Starting phenix.real_space_refine
on Fri Aug 22 21:51:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wv4_37864/08_2025/8wv4_37864.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wv4_37864/08_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_37864/08_2025/8wv4_37864.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wv4_37864/08_2025/8wv4_37864.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wv4_37864/08_2025/8wv4_37864.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wv4_37864/08_2025/8wv4_37864.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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:
    B, C, D, E
  Time building chain proxies: 1.25, per 1000 atoms: 0.15
  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 B  36 " - pdb=" SG  CYS B  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  36 " - pdb=" SG  CYS C  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  36 " - pdb=" SG  CYS D  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  36 " - pdb=" SG  CYS E  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: 0.65
  Conformation dependent library (CDL) restraints added in 446.4 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.28
  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: 1.26

  Time building geometry restraints manager: 0.87 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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:             1.560
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.900
  Find NCS groups from input model:        0.070
  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:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.860
-------------------------------------------------------------------------------
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   8395  Z= 0.112
  Angle     :  0.491   5.980  11415  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.008   0.001   ARG A 118 
 TYR   0.009   0.001   TYR A  54 
 PHE   0.009   0.001   PHE B 109 
 TRP   0.003   0.000   TRP D 110 
 HIS   0.002   0.001   HIS D  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 8390)
  covalent geometry    : angle       0.49079 (11405)
  SS BOND              : bond        0.00039 (    5)
  SS BOND              : angle       0.02738 (   10)
  hydrogen bonds       : bond        0.28617 (  290)
  hydrogen bonds       : angle       8.32903 (  735)

*********************** 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  : 0.263 
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: 0.0826
  time to fit residues: 27.5614
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  : 0.298 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0570
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    1.6104

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  59 GLN
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3149 r_free = 0.3149 target = 0.102068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.082560 restraints weight = 12667.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.2803 rms_B_bonded: 2.81
r_work: 0.2661 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   8395  Z= 0.189
  Angle     :  0.545   4.093  11415  Z= 0.305
  Chirality :  0.050   0.169   1235
  Planarity :  0.004   0.033   1450
  Dihedral  :  4.544  33.718   1108
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 10.44 %
    Favored  : 88.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.82 (0.24), residues: 1020
  helix:  2.71 (0.68), residues: 55
  sheet: -0.90 (0.27), residues: 335
  loop : -1.82 (0.22), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 118 
 TYR   0.017   0.002   TYR B  54 
 PHE   0.010   0.002   PHE E 109 
 TRP   0.008   0.001   TRP A 205 
 HIS   0.007   0.002   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 8390)
  covalent geometry    : angle       0.54487 (11405)
  SS BOND              : bond        0.00168 (    5)
  SS BOND              : angle       0.48438 (   10)
  hydrogen bonds       : bond        0.05010 (  290)
  hydrogen bonds       : angle       5.66777 (  735)

