Starting phenix.real_space_refine
on Wed Feb 12 17:11:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wv4_37864/02_2025/8wv4_37864.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wv4_37864/02_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_37864/02_2025/8wv4_37864.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wv4_37864/02_2025/8wv4_37864.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wv4_37864/02_2025/8wv4_37864.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wv4_37864/02_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-5592/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: 3.90, per 1000 atoms: 0.48
  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=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  36 " - pdb=" SG  CYS A  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: 1.96
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 1.18
  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: 2.55

  Time building geometry restraints manager: 2.30 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: 4517
       17.50 -    35.00: 281
       35.00 -    52.49: 35
       52.49 -    69.99: 20
       69.99 -    87.49: 30
  Dihedral angle restraints: 4883
    sinusoidal: 1928
      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 4880 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: 150
        2.53 -     3.12: 5816
        3.12 -     3.72: 12054
        3.72 -     4.31: 17672
        4.31 -     4.90: 30425
  Nonbonded interactions: 66117
  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 66112 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: 0.07
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:             0.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.520
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  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:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.680
-------------------------------------------------------------------------------
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= 0.142
  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  : 0.937 
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: 0.1979
  time to fit residues: 65.6302
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  : 0.873 
-------------------------------------------------------------------------------
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
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3106 r_free = 0.3106 target = 0.099322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.079749 restraints weight = 12791.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.2715 rms_B_bonded: 2.80
r_work: 0.2577 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.2459

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= 0.475
  Angle     :  0.616   4.643  11405  Z= 0.342
  Chirality :  0.052   0.166   1235
  Planarity :  0.005   0.042   1450
  Dihedral  :  5.004  36.753   1108
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  :  9.56 %
    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 (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:  2.67 (0.67), residues: 55
  sheet: -1.09 (0.25), residues: 390
  loop : -1.90 (0.24), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP D 205 
 HIS   0.010   0.002   HIS B  38 
 PHE   0.011   0.002   PHE C 109 
 TYR   0.019   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
  164 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 150
  time to evaluate  : 0.914 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8749 (tt0) cc_final: 0.8371 (tt0)
REVERT: A  172 ASN cc_start: 0.8612 (t0) cc_final: 0.8388 (t0)
REVERT: A  175 TYR cc_start: 0.8992 (t80) cc_final: 0.8718 (t80)
REVERT: B   59 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7839 (tp-100)
REVERT: B  137 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8287 (mm-40)
REVERT: C  190 LEU cc_start: 0.9184 (tp) cc_final: 0.8890 (mp)
REVERT: D   16 ASP cc_start: 0.8613 (p0) cc_final: 0.8404 (p0)
REVERT: D   62 GLU cc_start: 0.8813 (tp30) cc_final: 0.8434 (tp30)
REVERT: D  125 TYR cc_start: 0.8880 (t80) cc_final: 0.7945 (t80)
REVERT: D  137 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8301 (mm-40)
REVERT: D  193 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7624 (tm-30)
REVERT: E   49 TYR cc_start: 0.9160 (p90) cc_final: 0.8875 (p90)
REVERT: E  163 ASP cc_start: 0.8276 (p0) cc_final: 0.8068 (p0)
REVERT: E  172 ASN cc_start: 0.8727 (t0) cc_final: 0.8521 (t0)
  outliers start: 14
  outliers final: 9
  residues processed: 163
  average time/residue: 0.2087
  time to fit residues: 45.9116
Evaluate side-chains
  149 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 138
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
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 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:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 76 optimal weight:    0.5980
   chunk 90 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 94 optimal weight:    0.0370
   chunk 36 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 58 optimal weight:    0.0770
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.3816

-------------------------------------------------------------------------------
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 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 = 0.3157 r_free = 0.3157 target = 0.102716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.083214 restraints weight = 12954.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.2800 rms_B_bonded: 2.88
r_work: 0.2661 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.2540

