Starting phenix.real_space_refine
on Fri Dec 27 08:46:27 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8a7t_15225/12_2024/8a7t_15225.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8a7t_15225/12_2024/8a7t_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_15225/12_2024/8a7t_15225.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8a7t_15225/12_2024/8a7t_15225.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8a7t_15225/12_2024/8a7t_15225.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8a7t_15225/12_2024/8a7t_15225.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

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

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 2.65, per 1000 atoms: 0.72
  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: 0.97
  Conformation dependent library (CDL) restraints added in 433.1 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 18 sheets defined
      0.0% alpha, 45.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.53
  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: 0.79

  Time building geometry restraints manager: 1.12 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: 0.00
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:             0.780
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.870
  Find NCS groups from input model:        0.120
  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:11.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.930
-------------------------------------------------------------------------------
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  : 0.422 
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: 1.2735
  time to fit residues: 164.8259
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  : 0.436 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
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  : 0.459 
Fit side-chains
REVERT: A   12 ARG cc_start: 0.7910 (ttt180) cc_final: 0.5662 (tpm-80)
REVERT: A   36 GLU cc_start: 0.7858 (tt0) cc_final: 0.7213 (mt-10)
REVERT: A   38 ASP cc_start: 0.7796 (p0) cc_final: 0.7442 (p0)
REVERT: A   50 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7983 (mt-10)
REVERT: A   58 LYS cc_start: 0.8015 (mmtt) cc_final: 0.6052 (pmtt)
REVERT: B   58 LYS cc_start: 0.8383 (mmtm) cc_final: 0.6653 (mptt)
REVERT: C    6 LYS cc_start: 0.5882 (mptt) cc_final: 0.5021 (tttt)
REVERT: C   16 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7883 (mt-10)
REVERT: C   36 GLU cc_start: 0.7248 (tt0) cc_final: 0.6485 (mt-10)
REVERT: C   48 LYS cc_start: 0.7680 (mttt) cc_final: 0.7374 (mmtp)
REVERT: C   50 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7622 (mt-10)
REVERT: C   51 HIS cc_start: 0.7460 (m90) cc_final: 0.6847 (m-70)
REVERT: D   36 GLU cc_start: 0.7663 (tt0) cc_final: 0.7335 (mt-10)
REVERT: D   47 GLU cc_start: 0.7817 (tp30) cc_final: 0.7416 (tp30)
REVERT: D   48 LYS cc_start: 0.8484 (mtmt) cc_final: 0.8238 (mtpp)
REVERT: D   74 GLU cc_start: 0.7701 (pm20) cc_final: 0.7424 (pm20)
REVERT: E    6 LYS cc_start: 0.6234 (mttt) cc_final: 0.5949 (mptt)
REVERT: E   36 GLU cc_start: 0.7382 (tt0) cc_final: 0.6527 (mt-10)
REVERT: E   48 LYS cc_start: 0.7595 (mttt) cc_final: 0.7372 (mmpt)
REVERT: E   50 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7543 (mt-10)
REVERT: F   75 LYS cc_start: 0.8060 (mtmt) cc_final: 0.7831 (mtpp)
REVERT: F   81 ARG cc_start: 0.5285 (OUTLIER) cc_final: 0.4856 (mmm160)
  outliers start: 11
  outliers final: 5
  residues processed: 131
  average time/residue: 1.4527
  time to fit residues: 194.9735
Evaluate side-chains
  120 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 114
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 SER
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 31 optimal weight:    3.9990
   chunk 25 optimal weight:   20.0000
   chunk 10 optimal weight:    0.5980
   chunk 38 optimal weight:    5.9990
   chunk 41 optimal weight:    6.9990
   chunk 34 optimal weight:    7.9990
   chunk 37 optimal weight:    5.9990
   chunk 13 optimal weight:    9.9990
   chunk 30 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 19 optimal weight:   10.0000
   overall best weight:    3.7188