*********************** 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
  173 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 167
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8703 (tt0) cc_final: 0.8465 (tt0)
REVERT: A  172 ASN cc_start: 0.8579 (t0) cc_final: 0.8358 (t0)
REVERT: A  175 TYR cc_start: 0.8959 (t80) cc_final: 0.8650 (t80)
REVERT: B   59 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7760 (tp-100)
REVERT: B  137 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8144 (mm-40)
REVERT: C   16 ASP cc_start: 0.8603 (p0) cc_final: 0.8368 (p0)
REVERT: C  137 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8252 (mm110)
REVERT: D   16 ASP cc_start: 0.8516 (p0) cc_final: 0.8283 (p0)
REVERT: D   62 GLU cc_start: 0.8658 (tp30) cc_final: 0.7918 (tp30)
REVERT: D  125 TYR cc_start: 0.8853 (t80) cc_final: 0.8041 (t80)
REVERT: D  137 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8289 (mm-40)
REVERT: E  137 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8220 (mm-40)
REVERT: E  163 ASP cc_start: 0.8250 (p0) cc_final: 0.8046 (p0)
REVERT: E  172 ASN cc_start: 0.8698 (t0) cc_final: 0.8490 (t0)
  outliers start: 6
  outliers final: 2
  residues processed: 172
  average time/residue: 0.0694
  time to fit residues: 16.2141
Evaluate side-chains
  143 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 140
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 GLN
Chi-restraints excluded: chain B residue  139 GLN
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 29 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 24 optimal weight:    0.2980
   chunk 81 optimal weight:    0.5980
   chunk 65 optimal weight:    5.9990
   chunk 97 optimal weight:    0.7980
   chunk 7 optimal weight:    0.1980
   chunk 86 optimal weight:    6.9990
   chunk 48 optimal weight:    0.6980
   chunk 32 optimal weight:    5.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 139 GLN
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 = 0.3174 r_free = 0.3174 target = 0.103796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.084495 restraints weight = 12660.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.2848 rms_B_bonded: 2.83
r_work: 0.2710 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8395  Z= 0.099
  Angle     :  0.486   4.041  11415  Z= 0.269
  Chirality :  0.048   0.165   1235
  Planarity :  0.003   0.028   1450
  Dihedral  :  3.844  13.658   1100
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 10.44 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.33 (0.26), residues: 1020
  helix:  3.00 (0.68), residues: 55
  sheet: -0.67 (0.32), residues: 280
  loop : -1.37 (0.22), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C   6 
 TYR   0.015   0.001   TYR B  54 
 PHE   0.014   0.001   PHE A 180 
 TRP   0.006   0.001   TRP C 162 
 HIS   0.003   0.001   HIS E  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 8390)
  covalent geometry    : angle       0.48631 (11405)
  SS BOND              : bond        0.00248 (    5)
  SS BOND              : angle       0.61716 (   10)
  hydrogen bonds       : bond        0.04256 (  290)
  hydrogen bonds       : angle       5.30419 (  735)

*********************** 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
  182 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 167
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8634 (tt0) cc_final: 0.8284 (tt0)
REVERT: A  172 ASN cc_start: 0.8586 (t0) cc_final: 0.8376 (t0)
REVERT: A  175 TYR cc_start: 0.8880 (t80) cc_final: 0.8570 (t80)
REVERT: B   28 LYS cc_start: 0.8284 (tptt) cc_final: 0.7947 (tppt)
REVERT: C   16 ASP cc_start: 0.8559 (p0) cc_final: 0.8341 (p0)
REVERT: C  137 GLN cc_start: 0.8332 (mm-40) cc_final: 0.7881 (mm-40)
REVERT: C  186 ASN cc_start: 0.8834 (t0) cc_final: 0.8360 (t0)
REVERT: D   16 ASP cc_start: 0.8443 (p0) cc_final: 0.8036 (p0)
REVERT: D   62 GLU cc_start: 0.8577 (tp30) cc_final: 0.8044 (tp30)
REVERT: D  125 TYR cc_start: 0.8827 (t80) cc_final: 0.7908 (t80)
REVERT: D  137 GLN cc_start: 0.8437 (mm-40) cc_final: 0.8151 (mm-40)
REVERT: E  137 GLN cc_start: 0.8398 (mm-40) cc_final: 0.8186 (mm-40)
REVERT: E  163 ASP cc_start: 0.8109 (p0) cc_final: 0.7875 (p0)
REVERT: E  172 ASN cc_start: 0.8677 (t0) cc_final: 0.8468 (t0)
  outliers start: 15
  outliers final: 10
  residues processed: 179
  average time/residue: 0.0806
  time to fit residues: 19.5345
Evaluate side-chains
  155 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 145
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
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   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 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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 7 optimal weight:    6.9990
   chunk 99 optimal weight:    7.9990
   chunk 40 optimal weight:    6.9990
   chunk 41 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0570
   chunk 97 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 21 optimal weight:    6.9990
   overall best weight:    1.3704

