Starting phenix.real_space_refine
on Wed Mar 12 17:44:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wv4_37864/03_2025/8wv4_37864.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wv4_37864/03_2025/8wv4_37864.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wv4_37864/03_2025/8wv4_37864.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wv4_37864/03_2025/8wv4_37864.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wv4_37864/03_2025/8wv4_37864.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wv4_37864/03_2025/8wv4_37864.cif"
  }
  resolution = 3.3
  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=   0.008
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: 5
    Type Number    sf(0)   Gaussians
     Ca     10      9.91       5
     S      20      5.16       5
     C    5290      2.51       5
     N    1305      2.21       5
     O    1545      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 80 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8170
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1632
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 194}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 3.31, per 1000 atoms: 0.41
  Number of scatterers: 8170
  At special positions: 0
  Unit cell: (113.42, 115.56, 52.43, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca     10     19.99
     S      20     16.00
     O    1545      8.00
     N    1305      7.00
     C    5290      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  36 " - pdb=" SG  CYS A  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  36 " - pdb=" SG  CYS C  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  36 " - pdb=" SG  CYS B  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  36 " - pdb=" SG  CYS E  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  36 " - pdb=" SG  CYS D  97 " 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: 1.72
  Conformation dependent library (CDL) restraints added in 990.3 milliseconds
  

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1890

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 15 sheets defined
      6.8% alpha, 36.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 46
    Processing helix  chain 'A' and resid 167 through 176
    Processing helix  chain 'B' and resid 43 through 46
    Processing helix  chain 'B' and resid 167 through 176
    Processing helix  chain 'C' and resid 43 through 46
    Processing helix  chain 'C' and resid 167 through 176
    Processing helix  chain 'D' and resid 43 through 46
    Processing helix  chain 'D' and resid 167 through 176
    Processing helix  chain 'E' and resid 43 through 46
    Processing helix  chain 'E' and resid 167 through 176
    Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 115
    Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 115
      removed outlier: 3.892A  pdb=" N   ILE A 106 " --> pdb=" O   GLU A 101 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   PHE A  39 " --> pdb=" O   VAL A  94 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   THR A  34 " --> pdb=" O   TRP A 162 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   HIS A  38 " --> pdb=" O   ASN A 158 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   ASN A 158 " --> pdb=" O   HIS A  38 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   TYR A  40 " --> pdb=" O   ILE A 156 " (cutoff:3.500A)
      removed outlier: 5.383A  pdb=" N   ILE A 156 " --> pdb=" O   TYR A  40 " (cutoff:3.500A)
      removed outlier: 5.008A  pdb=" N   ASN A 158 " --> pdb=" O   LYS A   7 " (cutoff:3.500A)
      removed outlier: 10.164A  pdb=" N   LYS A   7 " --> pdb=" O   ASN A 158 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 85
      removed outlier: 3.607A  pdb=" N   SER A  80 " --> pdb=" O   VAL A  77 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   PHE A  52 " --> pdb=" O   ILE A  65 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   TRP A  67 " --> pdb=" O   SER A  50 " (cutoff:3.500A)
      removed outlier: 5.975A  pdb=" N   SER A  50 " --> pdb=" O   TRP A  67 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ALA A  55 " --> pdb=" O   SER A 132 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ILE A 133 " --> pdb=" O   LEU A  22 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   VAL A  20 " --> pdb=" O   LEU A 135 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   LYS A 191 " --> pdb=" O   LYS A  23 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115
    Processing sheet with id=AA5, first strand: chain 'B' and resid 114 through 115
      removed outlier: 3.892A  pdb=" N   ILE B 106 " --> pdb=" O   GLU B 101 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   PHE B  39 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   THR B  34 " --> pdb=" O   TRP B 162 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   HIS B  38 " --> pdb=" O   ASN B 158 " (cutoff:3.500A)
      removed outlier: 4.849A  pdb=" N   ASN B 158 " --> pdb=" O   HIS B  38 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   TYR B  40 " --> pdb=" O   ILE B 156 " (cutoff:3.500A)
      removed outlier: 5.382A  pdb=" N   ILE B 156 " --> pdb=" O   TYR B  40 " (cutoff:3.500A)
      removed outlier: 5.010A  pdb=" N   ASN B 158 " --> pdb=" O   LYS B   7 " (cutoff:3.500A)
      removed outlier: 10.164A  pdb=" N   LYS B   7 " --> pdb=" O   ASN B 158 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 80 through 85
      removed outlier: 3.606A  pdb=" N   SER B  80 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   PHE B  52 " --> pdb=" O   ILE B  65 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   TRP B  67 " --> pdb=" O   SER B  50 " (cutoff:3.500A)