-------------------------------------------------------------------------------
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  31 HIS
** D  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  21 ASN
** E  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  24 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.3680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3807  Z= 0.261
  Angle     :  0.559   4.388   5157  Z= 0.291
  Chirality :  0.045   0.136    534
  Planarity :  0.003   0.021    666
  Dihedral  :  4.437  14.694    486
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 12.14 %
    Favored  : 84.52 %
  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 (0.31), 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   0.003   0.001   TRP B  60 
 HIS   0.005   0.001   HIS C  13 
 PHE   0.010   0.002   PHE D  30 
 TYR   0.014   0.002   TYR B  67 
 ARG   0.002   0.000   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
  129 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 ARG cc_start: 0.7993 (ttt180) cc_final: 0.5785 (tpm-80)
REVERT: A   36 GLU cc_start: 0.7831 (tt0) cc_final: 0.7094 (mt-10)
REVERT: A   44 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7064 (mm-30)
REVERT: A   50 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8048 (mt-10)
REVERT: A   58 LYS cc_start: 0.7964 (mmtt) cc_final: 0.6061 (pmtt)
REVERT: A   71 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8490 (p)
REVERT: B   58 LYS cc_start: 0.8434 (mmtm) cc_final: 0.6698 (mptt)
REVERT: B   81 ARG cc_start: 0.7295 (mtt180) cc_final: 0.6701 (ptt-90)
REVERT: C    6 LYS cc_start: 0.5816 (mptt) cc_final: 0.4958 (tttt)
REVERT: C   16 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7823 (mt-10)
REVERT: C   36 GLU cc_start: 0.7247 (tt0) cc_final: 0.6533 (mt-10)
REVERT: C   44 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6435 (mm-30)
REVERT: C   48 LYS cc_start: 0.7631 (mttt) cc_final: 0.7324 (mmtp)
REVERT: C   50 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7642 (mt-10)
REVERT: C   77 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7583 (mt-10)
REVERT: D   36 GLU cc_start: 0.7657 (tt0) cc_final: 0.7452 (mp0)
REVERT: D   38 ASP cc_start: 0.8597 (p0) cc_final: 0.8395 (p0)
REVERT: D   47 GLU cc_start: 0.7699 (tp30) cc_final: 0.7400 (tp30)
REVERT: D   48 LYS cc_start: 0.8471 (mtmt) cc_final: 0.8244 (mtpp)
REVERT: E    6 LYS cc_start: 0.6522 (mttt) cc_final: 0.6309 (mptp)
REVERT: E   36 GLU cc_start: 0.7378 (tt0) cc_final: 0.6567 (mt-10)
REVERT: E   48 LYS cc_start: 0.7560 (mttt) cc_final: 0.7345 (mmpt)
REVERT: E   50 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7706 (mt-10)
REVERT: F   36 GLU cc_start: 0.7579 (tt0) cc_final: 0.7330 (tt0)
REVERT: F   75 LYS cc_start: 0.8163 (mtmt) cc_final: 0.7913 (mtpp)
  outliers start: 14
  outliers final: 9
  residues processed: 118
  average time/residue: 1.4192
  time to fit residues: 171.6144
Evaluate side-chains
  122 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
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 B residue   52 SER
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue   77 GLU
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain F residue   61 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 4 optimal weight:    9.9990
   chunk 18 optimal weight:    5.9990
   chunk 25 optimal weight:   20.0000
   chunk 38 optimal weight:   10.0000
   chunk 40 optimal weight:    8.9990
   chunk 20 optimal weight:    0.9980
   chunk 36 optimal weight:    9.9990
   chunk 10 optimal weight:   20.0000
   chunk 33 optimal weight:    9.9990
   chunk 23 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    6.9988