-------------------------------------------------------------------------------
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 195 GLN
D 195 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.100770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.081575 restraints weight = 12869.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.2797 rms_B_bonded: 2.80
r_work: 0.2660 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.2660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.2714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8395  Z= 0.160
  Angle     :  0.513   4.369  11415  Z= 0.284
  Chirality :  0.049   0.195   1235
  Planarity :  0.004   0.029   1450
  Dihedral  :  4.041  18.829   1100
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 11.33 %
    Favored  : 86.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.07 (0.26), residues: 1020
  helix:  3.05 (0.68), residues: 55
  sheet: -0.63 (0.32), residues: 280
  loop : -1.09 (0.23), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E   6 
 TYR   0.017   0.002   TYR B  54 
 PHE   0.013   0.002   PHE A 180 
 TRP   0.006   0.001   TRP C 162 
 HIS   0.003   0.001   HIS D  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 8390)
  covalent geometry    : angle       0.51221 (11405)
  SS BOND              : bond        0.00445 (    5)
  SS BOND              : angle       0.78521 (   10)
  hydrogen bonds       : bond        0.04483 (  290)
  hydrogen bonds       : angle       5.17837 (  735)

*********************** 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
  164 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 147
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8640 (tt0) cc_final: 0.8196 (tt0)
REVERT: A  172 ASN cc_start: 0.8581 (t0) cc_final: 0.8369 (t0)
REVERT: A  175 TYR cc_start: 0.8951 (t80) cc_final: 0.8614 (t80)
REVERT: A  190 LEU cc_start: 0.9190 (tp) cc_final: 0.8843 (mp)
REVERT: B  137 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8052 (mm-40)
REVERT: D   16 ASP cc_start: 0.8506 (p0) cc_final: 0.8249 (p0)
REVERT: D   62 GLU cc_start: 0.8754 (tp30) cc_final: 0.8127 (tp30)
REVERT: D  125 TYR cc_start: 0.8836 (t80) cc_final: 0.8002 (t80)
REVERT: D  163 ASP cc_start: 0.8183 (p0) cc_final: 0.7977 (p0)
REVERT: E  163 ASP cc_start: 0.8183 (p0) cc_final: 0.7961 (p0)
REVERT: E  172 ASN cc_start: 0.8692 (t0) cc_final: 0.8484 (t0)
REVERT: E  186 ASN cc_start: 0.8936 (t0) cc_final: 0.8717 (t0)
  outliers start: 17
  outliers final: 13
  residues processed: 160
  average time/residue: 0.0833
  time to fit residues: 18.1180
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  : 0.304 
-------------------------------------------------------------------------------
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  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
Chi-restraints excluded: chain E residue   81 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 99 optimal weight:    6.9990
   chunk 46 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 84 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   chunk 25 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
B 150 GLN
B 195 GLN
C 137 GLN
D 195 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.098058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.079633 restraints weight = 12930.117|
|-----------------------------------------------------------------------------|
r_work (start): 0.2786 rms_B_bonded: 2.69
r_work: 0.2658 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2509 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
moved from start:          0.2943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   8395  Z= 0.231
  Angle     :  0.549   4.332  11415  Z= 0.305
  Chirality :  0.050   0.219   1235
  Planarity :  0.004   0.031   1450
  Dihedral  :  4.440  22.928   1100
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 12.33 %
    Favored  : 85.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.08 (0.26), residues: 1020
  helix:  3.12 (0.67), residues: 55
  sheet: -0.69 (0.32), residues: 280
  loop : -1.08 (0.22), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 118 
 TYR   0.019   0.002   TYR B  54 
 PHE   0.011   0.002   PHE A 180 
 TRP   0.007   0.001   TRP C 162 
 HIS   0.004   0.001   HIS D  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00558 ( 8390)
  covalent geometry    : angle       0.54883 (11405)
  SS BOND              : bond        0.00209 (    5)
  SS BOND              : angle       1.06299 (   10)
  hydrogen bonds       : bond        0.04717 (  290)
  hydrogen bonds       : angle       5.23487 (  735)

