT: A   12 ARG cc_start: 0.8045 (ttt180) cc_final: 0.5926 (tpm170)
REVERT: A   16 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8071 (pt0)
REVERT: A   36 GLU cc_start: 0.8193 (tt0) cc_final: 0.7418 (mt-10)
REVERT: A   44 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7201 (mm-30)
REVERT: A   50 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8537 (mt-10)
REVERT: A   58 LYS cc_start: 0.8128 (mmtt) cc_final: 0.6218 (pmtt)
REVERT: A   71 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8560 (p)
REVERT: A   74 GLU cc_start: 0.8188 (pt0) cc_final: 0.7839 (pt0)
REVERT: B   23 LEU cc_start: 0.8379 (tt) cc_final: 0.7897 (tt)
REVERT: B   58 LYS cc_start: 0.8684 (mmtm) cc_final: 0.6982 (mptt)
REVERT: B   81 ARG cc_start: 0.7639 (mtt180) cc_final: 0.6965 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5821 (mptt) cc_final: 0.4747 (mmmm)
REVERT: C   36 GLU cc_start: 0.7862 (tt0) cc_final: 0.7144 (mt-10)
REVERT: C   48 LYS cc_start: 0.7815 (tptm) cc_final: 0.7460 (tppp)
REVERT: C   50 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8152 (mt-10)
REVERT: C   71 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8354 (p)
REVERT: C   77 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8148 (mt-10)
REVERT: D   36 GLU cc_start: 0.8134 (tt0) cc_final: 0.7809 (mp0)
REVERT: D   38 ASP cc_start: 0.8778 (p0) cc_final: 0.8566 (p0)
REVERT: D   44 GLU cc_start: 0.7836 (tt0) cc_final: 0.7215 (mm-30)
REVERT: D   48 LYS cc_start: 0.8590 (mtmt) cc_final: 0.8320 (mtpp)
REVERT: E    6 LYS cc_start: 0.6540 (mttt) cc_final: 0.6091 (mptp)
REVERT: E   36 GLU cc_start: 0.7998 (tt0) cc_final: 0.7181 (mt-10)
REVERT: E   48 LYS cc_start: 0.5049 (OUTLIER) cc_final: 0.4727 (tptt)
REVERT: F   45 ARG cc_start: 0.8148 (mtp85) cc_final: 0.7487 (mtt-85)
  outliers start: 17
  outliers final: 9
  residues processed: 119
  average time/residue: 1.4206
  time to fit residues: 173.1388
Evaluate side-chains
  125 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    8.9990
   chunk 9 optimal weight:    8.9990
   chunk 6 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 7 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9990
   chunk 17 optimal weight:   10.0000
   chunk 34 optimal weight:   10.0000
   chunk 2 optimal weight:   20.0000
   chunk 35 optimal weight:    5.9990
   chunk 19 optimal weight:    9.9990
   overall best weight:    6.5990

-------------------------------------------------------------------------------
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**
** E  89 GLN ** 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 = 0.4046 r_free = 0.4046 target = 0.134681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.112702 restraints weight = 4884.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3771 rms_B_bonded: 2.21
r_work: 0.3652 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3540 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8661
moved from start:          0.4823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.041   3807  Z= 0.427
  Angle     :  0.663   7.887   5157  Z= 0.335
  Chirality :  0.047   0.149    534
  Planarity :  0.003   0.027    666
  Dihedral  :  4.943  14.512    486
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 18.33 %
    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: -3.97 (0.31), 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   0.004   0.001   TRP C  60 
 HIS   0.005   0.002   HIS A  31 
 PHE   0.016   0.002   PHE F  30 
 TYR   0.020   0.002   TYR B  67 
 ARG   0.003   0.001   ARG D  45 