      removed outlier: 5.975A  pdb=" N   SER B  50 " --> pdb=" O   TRP B  67 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ALA B  55 " --> pdb=" O   SER B 132 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ILE B 133 " --> pdb=" O   LEU B  22 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   VAL B  20 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   LYS B 191 " --> pdb=" O   LYS B  23 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 114 through 115
    Processing sheet with id=AA8, first strand: chain 'C' and resid 114 through 115
      removed outlier: 3.892A  pdb=" N   ILE C 106 " --> pdb=" O   GLU C 101 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   PHE C  39 " --> pdb=" O   VAL C  94 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   THR C  34 " --> pdb=" O   TRP C 162 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   HIS C  38 " --> pdb=" O   ASN C 158 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   ASN C 158 " --> pdb=" O   HIS C  38 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   TYR C  40 " --> pdb=" O   ILE C 156 " (cutoff:3.500A)
      removed outlier: 5.382A  pdb=" N   ILE C 156 " --> pdb=" O   TYR C  40 " (cutoff:3.500A)
      removed outlier: 5.009A  pdb=" N   ASN C 158 " --> pdb=" O   LYS C   7 " (cutoff:3.500A)
      removed outlier: 10.165A  pdb=" N   LYS C   7 " --> pdb=" O   ASN C 158 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 80 through 85
      removed outlier: 3.607A  pdb=" N   SER C  80 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   PHE C  52 " --> pdb=" O   ILE C  65 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   TRP C  67 " --> pdb=" O   SER C  50 " (cutoff:3.500A)
      removed outlier: 5.975A  pdb=" N   SER C  50 " --> pdb=" O   TRP C  67 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ALA C  55 " --> pdb=" O   SER C 132 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ILE C 133 " --> pdb=" O   LEU C  22 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL C  20 " --> pdb=" O   LEU C 135 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   LYS C 191 " --> pdb=" O   LYS C  23 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 115
    Processing sheet with id=AB2, first strand: chain 'D' and resid 114 through 115
      removed outlier: 3.892A  pdb=" N   ILE D 106 " --> pdb=" O   GLU D 101 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   PHE D  39 " --> pdb=" O   VAL D  94 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   THR D  34 " --> pdb=" O   TRP D 162 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   HIS D  38 " --> pdb=" O   ASN D 158 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   ASN D 158 " --> pdb=" O   HIS D  38 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   TYR D  40 " --> pdb=" O   ILE D 156 " (cutoff:3.500A)
      removed outlier: 5.382A  pdb=" N   ILE D 156 " --> pdb=" O   TYR D  40 " (cutoff:3.500A)
      removed outlier: 5.010A  pdb=" N   ASN D 158 " --> pdb=" O   LYS D   7 " (cutoff:3.500A)
      removed outlier: 10.165A  pdb=" N   LYS D   7 " --> pdb=" O   ASN D 158 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 80 through 85
      removed outlier: 3.606A  pdb=" N   SER D  80 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   PHE D  52 " --> pdb=" O   ILE D  65 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   TRP D  67 " --> pdb=" O   SER D  50 " (cutoff:3.500A)
      removed outlier: 5.974A  pdb=" N   SER D  50 " --> pdb=" O   TRP D  67 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ALA D  55 " --> pdb=" O   SER D 132 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ILE D 133 " --> pdb=" O   LEU D  22 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   VAL D  20 " --> pdb=" O   LEU D 135 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   LYS D 191 " --> pdb=" O   LYS D  23 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 114 through 115
    Processing sheet with id=AB5, first strand: chain 'E' and resid 114 through 115
      removed outlier: 3.892A  pdb=" N   ILE E 106 " --> pdb=" O   GLU E 101 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   PHE E  39 " --> pdb=" O   VAL E  94 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   THR E  34 " --> pdb=" O   TRP E 162 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   HIS E  38 " --> pdb=" O   ASN E 158 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   ASN E 158 " --> pdb=" O   HIS E  38 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   TYR E  40 " --> pdb=" O   ILE E 156 " (cutoff:3.500A)
      removed outlier: 5.383A  pdb=" N   ILE E 156 " --> pdb=" O   TYR E  40 " (cutoff:3.500A)
      removed outlier: 5.009A  pdb=" N   ASN E 158 " --> pdb=" O   LYS E   7 " (cutoff:3.500A)
      removed outlier: 10.165A  pdb=" N   LYS E   7 " --> pdb=" O   ASN E 158 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 80 through 85
      removed outlier: 3.606A  pdb=" N   SER E  80 " --> pdb=" O   VAL E  77 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   PHE E  52 " --> pdb=" O   ILE E  65 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   TRP E  67 " --> pdb=" O   SER E  50 " (cutoff:3.500A)
      removed outlier: 5.975A  pdb=" N   SER E  50 " --> pdb=" O   TRP E  67 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ALA E  55 " --> pdb=" O   SER E 132 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ILE E 133 " --> pdb=" O   LEU E  22 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL E  20 " --> pdb=" O   LEU E 135 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   LYS E 191 " --> pdb=" O   LYS E  23 " (cutoff:3.500A)

    300 hydrogen bonds defined for protein.