*********************** 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
  166 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 149
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8765 (tt0) cc_final: 0.8519 (tt0)
REVERT: A  172 ASN cc_start: 0.8708 (t0) cc_final: 0.8499 (t0)
REVERT: A  175 TYR cc_start: 0.9037 (t80) cc_final: 0.8701 (t80)
REVERT: A  190 LEU cc_start: 0.9297 (tp) cc_final: 0.8868 (mp)
REVERT: B  137 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8336 (mm-40)
REVERT: B  190 LEU cc_start: 0.9252 (tp) cc_final: 0.8919 (mp)
REVERT: D   62 GLU cc_start: 0.9081 (tp30) cc_final: 0.8606 (tp30)
REVERT: D  125 TYR cc_start: 0.8907 (t80) cc_final: 0.8087 (t80)
REVERT: D  190 LEU cc_start: 0.9216 (tp) cc_final: 0.8951 (mp)
REVERT: E  163 ASP cc_start: 0.8365 (p0) cc_final: 0.8054 (p0)
  outliers start: 17
  outliers final: 16
  residues processed: 161
  average time/residue: 0.1014
  time to fit residues: 21.9986
Evaluate side-chains
  163 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 147
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
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 B residue  169 ASP
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   81 GLU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 54 optimal weight:    0.0470
   chunk 10 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   chunk 44 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9980
   chunk 2 optimal weight:    0.0980
   chunk 17 optimal weight:    0.8980
   chunk 6 optimal weight:    5.9990
   chunk 94 optimal weight:    0.9980
   chunk 34 optimal weight:    8.9990
   chunk 52 optimal weight:    6.9990
   overall best weight:    0.5478

-------------------------------------------------------------------------------
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
** 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 = 0.3133 r_free = 0.3133 target = 0.101259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.082674 restraints weight = 12641.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.2837 rms_B_bonded: 2.75
r_work: 0.2706 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.2706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.3001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8395  Z= 0.100
  Angle     :  0.490   4.271  11415  Z= 0.272
  Chirality :  0.048   0.170   1235
  Planarity :  0.004   0.052   1450
  Dihedral  :  3.964  17.424   1100
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.00 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.94 (0.26), residues: 1020
  helix:  3.24 (0.68), residues: 55
  sheet: -1.05 (0.29), residues: 305
  loop : -0.72 (0.24), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E   6 
 TYR   0.018   0.001   TYR B  54 
 PHE   0.011   0.001   PHE A 180 
 TRP   0.007   0.001   TRP E 162 
 HIS   0.003   0.001   HIS E  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 8390)
  covalent geometry    : angle       0.48955 (11405)
  SS BOND              : bond        0.00162 (    5)
  SS BOND              : angle       0.95999 (   10)
  hydrogen bonds       : bond        0.03805 (  290)
  hydrogen bonds       : angle       5.08365 (  735)

*********************** 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
  176 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 159
  time to evaluate  : 0.345 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8556 (tt0) cc_final: 0.8297 (tt0)
REVERT: A  172 ASN cc_start: 0.8627 (t0) cc_final: 0.8427 (t0)
REVERT: A  175 TYR cc_start: 0.8926 (t80) cc_final: 0.8653 (t80)
REVERT: A  190 LEU cc_start: 0.9245 (tp) cc_final: 0.8815 (mp)
REVERT: B  137 GLN cc_start: 0.8454 (mm-40) cc_final: 0.8103 (mm-40)
REVERT: B  190 LEU cc_start: 0.9223 (tp) cc_final: 0.8934 (mp)
REVERT: C  175 TYR cc_start: 0.8939 (t80) cc_final: 0.8649 (t80)
REVERT: D   62 GLU cc_start: 0.8811 (tp30) cc_final: 0.8313 (tp30)
REVERT: D  125 TYR cc_start: 0.8791 (t80) cc_final: 0.7862 (t80)
REVERT: D  163 ASP cc_start: 0.8263 (p0) cc_final: 0.8055 (p0)
REVERT: E   83 LEU cc_start: 0.9269 (mm) cc_final: 0.8945 (mm)
REVERT: E  163 ASP cc_start: 0.8130 (p0) cc_final: 0.7886 (p0)
  outliers start: 17
  outliers final: 13
  residues processed: 170
  average time/residue: 0.0934
  time to fit residues: 21.7877
Evaluate side-chains
  164 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 151
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
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   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
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 77 optimal weight:    0.0770
   chunk 75 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9980
   chunk 64 optimal weight:    3.9990
   chunk 20 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9980
   chunk 5 optimal weight:    6.9990
   chunk 59 optimal weight:    5.9990
   chunk 98 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 71 optimal weight:    0.7980
   overall best weight:    1.3740