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= 0.155
  Angle     :  0.504   4.057  11405  Z= 0.282
  Chirality :  0.048   0.166   1235
  Planarity :  0.003   0.029   1450
  Dihedral  :  3.985  16.938   1100
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  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: -1.39 (0.25), residues: 1020
  helix:  3.10 (0.70), residues: 55
  sheet: -0.68 (0.32), residues: 280
  loop : -1.44 (0.22), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 110 
 HIS   0.002   0.001   HIS E  38 
 PHE   0.010   0.001   PHE A 180 
 TYR   0.014   0.001   TYR B  54 
 ARG   0.003   0.000   ARG E   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  : 0.891 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8642 (tt0) cc_final: 0.8255 (tt0)
REVERT: A  172 ASN cc_start: 0.8601 (t0) cc_final: 0.8399 (t0)
REVERT: A  175 TYR cc_start: 0.8913 (t80) cc_final: 0.8628 (t80)
REVERT: A  190 LEU cc_start: 0.9169 (tp) cc_final: 0.8862 (mp)
REVERT: C   62 GLU cc_start: 0.8724 (tp30) cc_final: 0.8496 (tp30)
REVERT: C  175 TYR cc_start: 0.8921 (t80) cc_final: 0.8666 (t80)
REVERT: C  186 ASN cc_start: 0.8917 (t0) cc_final: 0.8358 (t0)
REVERT: C  190 LEU cc_start: 0.9199 (tp) cc_final: 0.8899 (mp)
REVERT: D   16 ASP cc_start: 0.8490 (p0) cc_final: 0.8238 (p0)
REVERT: D   62 GLU cc_start: 0.8646 (tp30) cc_final: 0.8135 (tp30)
REVERT: D  125 TYR cc_start: 0.8845 (t80) cc_final: 0.7952 (t80)
REVERT: E  163 ASP cc_start: 0.8183 (p0) cc_final: 0.7941 (p0)
REVERT: E  180 PHE cc_start: 0.8232 (p90) cc_final: 0.7909 (p90)
  outliers start: 8
  outliers final: 5
  residues processed: 168
  average time/residue: 0.2245
  time to fit residues: 50.6929
Evaluate side-chains
  148 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 143
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain C residue  130 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 46 optimal weight:    7.9990
   chunk 2 optimal weight:    0.3980
   chunk 10 optimal weight:    4.9990
   chunk 90 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 34 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 21 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.6186

-------------------------------------------------------------------------------
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 = 0.3117 r_free = 0.3117 target = 0.100141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.081084 restraints weight = 12914.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.2760 rms_B_bonded: 2.80
r_work: 0.2622 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.2815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8390  Z= 0.294
  Angle     :  0.534   4.190  11405  Z= 0.298
  Chirality :  0.050   0.231   1235
  Planarity :  0.004   0.030   1450
  Dihedral  :  4.178  20.475   1100
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 11.00 %
    Favored  : 87.11 %
  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: -1.14 (0.26), residues: 1020
  helix:  3.11 (0.68), residues: 55
  sheet: -0.61 (0.32), residues: 280
  loop : -1.19 (0.22), residues: 685

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   0.017   0.002   TYR B  54 
 ARG   0.002   0.000   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: 17
    poor density    : 146
  time to evaluate  : 0.978 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8648 (tt0) cc_final: 0.8213 (tt0)
REVERT: A  172 ASN cc_start: 0.8633 (t0) cc_final: 0.8417 (t0)
REVERT: A  175 TYR cc_start: 0.8966 (t80) cc_final: 0.8646 (t80)
REVERT: A  190 LEU cc_start: 0.9225 (tp) cc_final: 0.8831 (mp)
REVERT: B  137 GLN cc_start: 0.8525 (mm-40) cc_final: 0.8115 (mm-40)
REVERT: B  190 LEU cc_start: 0.9185 (tp) cc_final: 0.8910 (mp)
REVERT: C  175 TYR cc_start: 0.8960 (t80) cc_final: 0.8683 (t80)
REVERT: C  190 LEU cc_start: 0.9208 (tp) cc_final: 0.8890 (mp)
REVERT: D   62 GLU cc_start: 0.8808 (tp30) cc_final: 0.8262 (tp30)
REVERT: D  125 TYR cc_start: 0.8840 (t80) cc_final: 0.8048 (t80)
REVERT: D  163 ASP cc_start: 0.8238 (p0) cc_final: 0.8025 (p0)
REVERT: E   49 TYR cc_start: 0.9120 (p90) cc_final: 0.8916 (p90)
REVERT: E  163 ASP cc_start: 0.8221 (p0) cc_final: 0.7992 (p0)
  outliers start: 17
  outliers final: 13
  residues processed: 159
  average time/residue: 0.2152
  time to fit residues: 46.0424
Evaluate side-chains
  158 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 145
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
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 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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 90 optimal weight:    2.9990
   chunk 55 optimal weight:    6.9990
   chunk 58 optimal weight:    4.9990
   chunk 79 optimal weight:    5.9990
   chunk 56 optimal weight:    0.0870
   chunk 47 optimal weight:    0.0570
   chunk 48 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0270
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.2338