    735 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: 2.13

  Time building geometry restraints manager: 2.09 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: 2539
        1.34 -     1.46: 2007
        1.46 -     1.58: 3814
        1.58 -     1.69: 0
        1.69 -     1.81: 30
  Bond restraints: 8390
  Sorted by residual:
  bond pdb=" CB  ASP D  60 "
       pdb=" CG  ASP D  60 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 2.50e-02 1.60e+03 1.15e+00
  bond pdb=" CB  ASP A  60 "
       pdb=" CG  ASP A  60 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 2.50e-02 1.60e+03 1.10e+00
  bond pdb=" CB  ASP C  60 "
       pdb=" CG  ASP C  60 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 2.50e-02 1.60e+03 1.10e+00
  bond pdb=" CB  ASP B  60 "
       pdb=" CG  ASP B  60 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 2.50e-02 1.60e+03 1.08e+00
  bond pdb=" CB  ASP E  60 "
       pdb=" CG  ASP E  60 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 2.50e-02 1.60e+03 1.08e+00
  ... (remaining 8385 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.20: 11043
        1.20 -     2.39: 290
        2.39 -     3.59: 62
        3.59 -     4.78: 5
        4.78 -     5.98: 5
  Bond angle restraints: 11405
  Sorted by residual:
  angle pdb=" N   GLY C  72 "
        pdb=" CA  GLY C  72 "
        pdb=" C   GLY C  72 "
      ideal   model   delta    sigma   weight residual
     110.20  113.10   -2.90 1.32e+00 5.74e-01 4.84e+00
  angle pdb=" N   GLY D  72 "
        pdb=" CA  GLY D  72 "
        pdb=" C   GLY D  72 "
      ideal   model   delta    sigma   weight residual
     110.20  113.10   -2.90 1.32e+00 5.74e-01 4.83e+00
  angle pdb=" N   GLY B  72 "
        pdb=" CA  GLY B  72 "
        pdb=" C   GLY B  72 "
      ideal   model   delta    sigma   weight residual
     110.20  113.09   -2.89 1.32e+00 5.74e-01 4.81e+00
  angle pdb=" N   GLY E  72 "
        pdb=" CA  GLY E  72 "
        pdb=" C   GLY E  72 "
      ideal   model   delta    sigma   weight residual
     110.20  113.09   -2.89 1.32e+00 5.74e-01 4.79e+00
  angle pdb=" N   GLY A  72 "
        pdb=" CA  GLY A  72 "
        pdb=" C   GLY A  72 "
      ideal   model   delta    sigma   weight residual
     110.20  113.08   -2.88 1.32e+00 5.74e-01 4.77e+00
  ... (remaining 11400 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.50: 4525
       17.50 -    35.00: 285
       35.00 -    52.49: 35
       52.49 -    69.99: 20
       69.99 -    87.49: 30
  Dihedral angle restraints: 4895
    sinusoidal: 1940
      harmonic: 2955
  Sorted by residual:
  dihedral pdb=" CA  PHE A 146 "
           pdb=" C   PHE A 146 "
           pdb=" N   GLU A 147 "
           pdb=" CA  GLU A 147 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.24  -21.76     0      5.00e+00 4.00e-02 1.89e+01
  dihedral pdb=" CA  PHE C 146 "
           pdb=" C   PHE C 146 "
           pdb=" N   GLU C 147 "
           pdb=" CA  GLU C 147 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.26  -21.74     0      5.00e+00 4.00e-02 1.89e+01
  dihedral pdb=" CA  PHE D 146 "
           pdb=" C   PHE D 146 "
           pdb=" N   GLU D 147 "
           pdb=" CA  GLU D 147 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.26  -21.74     0      5.00e+00 4.00e-02 1.89e+01
  ... (remaining 4892 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 657
       0.025 -    0.049: 312
       0.049 -    0.074: 113
       0.074 -    0.098: 68
       0.098 -    0.123: 85
  Chirality restraints: 1235
  Sorted by residual:
  chirality pdb=" CA  ILE D  63 "
            pdb=" N   ILE D  63 "
            pdb=" C   ILE D  63 "
            pdb=" CB  ILE D  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.75e-01
  chirality pdb=" CA  ILE C  63 "
            pdb=" N   ILE C  63 "
            pdb=" C   ILE C  63 "
            pdb=" CB  ILE C  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.72e-01
  chirality pdb=" CA  ILE A  63 "
            pdb=" N   ILE A  63 "
            pdb=" C   ILE A  63 "
            pdb=" CB  ILE A  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.72e-01
  ... (remaining 1232 not shown)

  Planarity restraints: 1450
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER E 167 "   -0.019 5.00e-02 4.00e+02   2.92e-02 1.36e+00
        pdb=" N   PRO E 168 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO E 168 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO E 168 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 167 "   -0.019 5.00e-02 4.00e+02   2.91e-02 1.36e+00
        pdb=" N   PRO B 168 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO B 168 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 168 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 167 "   -0.019 5.00e-02 4.00e+02   2.90e-02 1.35e+00
        pdb=" N   PRO A 168 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A 168 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 168 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 1447 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 146
        2.53 -     3.12: 5808
        3.12 -     3.72: 12054
        3.72 -     4.31: 17672
        4.31 -     4.90: 30425
  Nonbonded interactions: 66105
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A  60 "
            pdb=" OD1 ASN A  61 "
     model   vdw
     1.938 3.040
  nonbonded pdb=" OD1 ASP C  60 "
            pdb=" OD1 ASN C  61 "
     model   vdw
     1.939 3.040
  nonbonded pdb=" OD1 ASP E  60 "
            pdb=" OD1 ASN E  61 "
     model   vdw
     1.939 3.040
  nonbonded pdb=" OD1 ASP B  60 "
            pdb=" OD1 ASN B  61 "
     model   vdw
     1.940 3.040
  nonbonded pdb=" OD1 ASP D  60 "
            pdb=" OD1 ASN D  61 "
     model   vdw
     1.940 3.040
  ... (remaining 66100 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     18.840
  Find NCS groups from input model:        0.160
  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:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