-------------------------------------------------------------------------------
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 = 0.3127 r_free = 0.3127 target = 0.100789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.082310 restraints weight = 12872.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.2815 rms_B_bonded: 2.73
r_work: 0.2686 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2539 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.3023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8395  Z= 0.160
  Angle     :  0.521   4.471  11415  Z= 0.289
  Chirality :  0.049   0.177   1235
  Planarity :  0.004   0.037   1450
  Dihedral  :  4.084  18.267   1100
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 13.56 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.01 (0.27), residues: 1020
  helix:  3.24 (0.67), residues: 55
  sheet: -0.86 (0.27), residues: 395
  loop : -0.86 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E   6 
 TYR   0.022   0.002   TYR B  54 
 PHE   0.010   0.001   PHE A 180 
 TRP   0.006   0.001   TRP C 162 
 HIS   0.003   0.001   HIS D  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 8390)
  covalent geometry    : angle       0.52028 (11405)
  SS BOND              : bond        0.00249 (    5)
  SS BOND              : angle       1.11472 (   10)
  hydrogen bonds       : bond        0.04211 (  290)
  hydrogen bonds       : angle       5.06986 (  735)

*********************** 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
  163 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 145
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8715 (tt0) cc_final: 0.8454 (tt0)
REVERT: A  175 TYR cc_start: 0.8983 (t80) cc_final: 0.8627 (t80)
REVERT: A  190 LEU cc_start: 0.9266 (tp) cc_final: 0.8814 (mp)
REVERT: B  137 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8206 (mm-40)
REVERT: B  190 LEU cc_start: 0.9264 (tp) cc_final: 0.8939 (mp)
REVERT: C  175 TYR cc_start: 0.8985 (t80) cc_final: 0.8705 (t80)
REVERT: D   62 GLU cc_start: 0.8995 (tp30) cc_final: 0.8508 (tp30)
REVERT: D  125 TYR cc_start: 0.8870 (t80) cc_final: 0.7959 (t80)
REVERT: E   83 LEU cc_start: 0.9249 (mm) cc_final: 0.8971 (mm)
REVERT: E  163 ASP cc_start: 0.8301 (p0) cc_final: 0.8037 (p0)
  outliers start: 18
  outliers final: 16
  residues processed: 157
  average time/residue: 0.0916
  time to fit residues: 19.6854
Evaluate side-chains
  159 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 143
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
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   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  130 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 64 optimal weight:    0.5980
   chunk 53 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 88 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 92 optimal weight:    0.4980
   chunk 25 optimal weight:    6.9990
   overall best weight:    0.7180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.102249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.083094 restraints weight = 12772.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.2770 rms_B_bonded: 2.82
r_work: 0.2638 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.2638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.3107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8395  Z= 0.111
  Angle     :  0.498   4.492  11415  Z= 0.276
  Chirality :  0.048   0.176   1235
  Planarity :  0.003   0.032   1450
  Dihedral  :  3.904  15.850   1100
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 14.11 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.83 (0.27), residues: 1020
  helix:  3.25 (0.67), residues: 55
  sheet: -0.69 (0.28), residues: 365
  loop : -0.79 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C   6 
 TYR   0.021   0.001   TYR B  54 
 PHE   0.010   0.001   PHE A 180 
 TRP   0.006   0.001   TRP C 162 
 HIS   0.003   0.001   HIS E  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 8390)
  covalent geometry    : angle       0.49700 (11405)
  SS BOND              : bond        0.00382 (    5)
  SS BOND              : angle       1.08650 (   10)
  hydrogen bonds       : bond        0.03833 (  290)
  hydrogen bonds       : angle       5.02250 (  735)