*********************** 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
  132 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.5956 (mptp) cc_final: 0.5074 (mmmm)
REVERT: A   12 ARG cc_start: 0.8011 (ttt180) cc_final: 0.5882 (tpm170)
REVERT: A   16 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8001 (pt0)
REVERT: A   36 GLU cc_start: 0.8230 (tt0) cc_final: 0.7458 (mt-10)
REVERT: A   44 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7429 (mp0)
REVERT: A   50 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8553 (mt-10)
REVERT: A   58 LYS cc_start: 0.8191 (mmtt) cc_final: 0.6308 (pptt)
REVERT: A   74 GLU cc_start: 0.8258 (pt0) cc_final: 0.7865 (pt0)
REVERT: B   58 LYS cc_start: 0.8779 (mmtm) cc_final: 0.7031 (mptt)
REVERT: B   81 ARG cc_start: 0.7740 (mtt180) cc_final: 0.7008 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5768 (mptt) cc_final: 0.4836 (mmmm)
REVERT: C   16 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8045 (mt-10)
REVERT: C   36 GLU cc_start: 0.7956 (tt0) cc_final: 0.7232 (mt-10)
REVERT: C   48 LYS cc_start: 0.7778 (tptm) cc_final: 0.7551 (tppt)
REVERT: C   50 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8198 (mt-10)
REVERT: C   58 LYS cc_start: 0.8382 (mmmm) cc_final: 0.8178 (mttm)
REVERT: C   77 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8209 (mt-10)
REVERT: D   36 GLU cc_start: 0.8134 (tt0) cc_final: 0.7831 (mp0)
REVERT: D   38 ASP cc_start: 0.8855 (p0) cc_final: 0.8607 (p0)
REVERT: D   77 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8184 (tt0)
REVERT: E    6 LYS cc_start: 0.6598 (mttt) cc_final: 0.6152 (mptp)
REVERT: E   36 GLU cc_start: 0.8071 (tt0) cc_final: 0.7301 (mt-10)
REVERT: E   48 LYS cc_start: 0.4802 (OUTLIER) cc_final: 0.4379 (tptt)
REVERT: F   45 ARG cc_start: 0.8159 (mtp85) cc_final: 0.7594 (mtt-85)
  outliers start: 16
  outliers final: 11
  residues processed: 122
  average time/residue: 1.4159
  time to fit residues: 176.9510
Evaluate side-chains
  128 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue   44 GLU
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue   77 GLU
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain E residue   48 LYS
Chi-restraints excluded: chain F residue   50 GLU
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   61 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 41 optimal weight:    8.9990
   chunk 21 optimal weight:    8.9990
   chunk 4 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9980
   chunk 9 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9980
   chunk 2 optimal weight:    8.9990
   chunk 35 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    3.1986

-------------------------------------------------------------------------------
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 = 0.4086 r_free = 0.4086 target = 0.138795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.116936 restraints weight = 4738.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3829 rms_B_bonded: 2.22
r_work: 0.3707 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3596 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8613
moved from start:          0.4792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3807  Z= 0.244
  Angle     :  0.609   7.887   5157  Z= 0.302
  Chirality :  0.045   0.143    534
  Planarity :  0.003   0.026    666
  Dihedral  :  4.679  14.609    486
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 19.29 %
    Favored  : 77.14 %
  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: -3.90 (0.31), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.97 (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  31 
 PHE   0.010   0.001   PHE E  70 
 TYR   0.019   0.001   TYR E  10 
 ARG   0.002   0.000   ARG D  45 

*********************** 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: 15
    poor density    : 115
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.5928 (mptp) cc_final: 0.5022 (mmmm)
REVERT: A   12 ARG cc_start: 0.8017 (ttt180) cc_final: 0.5858 (tpm170)
REVERT: A   16 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8018 (pt0)
REVERT: A   36 GLU cc_start: 0.8195 (tt0) cc_final: 0.7448 (mt-10)
REVERT: A   44 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7081 (mm-30)
REVERT: A   58 LYS cc_start: 0.8171 (mmtt) cc_final: 0.6252 (pmtt)
REVERT: A   74 GLU cc_start: 0.8212 (pt0) cc_final: 0.7882 (pt0)
REVERT: B   58 LYS cc_start: 0.8701 (mmtm) cc_final: 0.6994 (mptt)
REVERT: B   81 ARG cc_start: 0.7700 (mtt180) cc_final: 0.6955 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5712 (mptt) cc_final: 0.4747 (mmmm)
REVERT: C   16 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8082 (mt-10)
REVERT: C   36 GLU cc_start: 0.7820 (tt0) cc_final: 0.7087 (mt-10)
REVERT: C   48 LYS cc_start: 0.7800 (tptm) cc_final: 0.7485 (tppp)
REVERT: C   50 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8189 (mt-10)
REVERT: C   71 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8348 (p)
REVERT: C   77 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8193 (mt-10)
REVERT: D   36 GLU cc_start: 0.8119 (tt0) cc_final: 0.7803 (mp0)
REVERT: D   38 ASP cc_start: 0.8801 (p0) cc_final: 0.8581 (p0)
REVERT: D   48 LYS cc_start: 0.8612 (mtmt) cc_final: 0.8352 (mtpp)
REVERT: E    6 LYS cc_start: 0.6487 (mttt) cc_final: 0.6092 (mptp)
REVERT: E   36 GLU cc_start: 0.8087 (tt0) cc_final: 0.7251 (mt-10)
REVERT: E   48 LYS cc_start: 0.4786 (OUTLIER) cc_final: 0.4363 (tptt)
REVERT: F   45 ARG cc_start: 0.8059 (mtp85) cc_final: 0.7475 (mtt-85)
  outliers start: 15
  outliers final: 11
  residues processed: 121
  average time/residue: 1.4559
  time to fit residues: 180.2757
Evaluate side-chains
  127 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue   44 GLU
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain 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   27 VAL
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:   10.0000
   chunk 1 optimal weight:    9.9990
   chunk 16 optimal weight:   10.0000
   chunk 23 optimal weight:    9.9990
   chunk 35 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   chunk 32 optimal weight:    7.9990
   chunk 14 optimal weight:    7.9990
   chunk 39 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 34 optimal weight:    6.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4046 r_free = 0.4046 target = 0.135204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.113372 restraints weight = 4863.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3785 rms_B_bonded: 2.19
r_work: 0.3663 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3552 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.4959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   3807  Z= 0.397
  Angle     :  0.691   7.918   5157  Z= 0.342
  Chirality :  0.048   0.232    534
  Planarity :  0.003   0.028    666
  Dihedral  :  4.892  14.211    486
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 19.29 %
    Favored  : 76.19 %
  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: -3.97 (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   0.004   0.001   TRP C  60 
 HIS   0.004   0.002   HIS C  31 
 PHE   0.015   0.002   PHE F  30 
 TYR   0.020   0.002   TYR B  67 
 ARG   0.003   0.001   ARG D  45 