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      :  0.002   0.037   8390  Z= 0.146
  Angle     :  0.491   5.980  11405  Z= 0.287
  Chirality :  0.044   0.123   1235
  Planarity :  0.003   0.029   1450
  Dihedral  : 14.128  87.489   2990
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  :  3.33 %
    Favored  : 93.33 %
  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: -2.63 (0.23), residues: 1020
  helix:  1.99 (0.64), residues: 55
  sheet: -1.44 (0.27), residues: 320
  loop : -2.37 (0.20), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP D 110 
 HIS   0.002   0.001   HIS D  38 
 PHE   0.009   0.001   PHE B 109 
 TYR   0.009   0.001   TYR A  54 
 ARG   0.008   0.001   ARG A 118 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 225
  time to evaluate  : 0.921 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8276 (tt0) cc_final: 0.7927 (tt0)
REVERT: A  172 ASN cc_start: 0.8477 (t0) cc_final: 0.8259 (t0)
REVERT: A  175 TYR cc_start: 0.8828 (t80) cc_final: 0.8556 (t80)
REVERT: B    4 MET cc_start: 0.7729 (mtp) cc_final: 0.7506 (mtp)
REVERT: B   62 GLU cc_start: 0.8034 (tp30) cc_final: 0.7804 (tp30)
REVERT: B  137 GLN cc_start: 0.8377 (mm-40) cc_final: 0.8086 (mm-40)
REVERT: C   62 GLU cc_start: 0.8094 (tp30) cc_final: 0.7863 (tp30)
REVERT: C  137 GLN cc_start: 0.8391 (mm-40) cc_final: 0.8004 (mm-40)
REVERT: C  175 TYR cc_start: 0.8830 (t80) cc_final: 0.8533 (t80)
REVERT: D   62 GLU cc_start: 0.8029 (tp30) cc_final: 0.7267 (tp30)
REVERT: D  125 TYR cc_start: 0.8633 (t80) cc_final: 0.7829 (t80)
REVERT: D  137 GLN cc_start: 0.8392 (mm-40) cc_final: 0.8190 (mm-40)
REVERT: E   62 GLU cc_start: 0.8079 (tp30) cc_final: 0.7846 (tp30)
REVERT: E  137 GLN cc_start: 0.8355 (mm-40) cc_final: 0.8067 (mm-40)
REVERT: E  172 ASN cc_start: 0.8602 (t0) cc_final: 0.8372 (t0)
  outliers start: 30
  outliers final: 8
  residues processed: 245
  average time/residue: 0.1908
  time to fit residues: 63.6792
Evaluate side-chains
  163 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 155
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   53 SER
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   53 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 75 optimal weight:    6.9990
   chunk 42 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   chunk 78 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0970
   chunk 58 optimal weight:    3.9990
   chunk 90 optimal weight:    4.9990
   overall best weight:    2.8186

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
B  59 GLN
B 195 GLN
C  59 GLN
** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 195 GLN
D  59 GLN
E  59 GLN
** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.098639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.079409 restraints weight = 12604.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.2717 rms_B_bonded: 2.74
r_work: 0.2579 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2426 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.2548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.045   8390  Z= 0.470
  Angle     :  0.609   4.390  11405  Z= 0.340
  Chirality :  0.052   0.167   1235
  Planarity :  0.005   0.037   1450
  Dihedral  :  5.069  36.786   1108
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  :  9.89 %
    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: -1.97 (0.25), residues: 1020
  helix:  2.69 (0.67), residues: 55
  sheet: -1.11 (0.25), residues: 390
  loop : -1.89 (0.24), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP D 205 
 HIS   0.007   0.002   HIS B  38 
 PHE   0.013   0.002   PHE C 109 
 TYR   0.021   0.002   TYR D  54 
 ARG   0.004   0.001   ARG A 118 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 154
  time to evaluate  : 1.313 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8898 (tt0) cc_final: 0.8501 (tt0)
REVERT: A  172 ASN cc_start: 0.8685 (t0) cc_final: 0.8472 (t0)
REVERT: A  175 TYR cc_start: 0.9030 (t80) cc_final: 0.8716 (t80)
REVERT: A  190 LEU cc_start: 0.9172 (tp) cc_final: 0.8813 (mp)
REVERT: B   59 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7903 (tp-100)
REVERT: B  137 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8388 (mm-40)
REVERT: C  190 LEU cc_start: 0.9197 (tp) cc_final: 0.8843 (mp)
REVERT: D   62 GLU cc_start: 0.8946 (tp30) cc_final: 0.8639 (tp30)
REVERT: D  125 TYR cc_start: 0.8905 (t80) cc_final: 0.8026 (t80)
REVERT: D  137 GLN cc_start: 0.8660 (mm-40) cc_final: 0.8407 (mm-40)
REVERT: D  193 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7831 (tm-30)
REVERT: E   49 TYR cc_start: 0.9227 (p90) cc_final: 0.8969 (p90)
REVERT: E  163 ASP cc_start: 0.8441 (p0) cc_final: 0.8195 (p0)
  outliers start: 16
  outliers final: 10
  residues processed: 168
  average time/residue: 0.2035
  time to fit residues: 46.3205
Evaluate side-chains
  152 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 140
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 HIS
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue  130 GLU
Chi-restraints excluded: chain B residue   59 GLN
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  130 GLU
Chi-restraints excluded: chain D residue   76 THR
Chi-restraints excluded: chain D residue  193 GLU
Chi-restraints excluded: chain E residue   76 THR
Chi-restraints excluded: chain E residue  130 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 24 optimal weight:    0.4980
   chunk 2 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 90 optimal weight:    0.6980
   chunk 61 optimal weight:    4.9990
   chunk 94 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 31 optimal weight:    0.5980
   chunk 58 optimal weight:    0.0570
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
B 195 GLN
C 137 GLN
** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 195 GLN
D 195 GLN