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.4242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.039   3807  Z= 0.453
  Angle     :  0.655   6.320   5157  Z= 0.340
  Chirality :  0.048   0.149    534
  Planarity :  0.004   0.026    666
  Dihedral  :  4.978  15.500    486
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 13.57 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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   0.004   0.001   TRP C  60 
 HIS   0.005   0.002   HIS A  31 
 PHE   0.015   0.002   PHE F  30 
 TYR   0.017   0.002   TYR B  67 
 ARG   0.003   0.001   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
  138 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.5926 (mptp) cc_final: 0.5111 (mmmm)
REVERT: A   12 ARG cc_start: 0.8005 (ttt180) cc_final: 0.5793 (tpm170)
REVERT: A   36 GLU cc_start: 0.7853 (tt0) cc_final: 0.7017 (mt-10)
REVERT: A   50 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8076 (mt-10)
REVERT: A   58 LYS cc_start: 0.8069 (mmtt) cc_final: 0.6014 (pmtt)
REVERT: A   74 GLU cc_start: 0.8053 (pt0) cc_final: 0.7479 (pt0)
REVERT: B   58 LYS cc_start: 0.8517 (mmtm) cc_final: 0.6810 (mptt)
REVERT: B   81 ARG cc_start: 0.7362 (mtt180) cc_final: 0.6960 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5784 (mptt) cc_final: 0.4923 (mmmm)
REVERT: C   12 ARG cc_start: 0.8138 (ptm-80) cc_final: 0.7820 (ptm-80)
REVERT: C   16 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7482 (mt-10)
REVERT: C   21 ASN cc_start: 0.8601 (t0) cc_final: 0.8369 (m-40)
REVERT: C   36 GLU cc_start: 0.7330 (tt0) cc_final: 0.6568 (mt-10)
REVERT: C   50 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7819 (mt-10)
REVERT: D   38 ASP cc_start: 0.8619 (p0) cc_final: 0.8352 (p0)
REVERT: D   74 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7331 (mp0)
REVERT: E    6 LYS cc_start: 0.6501 (mttt) cc_final: 0.6165 (mptp)
REVERT: E   12 ARG cc_start: 0.8270 (ptm-80) cc_final: 0.8007 (ptm-80)
REVERT: E   36 GLU cc_start: 0.7446 (tt0) cc_final: 0.6616 (mt-10)
REVERT: F   75 LYS cc_start: 0.8204 (mtmt) cc_final: 0.7953 (mtpp)
  outliers start: 20
  outliers final: 10
  residues processed: 127
  average time/residue: 1.4866
  time to fit residues: 193.1648
Evaluate side-chains
  125 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain D residue   74 GLU
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 30 optimal weight:    8.9990
   chunk 16 optimal weight:    6.9990
   chunk 34 optimal weight:    0.0370
   chunk 28 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 20 optimal weight:    0.7980
   chunk 36 optimal weight:   10.0000
   chunk 10 optimal weight:    6.9990
   chunk 13 optimal weight:   10.0000
   chunk 8 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    3.5664

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.4423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3807  Z= 0.249
  Angle     :  0.572   8.698   5157  Z= 0.290
  Chirality :  0.045   0.136    534
  Planarity :  0.003   0.021    666
  Dihedral  :  4.672  15.623    486
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 17.38 %
    Favored  : 79.05 %
  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: -4.06 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.08 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E  60 
 HIS   0.004   0.001   HIS C  31 
 PHE   0.010   0.002   PHE F  30 
 TYR   0.016   0.002   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
  133 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.6003 (OUTLIER) cc_final: 0.5144 (mmmm)
REVERT: A   12 ARG cc_start: 0.7982 (ttt180) cc_final: 0.5823 (tpm170)
REVERT: A   36 GLU cc_start: 0.7782 (tt0) cc_final: 0.7001 (mt-10)
REVERT: A   44 GLU cc_start: 0.7814 (mp0) cc_final: 0.7133 (mm-30)
REVERT: A   50 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8115 (mt-10)
REVERT: A   58 LYS cc_start: 0.8036 (mmtt) cc_final: 0.6086 (pmtt)
REVERT: A   74 GLU cc_start: 0.8017 (pt0) cc_final: 0.7510 (pt0)
REVERT: B   45 ARG cc_start: 0.8232 (mtp85) cc_final: 0.7999 (mtp85)
REVERT: B   58 LYS cc_start: 0.8474 (mmtm) cc_final: 0.6777 (mptt)
REVERT: B   81 ARG cc_start: 0.7367 (mtt180) cc_final: 0.6886 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5765 (mptt) cc_final: 0.4928 (mmmm)
REVERT: C   36 GLU cc_start: 0.7283 (tt0) cc_final: 0.6580 (mt-10)
REVERT: C   44 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6824 (mm-30)
REVERT: C   48 LYS cc_start: 0.7737 (tptm) cc_final: 0.7369 (tppp)
REVERT: C   50 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7830 (mt-10)
REVERT: C   77 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7585 (mt-10)
REVERT: D   44 GLU cc_start: 0.7626 (tt0) cc_final: 0.7017 (mm-30)
REVERT: D   48 LYS cc_start: 0.8436 (mtmt) cc_final: 0.8158 (mtpp)
REVERT: E    6 LYS cc_start: 0.6476 (mttt) cc_final: 0.6137 (mptp)
REVERT: E   36 GLU cc_start: 0.7452 (tt0) cc_final: 0.6632 (mt-10)
REVERT: E   44 GLU cc_start: 0.7709 (mp0) cc_final: 0.7495 (mp0)
REVERT: E   48 LYS cc_start: 0.5417 (mmtt) cc_final: 0.5193 (tptt)
REVERT: F   75 LYS cc_start: 0.8081 (mtmt) cc_final: 0.7851 (mtpp)
  outliers start: 15
  outliers final: 8
  residues processed: 123
  average time/residue: 1.4651
  time to fit residues: 184.5293
Evaluate side-chains
  123 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
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   88 SER
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue   77 GLU
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain 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 10 optimal weight:    0.8980
   chunk 40 optimal weight:   10.0000
   chunk 33 optimal weight:    9.9990
   chunk 18 optimal weight:    9.9990
   chunk 3 optimal weight:    8.9990
   chunk 13 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 39 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 23 optimal weight:    4.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    4.3186