*********************** 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
  162 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 147
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8561 (tt0) cc_final: 0.8268 (tt0)
REVERT: A  175 TYR cc_start: 0.8887 (t80) cc_final: 0.8577 (t80)
REVERT: A  190 LEU cc_start: 0.9213 (tp) cc_final: 0.8785 (mp)
REVERT: B  137 GLN cc_start: 0.8469 (mm-40) cc_final: 0.7997 (mm-40)
REVERT: B  190 LEU cc_start: 0.9216 (tp) cc_final: 0.8905 (mp)
REVERT: C  175 TYR cc_start: 0.8898 (t80) cc_final: 0.8617 (t80)
REVERT: D   62 GLU cc_start: 0.8817 (tp30) cc_final: 0.8355 (tp30)
REVERT: D  125 TYR cc_start: 0.8804 (t80) cc_final: 0.7901 (t80)
REVERT: E   83 LEU cc_start: 0.9209 (mm) cc_final: 0.8946 (mm)
REVERT: E  163 ASP cc_start: 0.8147 (p0) cc_final: 0.7897 (p0)
  outliers start: 15
  outliers final: 15
  residues processed: 157
  average time/residue: 0.0935
  time to fit residues: 19.7413
Evaluate side-chains
  159 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 144
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
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   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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 74 optimal weight:    7.9990
   chunk 13 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 86 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 97 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
B 195 GLN
** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3075 r_free = 0.3075 target = 0.097391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.078890 restraints weight = 12894.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.2787 rms_B_bonded: 2.71
r_work: 0.2658 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2510 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.3185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.045   8395  Z= 0.285
  Angle     :  0.591   4.453  11415  Z= 0.327
  Chirality :  0.051   0.186   1235
  Planarity :  0.004   0.032   1450
  Dihedral  :  4.546  21.182   1100
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 14.33 %
    Favored  : 83.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.12 (0.26), residues: 1020
  helix:  3.23 (0.66), residues: 55
  sheet: -0.93 (0.26), residues: 395
  loop : -0.95 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 118 
 TYR   0.027   0.002   TYR B 125 
 PHE   0.009   0.002   PHE A 180 
 TRP   0.007   0.001   TRP B 162 
 HIS   0.005   0.002   HIS D  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00688 ( 8390)
  covalent geometry    : angle       0.58972 (11405)
  SS BOND              : bond        0.00607 (    5)
  SS BOND              : angle       1.50486 (   10)
  hydrogen bonds       : bond        0.04768 (  290)
  hydrogen bonds       : angle       5.21069 (  735)

*********************** 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
  155 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 139
  time to evaluate  : 0.352 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8765 (tt0) cc_final: 0.8472 (tt0)
REVERT: A  175 TYR cc_start: 0.9030 (t80) cc_final: 0.8724 (t80)
REVERT: A  190 LEU cc_start: 0.9260 (tp) cc_final: 0.8792 (mp)
REVERT: B  137 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8311 (mm-40)
REVERT: D   62 GLU cc_start: 0.9118 (tp30) cc_final: 0.8797 (tp30)
REVERT: E  163 ASP cc_start: 0.8394 (p0) cc_final: 0.8085 (p0)
  outliers start: 16
  outliers final: 15
  residues processed: 150
  average time/residue: 0.1039
  time to fit residues: 20.8155
Evaluate side-chains
  153 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 138
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
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   81 GLU
Chi-restraints excluded: chain A residue  198 VAL
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   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 14 optimal weight:    0.0000
   chunk 62 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 85 optimal weight:    4.9990
   chunk 56 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0070
   chunk 35 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.5406