E  59 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.101982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.082718 restraints weight = 12789.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.2822 rms_B_bonded: 2.82
r_work: 0.2685 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8390  Z= 0.168
  Angle     :  0.499   4.138  11405  Z= 0.278
  Chirality :  0.048   0.163   1235
  Planarity :  0.003   0.030   1450
  Dihedral  :  4.050  18.447   1100
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 11.22 %
    Favored  : 87.89 %
  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: -1.41 (0.25), residues: 1020
  helix:  2.97 (0.69), residues: 55
  sheet: -0.76 (0.32), residues: 280
  loop : -1.41 (0.22), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 162 
 HIS   0.002   0.001   HIS E  38 
 PHE   0.009   0.001   PHE B 109 
 TYR   0.014   0.001   TYR B  54 
 ARG   0.003   0.000   ARG C   6 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 162
  time to evaluate  : 1.022 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8613 (tt0) cc_final: 0.8206 (tt0)
REVERT: A  175 TYR cc_start: 0.8926 (t80) cc_final: 0.8660 (t80)
REVERT: A  190 LEU cc_start: 0.9202 (tp) cc_final: 0.8868 (mp)
REVERT: B  137 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8034 (mm-40)
REVERT: C   62 GLU cc_start: 0.8764 (tp30) cc_final: 0.8547 (tp30)
REVERT: C  190 LEU cc_start: 0.9177 (tp) cc_final: 0.8908 (mp)
REVERT: D   16 ASP cc_start: 0.8514 (p0) cc_final: 0.8257 (p0)
REVERT: D   62 GLU cc_start: 0.8664 (tp30) cc_final: 0.8156 (tp30)
REVERT: D  125 TYR cc_start: 0.8820 (t80) cc_final: 0.7878 (t80)
REVERT: E  163 ASP cc_start: 0.8180 (p0) cc_final: 0.7949 (p0)
REVERT: E  180 PHE cc_start: 0.8352 (p90) cc_final: 0.7981 (p90)
  outliers start: 8
  outliers final: 4
  residues processed: 168
  average time/residue: 0.2337
  time to fit residues: 52.9997
Evaluate side-chains
  150 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 146
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 HIS
Chi-restraints excluded: chain B residue   81 GLU
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  169 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 2 optimal weight:    6.9990
   chunk 10 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9980
   chunk 1 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 34 optimal weight:    7.9990
   chunk 42 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   chunk 21 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
B  59 GLN
B 150 GLN
B 195 GLN
C 195 GLN
D 195 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.099451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.080480 restraints weight = 12740.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.2742 rms_B_bonded: 2.76
r_work: 0.2605 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2452 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.2452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
moved from start:          0.2865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   8390  Z= 0.341
  Angle     :  0.542   4.208  11405  Z= 0.303
  Chirality :  0.050   0.234   1235
  Planarity :  0.004   0.055   1450
  Dihedral  :  4.318  22.373   1100
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.44 %
    Favored  : 86.89 %
  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: -1.21 (0.25), residues: 1020
  helix:  2.99 (0.68), residues: 55
  sheet: -0.69 (0.32), residues: 280
  loop : -1.22 (0.22), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 162 
 HIS   0.004   0.001   HIS D  38 
 PHE   0.009   0.002   PHE A  66 
 TYR   0.017   0.002   TYR B  54 
 ARG   0.003   0.001   ARG E   6 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 148
  time to evaluate  : 0.961 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8781 (tt0) cc_final: 0.8374 (tt0)
REVERT: A  175 TYR cc_start: 0.9015 (t80) cc_final: 0.8670 (t80)
REVERT: A  190 LEU cc_start: 0.9258 (tp) cc_final: 0.8824 (mp)
REVERT: B  137 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8288 (mm-40)
REVERT: B  190 LEU cc_start: 0.9221 (tp) cc_final: 0.8897 (mp)
REVERT: C  190 LEU cc_start: 0.9218 (tp) cc_final: 0.8825 (mp)
REVERT: D   16 ASP cc_start: 0.8597 (p0) cc_final: 0.8373 (p0)
REVERT: D   62 GLU cc_start: 0.9064 (tp30) cc_final: 0.8570 (tp30)
REVERT: D  125 TYR cc_start: 0.8878 (t80) cc_final: 0.8067 (t80)
REVERT: E   49 TYR cc_start: 0.9208 (p90) cc_final: 0.8965 (p90)
REVERT: E  163 ASP cc_start: 0.8414 (p0) cc_final: 0.8142 (p0)
  outliers start: 15
  outliers final: 13
  residues processed: 159
  average time/residue: 0.2459
  time to fit residues: 52.5424
Evaluate side-chains
  157 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 144
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   38 HIS
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue   81 GLU
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   81 GLU
Chi-restraints excluded: chain D residue   76 THR
Chi-restraints excluded: chain D residue   81 GLU
Chi-restraints excluded: chain E residue   76 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 90 optimal weight:    2.9990
   chunk 55 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 79 optimal weight:    4.9990
   chunk 56 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 74 optimal weight:    8.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
B 195 GLN
D 195 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.099139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.080311 restraints weight = 12727.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.2708 rms_B_bonded: 2.75
r_work: 0.2574 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2426 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.2958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   8390  Z= 0.325
  Angle     :  0.535   4.243  11405  Z= 0.300
  Chirality :  0.049   0.199   1235
  Planarity :  0.004   0.052   1450
  Dihedral  :  4.359  21.080   1100