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.4545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   3807  Z= 0.297
  Angle     :  0.598   8.209   5157  Z= 0.303
  Chirality :  0.045   0.141    534
  Planarity :  0.003   0.020    666
  Dihedral  :  4.719  14.947    486
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 17.86 %
    Favored  : 78.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.03 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.07 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A  60 
 HIS   0.004   0.001   HIS C  13 
 PHE   0.012   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
  127 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.6075 (OUTLIER) cc_final: 0.5182 (mmmm)
REVERT: A   12 ARG cc_start: 0.7970 (ttt180) cc_final: 0.5849 (tpm170)
REVERT: A   16 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7820 (pt0)
REVERT: A   36 GLU cc_start: 0.7771 (tt0) cc_final: 0.6984 (mt-10)
REVERT: A   44 GLU cc_start: 0.7791 (mp0) cc_final: 0.7475 (mp0)
REVERT: A   50 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8146 (mt-10)
REVERT: A   58 LYS cc_start: 0.8049 (mmtt) cc_final: 0.6115 (pmtt)
REVERT: A   74 GLU cc_start: 0.8034 (pt0) cc_final: 0.7567 (pt0)
REVERT: B   38 ASP cc_start: 0.8539 (p0) cc_final: 0.7988 (p0)
REVERT: B   45 ARG cc_start: 0.8234 (mtp85) cc_final: 0.7998 (mtp85)
REVERT: B   58 LYS cc_start: 0.8566 (mmtm) cc_final: 0.6831 (mptt)
REVERT: B   81 ARG cc_start: 0.7435 (mtt180) cc_final: 0.6933 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5815 (mptt) cc_final: 0.4976 (mmmm)
REVERT: C   36 GLU cc_start: 0.7318 (tt0) cc_final: 0.6612 (mt-10)
REVERT: C   48 LYS cc_start: 0.7694 (tptm) cc_final: 0.7299 (tppp)
REVERT: C   50 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7819 (mt-10)
REVERT: C   77 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7595 (mt-10)
REVERT: D   48 LYS cc_start: 0.8439 (mtmt) cc_final: 0.8158 (mtpp)
REVERT: D   74 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7288 (mp0)
REVERT: E    6 LYS cc_start: 0.6476 (mttt) cc_final: 0.6155 (mptp)
REVERT: E   36 GLU cc_start: 0.7473 (tt0) cc_final: 0.6678 (mt-10)
REVERT: F   75 LYS cc_start: 0.8156 (mtmt) cc_final: 0.7902 (mtpp)
  outliers start: 14
  outliers final: 9
  residues processed: 118
  average time/residue: 1.4244
  time to fit residues: 172.1766
Evaluate side-chains
  125 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
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   57 SER
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue   77 GLU
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain D residue   74 GLU
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 22 optimal weight:    5.9990
   chunk 34 optimal weight:    7.9990
   chunk 40 optimal weight:    6.9990
   chunk 25 optimal weight:   20.0000
   chunk 24 optimal weight:   10.0000
   chunk 18 optimal weight:   20.0000
   chunk 16 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9990
   chunk 7 optimal weight:    5.9990
   chunk 27 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   overall best weight:    5.1990