-------------------------------------------------------------------------------
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 = 0.3113 r_free = 0.3113 target = 0.099925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.080800 restraints weight = 12827.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.2797 rms_B_bonded: 2.80
r_work: 0.2659 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.2883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8390  Z= 0.235
  Angle     :  0.513   4.198  11405  Z= 0.287
  Chirality :  0.049   0.172   1235
  Planarity :  0.004   0.060   1450
  Dihedral  :  4.089  19.642   1100
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 12.00 %
    Favored  : 86.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.03 (0.26), residues: 1020
  helix:  3.26 (0.69), residues: 55
  sheet: -0.65 (0.28), residues: 355
  loop : -1.07 (0.24), residues: 610

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   0.001   PHE B  33 
 TYR   0.018   0.001   TYR B  54 
 ARG   0.003   0.000   ARG E   6 

*********************** 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
  171 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 155
  time to evaluate  : 0.955 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8618 (tt0) cc_final: 0.8161 (tt0)
REVERT: A  172 ASN cc_start: 0.8608 (t0) cc_final: 0.8402 (t0)
REVERT: A  175 TYR cc_start: 0.8948 (t80) cc_final: 0.8637 (t80)
REVERT: A  190 LEU cc_start: 0.9203 (tp) cc_final: 0.8824 (mp)
REVERT: B  137 GLN cc_start: 0.8510 (mm-40) cc_final: 0.8106 (mm-40)
REVERT: B  190 LEU cc_start: 0.9208 (tp) cc_final: 0.8893 (mp)
REVERT: C  175 TYR cc_start: 0.8960 (t80) cc_final: 0.8689 (t80)
REVERT: C  186 ASN cc_start: 0.8945 (t0) cc_final: 0.8425 (t0)
REVERT: C  190 LEU cc_start: 0.9182 (tp) cc_final: 0.8810 (mp)
REVERT: D   62 GLU cc_start: 0.8871 (tp30) cc_final: 0.8325 (tp30)
REVERT: D  125 TYR cc_start: 0.8827 (t80) cc_final: 0.7999 (t80)
REVERT: D  163 ASP cc_start: 0.8233 (p0) cc_final: 0.8020 (p0)
REVERT: D  190 LEU cc_start: 0.9172 (tp) cc_final: 0.8962 (mp)
REVERT: E  163 ASP cc_start: 0.8207 (p0) cc_final: 0.7961 (p0)
REVERT: E  186 ASN cc_start: 0.8898 (t0) cc_final: 0.8688 (t0)
  outliers start: 16
  outliers final: 14
  residues processed: 166
  average time/residue: 0.2062
  time to fit residues: 46.0464
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  : 0.906 
-------------------------------------------------------------------------------
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  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=3.00
-------------------------------------------------------------------------------
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:    0.0370
   chunk 71 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 87 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   chunk 66 optimal weight:    6.9990
   chunk 82 optimal weight:    0.9980
   chunk 97 optimal weight:    0.8980
   overall best weight:    1.5862