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 11.78 %
    Favored  : 86.11 %
  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: -1.16 (0.26), residues: 1020
  helix:  3.11 (0.68), residues: 55
  sheet: -0.86 (0.31), residues: 290
  loop : -1.09 (0.23), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 162 
 HIS   0.003   0.001   HIS D  38 
 PHE   0.008   0.002   PHE C  39 
 TYR   0.018   0.002   TYR B  54 
 ARG   0.002   0.000   ARG C 118 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 146
  time to evaluate  : 0.913 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8755 (tt0) cc_final: 0.8326 (tt0)
REVERT: A  175 TYR cc_start: 0.9014 (t80) cc_final: 0.8681 (t80)
REVERT: A  190 LEU cc_start: 0.9264 (tp) cc_final: 0.8812 (mp)
REVERT: B  137 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8326 (mm-40)
REVERT: B  190 LEU cc_start: 0.9237 (tp) cc_final: 0.8847 (mp)
REVERT: C  190 LEU cc_start: 0.9307 (tp) cc_final: 0.8896 (mp)
REVERT: D   16 ASP cc_start: 0.8576 (p0) cc_final: 0.8363 (p0)
REVERT: D   62 GLU cc_start: 0.9084 (tp30) cc_final: 0.8628 (tp30)
REVERT: D  125 TYR cc_start: 0.8896 (t80) cc_final: 0.8012 (t80)
REVERT: E   49 TYR cc_start: 0.9212 (p90) cc_final: 0.8905 (p90)
REVERT: E  163 ASP cc_start: 0.8350 (p0) cc_final: 0.8077 (p0)
  outliers start: 19
  outliers final: 17
  residues processed: 160
  average time/residue: 0.2371
  time to fit residues: 51.6122
Evaluate side-chains
  159 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 142
  time to evaluate  : 1.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   38 HIS
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue   81 GLU
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain C residue   38 HIS
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   81 GLU
Chi-restraints excluded: chain D residue   76 THR
Chi-restraints excluded: chain D residue   81 GLU
Chi-restraints excluded: chain D residue   82 ILE
Chi-restraints excluded: chain E residue   76 THR
Chi-restraints excluded: chain E residue   81 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    6.9990
   chunk 60 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9980
   chunk 71 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 87 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   chunk 82 optimal weight:    0.0870
   chunk 97 optimal weight:    3.9990
   overall best weight:    1.8164

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
B 195 GLN
D 195 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.099092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.080843 restraints weight = 12661.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.2760 rms_B_bonded: 2.70
r_work: 0.2622 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2468 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.3068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   8390  Z= 0.310
  Angle     :  0.532   4.367  11405  Z= 0.298
  Chirality :  0.049   0.177   1235
  Planarity :  0.004   0.038   1450
  Dihedral  :  4.352  20.893   1100
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 12.33 %
    Favored  : 85.33 %
  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: -1.24 (0.26), residues: 1020
  helix:  3.17 (0.68), residues: 55
  sheet: -0.98 (0.26), residues: 395
  loop : -1.06 (0.25), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 162 
 HIS   0.003   0.001   HIS E  38 
 PHE   0.009   0.002   PHE B 109 
 TYR   0.019   0.002   TYR B  54 
 ARG   0.002   0.000   ARG C 118 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 145
  time to evaluate  : 0.906 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8736 (tt0) cc_final: 0.8299 (tt0)
REVERT: A  175 TYR cc_start: 0.8995 (t80) cc_final: 0.8743 (t80)
REVERT: B   38 HIS cc_start: 0.8726 (OUTLIER) cc_final: 0.8332 (t70)
REVERT: B  137 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8330 (mm-40)
REVERT: B  190 LEU cc_start: 0.9243 (tp) cc_final: 0.8874 (mp)
REVERT: D   62 GLU cc_start: 0.9080 (tp30) cc_final: 0.8640 (tp30)
REVERT: D  125 TYR cc_start: 0.8891 (t80) cc_final: 0.8000 (t80)
REVERT: E   49 TYR cc_start: 0.9215 (p90) cc_final: 0.8884 (p90)
REVERT: E  163 ASP cc_start: 0.8392 (p0) cc_final: 0.8131 (p0)
  outliers start: 21
  outliers final: 18
  residues processed: 161
  average time/residue: 0.2050
  time to fit residues: 44.5637
Evaluate side-chains
  158 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   38 HIS
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain B residue   38 HIS
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue   81 GLU
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain C residue   38 HIS
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   81 GLU
Chi-restraints excluded: chain D residue   76 THR
Chi-restraints excluded: chain D residue   81 GLU
Chi-restraints excluded: chain D residue   82 ILE
Chi-restraints excluded: chain E residue   76 THR
Chi-restraints excluded: chain E residue   81 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 4 optimal weight:    0.0970
   chunk 33 optimal weight:    3.9990
   chunk 75 optimal weight:    6.9990
   chunk 52 optimal weight:    0.0370
   chunk 84 optimal weight:    0.1980
   chunk 35 optimal weight:    5.9990
   chunk 80 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.4456

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
D 195 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.101762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.083484 restraints weight = 12583.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.2865 rms_B_bonded: 2.69
r_work: 0.2736 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2588 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.3044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8390  Z= 0.154
  Angle     :  0.491   4.467  11405  Z= 0.273
  Chirality :  0.048   0.179   1235
  Planarity :  0.003   0.030   1450
  Dihedral  :  3.908  15.557   1100