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.4687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   3807  Z= 0.346
  Angle     :  0.618   8.058   5157  Z= 0.314
  Chirality :  0.046   0.143    534
  Planarity :  0.003   0.023    666
  Dihedral  :  4.806  14.726    486
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 18.57 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.00 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.04 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C  60 
 HIS   0.004   0.001   HIS C  31 
 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 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
  131 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.6022 (OUTLIER) cc_final: 0.5121 (mmmm)
REVERT: A   12 ARG cc_start: 0.7972 (ttt180) cc_final: 0.5866 (tpm170)
REVERT: A   16 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7817 (pt0)
REVERT: A   36 GLU cc_start: 0.7771 (tt0) cc_final: 0.6987 (mt-10)
REVERT: A   44 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6862 (mm-30)
REVERT: A   50 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8330 (mt-10)
REVERT: A   58 LYS cc_start: 0.8044 (mmtt) cc_final: 0.6120 (pmtt)
REVERT: A   74 GLU cc_start: 0.8045 (pt0) cc_final: 0.7603 (pt0)
REVERT: B   38 ASP cc_start: 0.8539 (p0) cc_final: 0.7994 (p0)
REVERT: B   45 ARG cc_start: 0.8287 (mtp85) cc_final: 0.8024 (mtp85)
REVERT: B   48 LYS cc_start: 0.8713 (mtpt) cc_final: 0.8485 (mtpp)
REVERT: B   58 LYS cc_start: 0.8513 (mmtm) cc_final: 0.6797 (mptt)
REVERT: B   81 ARG cc_start: 0.7477 (mtt180) cc_final: 0.6920 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5914 (mptt) cc_final: 0.4957 (mmmm)
REVERT: C   36 GLU cc_start: 0.7404 (tt0) cc_final: 0.6660 (mt-10)
REVERT: C   48 LYS cc_start: 0.7691 (tptm) cc_final: 0.7334 (tppp)
REVERT: C   50 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7912 (mt-10)
REVERT: D   48 LYS cc_start: 0.8449 (mtmt) cc_final: 0.8205 (mtpp)
REVERT: D   74 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7287 (mp0)
REVERT: E    6 LYS cc_start: 0.6393 (mttt) cc_final: 0.6060 (mptp)
REVERT: E   36 GLU cc_start: 0.7526 (tt0) cc_final: 0.6756 (mt-10)
REVERT: F   45 ARG cc_start: 0.7975 (mtp85) cc_final: 0.7435 (mtt-85)
REVERT: F   75 LYS cc_start: 0.8163 (mtmt) cc_final: 0.7892 (mtpp)
  outliers start: 14
  outliers final: 9
  residues processed: 121
  average time/residue: 1.4392
  time to fit residues: 178.3177
Evaluate side-chains
  128 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
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   88 SER
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain D residue   74 GLU
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   61 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 31 optimal weight:    7.9990
   chunk 36 optimal weight:    8.9990
   chunk 38 optimal weight:    5.9990
   chunk 35 optimal weight:    0.2980
   chunk 37 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 29 optimal weight:    0.6980
   chunk 11 optimal weight:   10.0000
   chunk 34 optimal weight:    4.9990
   overall best weight:    2.3986

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

Flipped N/Q/H residues before XYZ refinement:
D  76 ASN
F  24 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.4679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3807  Z= 0.198
  Angle     :  0.555   7.808   5157  Z= 0.280
  Chirality :  0.044   0.137    534
  Planarity :  0.002   0.021    666
  Dihedral  :  4.519  14.415    486
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 18.81 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.90 (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   0.000   TRP F  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   0.001   0.000   ARG A  12 