-------------------------------------------------------------------------------
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 = 0.3103 r_free = 0.3103 target = 0.099124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.079938 restraints weight = 12834.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.2779 rms_B_bonded: 2.80
r_work: 0.2640 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.3012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8390  Z= 0.282
  Angle     :  0.525   4.402  11405  Z= 0.294
  Chirality :  0.049   0.177   1235
  Planarity :  0.004   0.049   1450
  Dihedral  :  4.180  19.830   1100
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  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 (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:  3.29 (0.68), residues: 55
  sheet: -0.90 (0.27), residues: 395
  loop : -1.04 (0.25), 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 C  39 
 TYR   0.020   0.002   TYR B  54 
 ARG   0.003   0.000   ARG E   6 

*********************** 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
  167 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 150
  time to evaluate  : 0.913 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8591 (tt0) cc_final: 0.8131 (tt0)
REVERT: A  175 TYR cc_start: 0.8966 (t80) cc_final: 0.8651 (t80)
REVERT: A  190 LEU cc_start: 0.9272 (tp) cc_final: 0.8836 (mp)
REVERT: B  137 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8150 (mm-40)
REVERT: B  190 LEU cc_start: 0.9221 (tp) cc_final: 0.8865 (mp)
REVERT: C  175 TYR cc_start: 0.8964 (t80) cc_final: 0.8689 (t80)
REVERT: C  190 LEU cc_start: 0.9276 (tp) cc_final: 0.8892 (mp)
REVERT: D   62 GLU cc_start: 0.8918 (tp30) cc_final: 0.8385 (tp30)
REVERT: D  125 TYR cc_start: 0.8824 (t80) cc_final: 0.7968 (t80)
REVERT: D  163 ASP cc_start: 0.8207 (p0) cc_final: 0.7971 (p0)
REVERT: D  190 LEU cc_start: 0.9224 (tp) cc_final: 0.8958 (mp)
REVERT: E   85 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8544 (mp0)
REVERT: E  163 ASP cc_start: 0.8217 (p0) cc_final: 0.7974 (p0)
  outliers start: 17
  outliers final: 16
  residues processed: 161
  average time/residue: 0.2207
  time to fit residues: 47.5220
Evaluate side-chains
  161 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 145
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
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  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   36 CYS
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 67 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 75 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0040
   chunk 84 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 80 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   chunk 87 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    1.9798

-------------------------------------------------------------------------------
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 = 0.3088 r_free = 0.3088 target = 0.098118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.079049 restraints weight = 12939.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.2734 rms_B_bonded: 2.79
r_work: 0.2595 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.3100