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 13.11 %
    Favored  : 85.11 %
  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: -1.01 (0.26), residues: 1020
  helix:  3.21 (0.68), residues: 55
  sheet: -1.18 (0.27), residues: 335
  loop : -0.68 (0.25), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 162 
 HIS   0.004   0.001   HIS E  38 
 PHE   0.010   0.001   PHE A  33 
 TYR   0.020   0.001   TYR B  54 
 ARG   0.003   0.000   ARG E   6 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 166
  time to evaluate  : 0.995 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8687 (tt0) cc_final: 0.8414 (tt0)
REVERT: A  175 TYR cc_start: 0.8947 (t80) cc_final: 0.8655 (t80)
REVERT: B  137 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8100 (mm-40)
REVERT: B  190 LEU cc_start: 0.9266 (tp) cc_final: 0.8935 (mp)
REVERT: C  175 TYR cc_start: 0.8987 (t80) cc_final: 0.8677 (t80)
REVERT: D   62 GLU cc_start: 0.8939 (tp30) cc_final: 0.8527 (tp30)
REVERT: D  125 TYR cc_start: 0.8866 (t80) cc_final: 0.7992 (t80)
REVERT: E   83 LEU cc_start: 0.9300 (mm) cc_final: 0.8967 (mm)
REVERT: E  163 ASP cc_start: 0.8295 (p0) cc_final: 0.8024 (p0)
  outliers start: 16
  outliers final: 13
  residues processed: 177
  average time/residue: 0.2946
  time to fit residues: 69.6021
Evaluate side-chains
  155 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 142
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 HIS
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain B residue   81 GLU
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   81 GLU
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain D residue   76 THR
Chi-restraints excluded: chain D residue   81 GLU
Chi-restraints excluded: chain E residue   76 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 89 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 79 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0370
   chunk 64 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 20 optimal weight:    6.9990
   overall best weight:    1.5464

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

Flipped N/Q/H residues before XYZ refinement:
B  59 GLN
B 195 GLN
D 195 GLN
** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.100284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.081895 restraints weight = 12835.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.2838 rms_B_bonded: 2.69
r_work: 0.2711 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2562 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.3158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8390  Z= 0.275
  Angle     :  0.532   4.941  11405  Z= 0.297
  Chirality :  0.049   0.180   1235
  Planarity :  0.004   0.031   1450
  Dihedral  :  4.126  17.844   1100
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.44 %
    Favored  : 84.67 %
  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: -1.01 (0.27), residues: 1020
  helix:  3.22 (0.67), residues: 55
  sheet: -0.87 (0.27), residues: 395
  loop : -0.86 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 162 
 HIS   0.003   0.001   HIS D  38 
 PHE   0.009   0.001   PHE E  52 
 TYR   0.024   0.002   TYR B  54 
 ARG   0.003   0.000   ARG E   6 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 141
  time to evaluate  : 1.088 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8696 (tt0) cc_final: 0.8423 (tt0)
REVERT: A  175 TYR cc_start: 0.8985 (t80) cc_final: 0.8684 (t80)
REVERT: A  190 LEU cc_start: 0.9281 (tp) cc_final: 0.8886 (mp)
REVERT: B  137 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8224 (mm-40)
REVERT: B  190 LEU cc_start: 0.9276 (tp) cc_final: 0.8951 (mp)
REVERT: D   62 GLU cc_start: 0.9019 (tp30) cc_final: 0.8569 (tp30)
REVERT: D  125 TYR cc_start: 0.8888 (t80) cc_final: 0.7957 (t80)
REVERT: E  163 ASP cc_start: 0.8352 (p0) cc_final: 0.8091 (p0)
  outliers start: 17
  outliers final: 17
  residues processed: 153
  average time/residue: 0.2168
  time to fit residues: 44.7135
Evaluate side-chains
  156 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 139
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 HIS
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue   81 GLU
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   81 GLU
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  130 GLU
Chi-restraints excluded: chain D residue   38 HIS
Chi-restraints excluded: chain D residue   76 THR
Chi-restraints excluded: chain D residue   81 GLU
Chi-restraints excluded: chain E residue   76 THR
Chi-restraints excluded: chain E residue   81 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 12 optimal weight:    6.9990
   chunk 18 optimal weight:    0.0980
   chunk 88 optimal weight:    0.0030
   chunk 5 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9990
   chunk 73 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 84 optimal weight:    3.9990
   overall best weight:    0.9794

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

Flipped N/Q/H residues before XYZ refinement:
** E 139 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 = 0.3131 r_free = 0.3131 target = 0.101319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.082038 restraints weight = 12920.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.2829 rms_B_bonded: 2.83
r_work: 0.2696 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.3141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8390  Z= 0.209
  Angle     :  0.510   4.429  11405  Z= 0.285
  Chirality :  0.049   0.178   1235
  Planarity :  0.003   0.030   1450
  Dihedral  :  4.015  16.277   1100
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 13.11 %
    Favored  : 84.89 %
  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: -0.98 (0.27), residues: 1020
  helix:  3.25 (0.68), residues: 55
  sheet: -0.87 (0.27), residues: 395
  loop : -0.82 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 162 
 HIS   0.003   0.001   HIS E  38 