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

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.6039 (OUTLIER) cc_final: 0.5162 (mmmm)
REVERT: A   12 ARG cc_start: 0.7916 (ttt180) cc_final: 0.5835 (tpm170)
REVERT: A   16 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7826 (pt0)
REVERT: A   36 GLU cc_start: 0.7715 (tt0) cc_final: 0.6973 (mt-10)
REVERT: A   44 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.6846 (mm-30)
REVERT: A   50 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8378 (mt-10)
REVERT: A   58 LYS cc_start: 0.8021 (mmtt) cc_final: 0.6076 (pmtt)
REVERT: A   74 GLU cc_start: 0.8022 (pt0) cc_final: 0.7711 (pt0)
REVERT: B   45 ARG cc_start: 0.8281 (mtp85) cc_final: 0.8015 (mtp85)
REVERT: B   58 LYS cc_start: 0.8525 (mmtm) cc_final: 0.6785 (mptt)
REVERT: B   81 ARG cc_start: 0.7458 (mtt180) cc_final: 0.6919 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5913 (mptt) cc_final: 0.4957 (mmmm)
REVERT: C   36 GLU cc_start: 0.7342 (tt0) cc_final: 0.6662 (mt-10)
REVERT: C   44 GLU cc_start: 0.7264 (mp0) cc_final: 0.5978 (mp0)
REVERT: C   48 LYS cc_start: 0.7712 (tptm) cc_final: 0.7394 (tppp)
REVERT: C   50 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7972 (mt-10)
REVERT: C   77 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7611 (mt-10)
REVERT: D   48 LYS cc_start: 0.8481 (mtmt) cc_final: 0.8205 (mtpp)
REVERT: E    6 LYS cc_start: 0.6469 (mttt) cc_final: 0.6158 (mptp)
REVERT: E   36 GLU cc_start: 0.7568 (tt0) cc_final: 0.6760 (mt-10)
REVERT: E   44 GLU cc_start: 0.7714 (mp0) cc_final: 0.7473 (mp0)
REVERT: F   75 LYS cc_start: 0.8068 (mtmt) cc_final: 0.7802 (mtpp)
  outliers start: 13
  outliers final: 9
  residues processed: 119
  average time/residue: 1.4427
  time to fit residues: 175.9817
Evaluate side-chains
  125 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
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   88 SER
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue   77 GLU
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain 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 35 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 27 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 38 optimal weight:    8.9990
   chunk 33 optimal weight:   10.0000
   chunk 3 optimal weight:    9.9990
   chunk 25 optimal weight:    5.9990
   overall best weight:    3.7388

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.4822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3807  Z= 0.263
  Angle     :  0.584   7.664   5157  Z= 0.296
  Chirality :  0.045   0.143    534
  Planarity :  0.002   0.023    666
  Dihedral  :  4.628  14.148    486
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 18.81 %
    Favored  : 78.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.87 (0.31), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.94 (0.24), 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   0.011   0.002   PHE F  30 
 TYR   0.017   0.002   TYR B  67 
 ARG   0.001   0.000   ARG A  12 

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

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.6056 (OUTLIER) cc_final: 0.5165 (mmmm)
REVERT: A   12 ARG cc_start: 0.7918 (ttt180) cc_final: 0.5805 (tpm170)
REVERT: A   16 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7809 (pt0)
REVERT: A   36 GLU cc_start: 0.7727 (tt0) cc_final: 0.6980 (mt-10)
REVERT: A   44 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.6870 (mm-30)
REVERT: A   50 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8361 (mt-10)
REVERT: A   58 LYS cc_start: 0.8029 (mmtt) cc_final: 0.6105 (pmtt)
REVERT: A   74 GLU cc_start: 0.8019 (pt0) cc_final: 0.7722 (pt0)
REVERT: B   45 ARG cc_start: 0.8288 (mtp85) cc_final: 0.8029 (mtp85)
REVERT: B   58 LYS cc_start: 0.8526 (mmtm) cc_final: 0.6770 (mptt)
REVERT: B   81 ARG cc_start: 0.7481 (mtt180) cc_final: 0.6933 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5866 (mptt) cc_final: 0.4953 (mmmm)
REVERT: C   36 GLU cc_start: 0.7362 (tt0) cc_final: 0.6669 (mt-10)
REVERT: C   44 GLU cc_start: 0.7161 (mp0) cc_final: 0.6076 (mp0)
REVERT: C   48 LYS cc_start: 0.7670 (tptm) cc_final: 0.7331 (tppp)
REVERT: C   50 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7971 (mt-10)
REVERT: C   77 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7604 (mt-10)
REVERT: D   48 LYS cc_start: 0.8490 (mtmt) cc_final: 0.8209 (mtpp)
REVERT: E    6 LYS cc_start: 0.6468 (mttt) cc_final: 0.6148 (mptp)
REVERT: E   36 GLU cc_start: 0.7579 (tt0) cc_final: 0.6781 (mt-10)
REVERT: E   44 GLU cc_start: 0.7666 (mp0) cc_final: 0.7423 (mp0)
REVERT: F   45 ARG cc_start: 0.7965 (mtp85) cc_final: 0.7381 (mtt-85)
REVERT: F   75 LYS cc_start: 0.8128 (mtmt) cc_final: 0.7866 (mtpp)
  outliers start: 12
  outliers final: 9
  residues processed: 117
  average time/residue: 1.4433
  time to fit residues: 173.2040
Evaluate side-chains
  123 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
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   88 SER
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue   77 GLU
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain 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 20 optimal weight:    9.9990
   chunk 26 optimal weight:    9.9990
   chunk 35 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 30 optimal weight:    0.0970
   chunk 4 optimal weight:    8.9990
   chunk 9 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 13 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    5.0186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.4841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   3807  Z= 0.334
  Angle     :  0.612   7.583   5157  Z= 0.312
  Chirality :  0.046   0.147    534
  Planarity :  0.003   0.027    666
  Dihedral  :  4.775  14.106    486
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 19.05 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.93 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.99 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  60 
 HIS   0.004   0.001   HIS A  31 
 PHE   0.014   0.002   PHE F  30 
 TYR   0.019   0.002   TYR B  67 
 ARG   0.002   0.000   ARG E  45 