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= 0.336
  Angle     :  0.546   4.404  11405  Z= 0.306
  Chirality :  0.050   0.179   1235
  Planarity :  0.004   0.043   1450
  Dihedral  :  4.336  20.844   1100
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 12.56 %
    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: -1.18 (0.26), residues: 1020
  helix:  3.32 (0.68), residues: 55
  sheet: -0.92 (0.27), residues: 395
  loop : -1.06 (0.25), 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   0.010   0.002   PHE E 199 
 TYR   0.020   0.002   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
  165 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 144
  time to evaluate  : 0.977 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8607 (tt0) cc_final: 0.8140 (tt0)
REVERT: A  175 TYR cc_start: 0.8972 (t80) cc_final: 0.8703 (t80)
REVERT: A  190 LEU cc_start: 0.9246 (tp) cc_final: 0.8845 (mp)
REVERT: B  137 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8198 (mm-40)
REVERT: B  190 LEU cc_start: 0.9226 (tp) cc_final: 0.8876 (mp)
REVERT: C  175 TYR cc_start: 0.8972 (t80) cc_final: 0.8701 (t80)
REVERT: D   62 GLU cc_start: 0.8965 (tp30) cc_final: 0.8481 (tp30)
REVERT: D  125 TYR cc_start: 0.8853 (t80) cc_final: 0.7980 (t80)
REVERT: D  190 LEU cc_start: 0.9221 (tp) cc_final: 0.8929 (mp)
REVERT: E  163 ASP cc_start: 0.8231 (p0) cc_final: 0.7992 (p0)
  outliers start: 21
  outliers final: 19
  residues processed: 158
  average time/residue: 0.2080
  time to fit residues: 44.4215
Evaluate side-chains
  162 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
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  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   36 CYS
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 58 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 89 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 79 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9980
   chunk 56 optimal weight:    0.7980
   chunk 20 optimal weight:    6.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
C  38 HIS
D 195 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.098807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.079697 restraints weight = 13104.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.2775 rms_B_bonded: 2.81
r_work: 0.2637 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.3142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8390  Z= 0.282
  Angle     :  0.537   4.348  11405  Z= 0.301
  Chirality :  0.049   0.180   1235
  Planarity :  0.004   0.038   1450
  Dihedral  :  4.251  19.875   1100
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.22 %
    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: -1.15 (0.26), residues: 1020
  helix:  3.38 (0.68), residues: 55
  sheet: -0.92 (0.27), residues: 395
  loop : -1.02 (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 C  38 
 PHE   0.009   0.001   PHE E  52 
 TYR   0.020   0.002   TYR B  54 
 ARG   0.003   0.000   ARG C   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
  166 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 149
  time to evaluate  : 0.985 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8587 (tt0) cc_final: 0.8115 (tt0)
REVERT: A  175 TYR cc_start: 0.8970 (t80) cc_final: 0.8703 (t80)
REVERT: B  137 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8180 (mm-40)
REVERT: B  190 LEU cc_start: 0.9234 (tp) cc_final: 0.8877 (mp)
REVERT: C  175 TYR cc_start: 0.8967 (t80) cc_final: 0.8691 (t80)
REVERT: D   62 GLU cc_start: 0.8925 (tp30) cc_final: 0.8432 (tp30)
REVERT: D  125 TYR cc_start: 0.8839 (t80) cc_final: 0.7961 (t80)
REVERT: D  163 ASP cc_start: 0.8282 (p0) cc_final: 0.8071 (p0)
REVERT: D  190 LEU cc_start: 0.9220 (tp) cc_final: 0.8930 (mp)
REVERT: E   83 LEU cc_start: 0.9281 (mm) cc_final: 0.8930 (mm)
REVERT: E  163 ASP cc_start: 0.8218 (p0) cc_final: 0.7971 (p0)
  outliers start: 17
  outliers final: 16
  residues processed: 160
  average time/residue: 0.2093
  time to fit residues: 45.0565
Evaluate side-chains
  160 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 144
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
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  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   36 CYS
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 12 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 45 optimal weight:    6.9990
   chunk 84 optimal weight:    3.9990
   overall best weight:    1.7984

-------------------------------------------------------------------------------
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 = 0.3093 r_free = 0.3093 target = 0.098490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.079272 restraints weight = 13266.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.2709 rms_B_bonded: 2.83
r_work: 0.2575 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.3166

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= 0.319
  Angle     :  0.561   5.044  11405  Z= 0.314
  Chirality :  0.050   0.183   1235
  Planarity :  0.004   0.037   1450
  Dihedral  :  4.312  20.103   1100
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.67 %
    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 (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: -1.15 (0.26), residues: 1020
  helix:  3.36 (0.68), residues: 55
  sheet: -0.92 (0.27), residues: 395
  loop : -1.03 (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 D  38 
 PHE   0.009   0.001   PHE E  52 
 TYR   0.021   0.002   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
  157 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 140
  time to evaluate  : 0.899 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8588 (tt0) cc_final: 0.8103 (tt0)
REVERT: A  175 TYR cc_start: 0.8969 (t80) cc_final: 0.8703 (t80)
REVERT: A  190 LEU cc_start: 0.9252 (tp) cc_final: 0.8838 (mp)
REVERT: B  137 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8186 (mm-40)
REVERT: C  175 TYR cc_start: 0.8963 (t80) cc_final: 0.8692 (t80)
REVERT: D   62 GLU cc_start: 0.8962 (tp30) cc_final: 0.8469 (tp30)
REVERT: D  125 TYR cc_start: 0.8844 (t80) cc_final: 0.7943 (t80)
REVERT: D  163 ASP cc_start: 0.8300 (p0) cc_final: 0.8086 (p0)
REVERT: D  190 LEU cc_start: 0.9207 (tp) cc_final: 0.8886 (mp)
REVERT: E  163 ASP cc_start: 0.8210 (p0) cc_final: 0.7970 (p0)
  outliers start: 17
  outliers final: 17
  residues processed: 151
  average time/residue: 0.2146
  time to fit residues: 43.4683
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  : 0.931 
-------------------------------------------------------------------------------
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  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   36 CYS
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 60 optimal weight:    6.9990
   chunk 93 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0040
   chunk 0 optimal weight:    5.9990
   chunk 72 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 82 optimal weight:    0.0040
   chunk 45 optimal weight:    6.9990
   chunk 95 optimal weight:    4.9990
   overall best weight:    0.5606