 PHE   0.008   0.001   PHE E  52 
 TYR   0.022   0.001   TYR B  54 
 ARG   0.003   0.000   ARG C   6 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 153
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLU cc_start: 0.8765 (mp0) cc_final: 0.8172 (mp0)
REVERT: A  101 GLU cc_start: 0.8522 (tt0) cc_final: 0.8239 (tt0)
REVERT: A  175 TYR cc_start: 0.8935 (t80) cc_final: 0.8640 (t80)
REVERT: B  137 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8050 (mm-40)
REVERT: B  190 LEU cc_start: 0.9227 (tp) cc_final: 0.8892 (mp)
REVERT: D   62 GLU cc_start: 0.8817 (tp30) cc_final: 0.8377 (tp30)
REVERT: D  125 TYR cc_start: 0.8817 (t80) cc_final: 0.7937 (t80)
REVERT: E   83 LEU cc_start: 0.9195 (mm) cc_final: 0.8968 (mm)
REVERT: E  163 ASP cc_start: 0.8210 (p0) cc_final: 0.7964 (p0)
  outliers start: 18
  outliers final: 17
  residues processed: 166
  average time/residue: 0.2132
  time to fit residues: 47.8423
Evaluate side-chains
  162 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 145
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 HIS
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue   81 GLU
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain C residue   38 HIS
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   81 GLU
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  130 GLU
Chi-restraints excluded: chain D residue   76 THR
Chi-restraints excluded: chain D residue   81 GLU
Chi-restraints excluded: chain E residue   76 THR
Chi-restraints excluded: chain E residue   81 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 60 optimal weight:    6.9990
   chunk 93 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 64 optimal weight:    4.9990
   chunk 54 optimal weight:    7.9990
   chunk 0 optimal weight:    6.9990
   chunk 72 optimal weight:    8.9990
   chunk 66 optimal weight:    4.9990
   chunk 82 optimal weight:    0.5980
   chunk 45 optimal weight:    4.9990
   chunk 95 optimal weight:    3.9990
   overall best weight:    3.7188

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

Flipped N/Q/H residues before XYZ refinement:
B 195 GLN
D 195 GLN
** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.096703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.078095 restraints weight = 12788.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.2756 rms_B_bonded: 2.68
r_work: 0.2624 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2473 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8641
moved from start:          0.3328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.051   8390  Z= 0.578
  Angle     :  0.648   5.005  11405  Z= 0.360
  Chirality :  0.054   0.195   1235
  Planarity :  0.004   0.031   1450
  Dihedral  :  4.807  24.008   1100
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.44 %
    Favored  : 84.67 %
  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: -1.35 (0.26), residues: 1020
  helix:  3.12 (0.66), residues: 55
  sheet: -0.56 (0.25), residues: 465
  loop : -1.68 (0.25), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 162 
 HIS   0.006   0.002   HIS D  38 
 PHE   0.010   0.002   PHE E  52 
 TYR   0.025   0.003   TYR B  54 
 ARG   0.003   0.001   ARG C 118 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 138
  time to evaluate  : 0.786 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8768 (tt0) cc_final: 0.8490 (tt0)
REVERT: A  175 TYR cc_start: 0.9064 (t80) cc_final: 0.8760 (t80)
REVERT: B  137 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8386 (mm-40)
REVERT: D   62 GLU cc_start: 0.9161 (tp30) cc_final: 0.8866 (tp30)
REVERT: E  163 ASP cc_start: 0.8473 (p0) cc_final: 0.8195 (p0)
  outliers start: 17
  outliers final: 16
  residues processed: 150
  average time/residue: 0.2188
  time to fit residues: 44.2378
Evaluate side-chains
  155 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 139
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 HIS
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue   81 GLU
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain C residue   38 HIS
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   81 GLU
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  130 GLU
Chi-restraints excluded: chain D residue   76 THR
Chi-restraints excluded: chain D residue   81 GLU
Chi-restraints excluded: chain E residue   76 THR
Chi-restraints excluded: chain E residue   81 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 94 optimal weight:    0.3980
   chunk 75 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9980
   chunk 64 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 76 optimal weight:    0.7980
   chunk 91 optimal weight:    0.2980
   chunk 5 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 195 GLN
D 195 GLN
** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.100559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.081566 restraints weight = 12797.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.2751 rms_B_bonded: 2.78
r_work: 0.2618 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2469 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.3241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8390  Z= 0.195
  Angle     :  0.539   4.899  11405  Z= 0.301
  Chirality :  0.049   0.181   1235
  Planarity :  0.003   0.032   1450
  Dihedral  :  4.232  19.184   1100
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 13.67 %
    Favored  : 84.33 %
  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: -1.11 (0.27), residues: 1020
  helix:  3.34 (0.68), residues: 55
  sheet: -0.74 (0.26), residues: 430
  loop : -1.11 (0.26), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 162 
 HIS   0.003   0.001   HIS E  38 
 PHE   0.010   0.001   PHE A  33 
 TYR   0.021   0.001   TYR B  54 
 ARG   0.004   0.000   ARG C   6 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3823.11 seconds
wall clock time: 68 minutes 39.02 seconds (4119.02 seconds total)