********************** 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
  134 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.5935 (OUTLIER) cc_final: 0.5028 (mmmm)
REVERT: A   12 ARG cc_start: 0.7949 (ttt180) cc_final: 0.5770 (tpm170)
REVERT: A   16 GLU cc_start: 0.8677 (mt-10) cc_final: 0.7991 (pt0)
REVERT: A   36 GLU cc_start: 0.8232 (tt0) cc_final: 0.7453 (mt-10)
REVERT: A   44 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7492 (mp0)
REVERT: A   58 LYS cc_start: 0.8189 (mmtt) cc_final: 0.6248 (pmtt)
REVERT: A   74 GLU cc_start: 0.8243 (pt0) cc_final: 0.7906 (pt0)
REVERT: B   58 LYS cc_start: 0.8768 (mmtm) cc_final: 0.7037 (mptt)
REVERT: B   81 ARG cc_start: 0.7811 (mtt180) cc_final: 0.7059 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5700 (mptt) cc_final: 0.4771 (mmmm)
REVERT: C   36 GLU cc_start: 0.7913 (tt0) cc_final: 0.7127 (mt-10)
REVERT: C   48 LYS cc_start: 0.7794 (tptm) cc_final: 0.7580 (tppt)
REVERT: C   50 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8268 (mt-10)
REVERT: C   77 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8206 (mt-10)
REVERT: D   36 GLU cc_start: 0.8128 (tt0) cc_final: 0.7809 (mp0)
REVERT: D   38 ASP cc_start: 0.8807 (p0) cc_final: 0.8577 (p0)
REVERT: D   77 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8172 (tt0)
REVERT: E    6 LYS cc_start: 0.6533 (mttt) cc_final: 0.6129 (mptp)
REVERT: E   36 GLU cc_start: 0.8175 (tt0) cc_final: 0.7330 (mt-10)
REVERT: E   48 LYS cc_start: 0.4781 (OUTLIER) cc_final: 0.4367 (tptt)
REVERT: F   45 ARG cc_start: 0.8112 (mtp85) cc_final: 0.7549 (mtt-85)
  outliers start: 19
  outliers final: 13
  residues processed: 122
  average time/residue: 1.4277
  time to fit residues: 178.4296
Evaluate side-chains
  130 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
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 B residue   23 LEU
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   27 VAL
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:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 13 optimal weight:   10.0000
   chunk 14 optimal weight:   10.0000
   chunk 9 optimal weight:    8.9990
   chunk 21 optimal weight:    9.9990
   chunk 32 optimal weight:    7.9990
   chunk 8 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   chunk 0 optimal weight:    0.9990
   chunk 16 optimal weight:    0.1980
   overall best weight:    3.4388

-------------------------------------------------------------------------------
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 = 0.4084 r_free = 0.4084 target = 0.138338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.116435 restraints weight = 4804.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3824 rms_B_bonded: 2.23
r_work: 0.3704 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3589 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8620
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   0.032   3807  Z= 0.257
  Angle     :  0.642   7.705   5157  Z= 0.315
  Chirality :  0.046   0.152    534
  Planarity :  0.003   0.027    666
  Dihedral  :  4.690  14.340    486
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 19.52 %
    Favored  : 76.19 %
  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: -3.91 (0.31), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.97 (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  31 
 PHE   0.009   0.002   PHE F  30 
 TYR   0.017   0.001   TYR B  67 
 ARG   0.002   0.000   ARG D  45 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3777.36 seconds
wall clock time: 66 minutes 59.00 seconds (4019.00 seconds total)