-------------------------------------------------------------------------------
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 = 0.3126 r_free = 0.3126 target = 0.100681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.082167 restraints weight = 12796.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.2866 rms_B_bonded: 2.76
r_work: 0.2730 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.3176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8390  Z= 0.178
  Angle     :  0.525   4.851  11405  Z= 0.293
  Chirality :  0.048   0.177   1235
  Planarity :  0.003   0.034   1450
  Dihedral  :  3.955  15.915   1100
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 13.78 %
    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 (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: -0.97 (0.26), residues: 1020
  helix:  3.40 (0.68), residues: 55
  sheet: -1.13 (0.28), residues: 335
  loop : -0.69 (0.25), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 162 
 HIS   0.003   0.001   HIS C  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 

********************** 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
  172 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 156
  time to evaluate  : 0.935 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.8552 (tt0) cc_final: 0.8279 (tt0)
REVERT: A  175 TYR cc_start: 0.8915 (t80) cc_final: 0.8641 (t80)
REVERT: B  137 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8063 (mm-40)
REVERT: B  190 LEU cc_start: 0.9250 (tp) cc_final: 0.8943 (mp)
REVERT: C  175 TYR cc_start: 0.8931 (t80) cc_final: 0.8659 (t80)
REVERT: D   62 GLU cc_start: 0.8778 (tp30) cc_final: 0.8299 (tp30)
REVERT: D  125 TYR cc_start: 0.8802 (t80) cc_final: 0.7850 (t80)
REVERT: D  190 LEU cc_start: 0.9184 (tp) cc_final: 0.8887 (mp)
REVERT: E   83 LEU cc_start: 0.9166 (mm) cc_final: 0.8927 (mm)
REVERT: E  163 ASP cc_start: 0.8174 (p0) cc_final: 0.7928 (p0)
  outliers start: 16
  outliers final: 12
  residues processed: 166
  average time/residue: 0.2211
  time to fit residues: 49.4826
Evaluate side-chains
  158 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 146
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
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  198 VAL
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain C residue   36 CYS
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   81 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 39 optimal weight:    8.9990
   chunk 94 optimal weight:    7.9990
   chunk 75 optimal weight:    3.9990
   chunk 83 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 91 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 66 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    1.6786

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.099058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.080065 restraints weight = 13079.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.2773 rms_B_bonded: 2.81
r_work: 0.2637 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.3239

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= 0.305
  Angle     :  0.560   5.637  11405  Z= 0.312
  Chirality :  0.050   0.183   1235
  Planarity :  0.004   0.035   1450
  Dihedral  :  4.202  17.515   1100
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 14.11 %
    Favored  : 84.11 %
  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: -1.09 (0.26), residues: 1020
  helix:  3.43 (0.67), residues: 55
  sheet: -0.88 (0.27), residues: 395
  loop : -0.98 (0.25), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 162 
 HIS   0.004   0.001   HIS D  38 
 PHE   0.009   0.001   PHE E  52 
 TYR   0.025   0.002   TYR B  54 
 ARG   0.003   0.000   ARG C   6 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3185.84 seconds
wall clock time: 57 minutes 40.61 seconds (3460.61 seconds total)