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.102438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.083336 restraints weight = 12682.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.2867 rms_B_bonded: 2.81
r_work: 0.2732 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.3187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8395  Z= 0.105
  Angle     :  0.509   4.848  11415  Z= 0.283
  Chirality :  0.048   0.177   1235
  Planarity :  0.003   0.030   1450
  Dihedral  :  4.012  16.348   1100
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 14.89 %
    Favored  : 83.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.96 (0.27), residues: 1020
  helix:  3.32 (0.68), residues: 55
  sheet: -0.83 (0.27), residues: 395
  loop : -0.83 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E   6 
 TYR   0.021   0.001   TYR B  54 
 PHE   0.010   0.001   PHE E  33 
 TRP   0.007   0.001   TRP D 162 
 HIS   0.003   0.001   HIS E  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 8390)
  covalent geometry    : angle       0.50814 (11405)
  SS BOND              : bond        0.00189 (    5)
  SS BOND              : angle       1.14106 (   10)
  hydrogen bonds       : bond        0.03784 (  290)
  hydrogen bonds       : angle       5.07924 (  735)

********************** 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
  158 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 143
  time to evaluate  : 0.333 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8563 (tt0) cc_final: 0.8285 (tt0)
REVERT: A  175 TYR cc_start: 0.8923 (t80) cc_final: 0.8645 (t80)
REVERT: A  190 LEU cc_start: 0.9234 (tp) cc_final: 0.8825 (mp)
REVERT: B  137 GLN cc_start: 0.8457 (mm-40) cc_final: 0.8038 (mm-40)
REVERT: B  190 LEU cc_start: 0.9243 (tp) cc_final: 0.8927 (mp)
REVERT: C  175 TYR cc_start: 0.8937 (t80) cc_final: 0.8688 (t80)
REVERT: D   62 GLU cc_start: 0.8794 (tp30) cc_final: 0.8320 (tp30)
REVERT: D  125 TYR cc_start: 0.8814 (t80) cc_final: 0.7859 (t80)
REVERT: E   83 LEU cc_start: 0.9223 (mm) cc_final: 0.8987 (mm)
REVERT: E  163 ASP cc_start: 0.8158 (p0) cc_final: 0.7909 (p0)
  outliers start: 15
  outliers final: 14
  residues processed: 153
  average time/residue: 0.0931
  time to fit residues: 19.1224
Evaluate side-chains
  163 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 149
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
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   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
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 41 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 67 optimal weight:    6.9990
   chunk 6 optimal weight:    4.9990
   chunk 81 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 40 optimal weight:    5.9990
   overall best weight:    1.1384

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.101154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.082075 restraints weight = 12822.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.2789 rms_B_bonded: 2.80
r_work: 0.2651 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.2651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.3188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8395  Z= 0.142
  Angle     :  0.522   4.687  11415  Z= 0.289
  Chirality :  0.049   0.185   1235
  Planarity :  0.004   0.030   1450
  Dihedral  :  4.044  16.518   1100
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 15.00 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.93 (0.27), residues: 1020
  helix:  3.32 (0.67), residues: 55
  sheet: -0.81 (0.27), residues: 395
  loop : -0.82 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E   6 
 TYR   0.030   0.002   TYR B  19 
 PHE   0.009   0.001   PHE B 146 
 TRP   0.007   0.001   TRP D 162 
 HIS   0.003   0.001   HIS E  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 8390)
  covalent geometry    : angle       0.52119 (11405)
  SS BOND              : bond        0.00376 (    5)
  SS BOND              : angle       1.24972 (   10)
  hydrogen bonds       : bond        0.04053 (  290)
  hydrogen bonds       : angle       5.03370 (  735)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1655.87 seconds
wall clock time: 29 minutes 9.68 seconds (1749.68 seconds total)