********************** 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
  130 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 118
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.6016 (OUTLIER) cc_final: 0.5112 (mmmm)
REVERT: A   12 ARG cc_start: 0.7913 (ttt180) cc_final: 0.5821 (tpm170)
REVERT: A   16 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7798 (pt0)
REVERT: A   36 GLU cc_start: 0.7732 (tt0) cc_final: 0.6970 (mt-10)
REVERT: A   44 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7395 (mp0)
REVERT: A   50 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8396 (mt-10)
REVERT: A   58 LYS cc_start: 0.8045 (mmtt) cc_final: 0.6129 (pmtt)
REVERT: A   74 GLU cc_start: 0.8019 (pt0) cc_final: 0.7711 (pt0)
REVERT: B   38 ASP cc_start: 0.8510 (p0) cc_final: 0.7937 (p0)
REVERT: B   48 LYS cc_start: 0.8710 (mtpt) cc_final: 0.8476 (mtpp)
REVERT: B   58 LYS cc_start: 0.8555 (mmtm) cc_final: 0.6812 (mptt)
REVERT: B   81 ARG cc_start: 0.7497 (mtt180) cc_final: 0.6904 (pmt-80)
REVERT: C    6 LYS cc_start: 0.5843 (mptt) cc_final: 0.4940 (mmmm)
REVERT: C   21 ASN cc_start: 0.8726 (t0) cc_final: 0.8464 (m-40)
REVERT: C   36 GLU cc_start: 0.7375 (tt0) cc_final: 0.6708 (mt-10)
REVERT: C   44 GLU cc_start: 0.7200 (mp0) cc_final: 0.6753 (mp0)
REVERT: C   48 LYS cc_start: 0.7657 (tptm) cc_final: 0.7356 (tppp)
REVERT: C   50 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7926 (mt-10)
REVERT: C   77 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7614 (mt-10)
REVERT: D   48 LYS cc_start: 0.8471 (mtmt) cc_final: 0.8230 (mtpp)
REVERT: E    6 LYS cc_start: 0.6477 (mttt) cc_final: 0.6163 (mptp)
REVERT: E   36 GLU cc_start: 0.7633 (tt0) cc_final: 0.6821 (mt-10)
REVERT: F   45 ARG cc_start: 0.7950 (mtp85) cc_final: 0.7346 (mtt-85)
REVERT: F   75 LYS cc_start: 0.8165 (mtmt) cc_final: 0.7882 (mtpp)
  outliers start: 12
  outliers final: 9
  residues processed: 121
  average time/residue: 1.4092
  time to fit residues: 174.7401
Evaluate side-chains
  129 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
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   88 SER
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue   77 GLU
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain 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 29 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 24 optimal weight:    6.9990
   chunk 38 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 28 optimal weight:    8.9990
   chunk 26 optimal weight:    7.9990
   chunk 25 optimal weight:    9.9990
   chunk 16 optimal weight:    8.9990
   chunk 15 optimal weight:    0.8980
   chunk 41 optimal weight:   10.0000
   overall best weight:    3.3586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.138203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.116893 restraints weight = 4804.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3822 rms_B_bonded: 2.17
r_work: 0.3701 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3593 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.4904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3807  Z= 0.243
  Angle     :  0.600   7.811   5157  Z= 0.298
  Chirality :  0.045   0.142    534
  Planarity :  0.002   0.027    666
  Dihedral  :  4.629  14.225    486
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 20.24 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.92 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.98 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A  60 
 HIS   0.003   0.001   HIS C  13 
 PHE   0.010   0.002   PHE F  30 
 TYR   0.017   0.002   TYR B  67 
 ARG   0.001   0.000   ARG E  45 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2799.83 seconds
wall clock time: 50 minutes 10.42 seconds (3010.42 seconds total)