Starting phenix.real_space_refine
on Sun Apr 27 21:10:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5oh0_3809/04_2025/5oh0_3809_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5oh0_3809/04_2025/5oh0_3809.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5oh0_3809/04_2025/5oh0_3809.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5oh0_3809/04_2025/5oh0_3809.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5oh0_3809/04_2025/5oh0_3809_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5oh0_3809/04_2025/5oh0_3809_neut.cif"
  }
  resolution = 4.2
  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=   0.001 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    4032      2.51       5
     N    1158      2.21       5
     O    1386      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 6588
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1098
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1098
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 2, 'TRANS': 154}
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 2.65, per 1000 atoms: 0.40
  Number of scatterers: 6588
  At special positions: 0
  Unit cell: (87.01, 84.75, 84.75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      12     16.00
     O    1386      8.00
     N    1158      7.00
     C    4032      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  21 " - pdb=" SG  CYS A  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  21 " - pdb=" SG  CYS C  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  21 " - pdb=" SG  CYS B  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  21 " - pdb=" SG  CYS E  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  21 " - pdb=" SG  CYS D  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  21 " - pdb=" SG  CYS F  61 " 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: 1.32
  Conformation dependent library (CDL) restraints added in 924.8 milliseconds
  

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1692

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 17 sheets defined
      5.2% alpha, 40.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 27
      No H-bonds generated for 'chain 'A' and resid 25 through 27'
    Processing helix  chain 'A' and resid 38 through 42
    Processing helix  chain 'B' and resid 25 through 27
      No H-bonds generated for 'chain 'B' and resid 25 through 27'
    Processing helix  chain 'B' and resid 38 through 42
    Processing helix  chain 'C' and resid 25 through 27
      No H-bonds generated for 'chain 'C' and resid 25 through 27'
    Processing helix  chain 'C' and resid 38 through 42
    Processing helix  chain 'D' and resid 25 through 27
      No H-bonds generated for 'chain 'D' and resid 25 through 27'
    Processing helix  chain 'D' and resid 38 through 42
    Processing helix  chain 'E' and resid 25 through 27
      No H-bonds generated for 'chain 'E' and resid 25 through 27'
    Processing helix  chain 'E' and resid 38 through 42
    Processing helix  chain 'F' and resid 25 through 28
      removed outlier: 4.033A  pdb=" N   VAL F  28 " --> pdb=" O   ALA F  25 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 25 through 28'
    Processing helix  chain 'F' and resid 38 through 42
    Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 23
      removed outlier: 6.519A  pdb=" N   THR A  48 " --> pdb=" O   ALA A 139 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   ALA A 139 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   SER A  50 " --> pdb=" O   TYR A 137 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   TYR A 137 " --> pdb=" O   SER A  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33
      removed outlier: 6.967A  pdb=" N   GLN A  30 " --> pdb=" O   HIS B  11 " (cutoff:3.500A)
      removed outlier: 8.208A  pdb=" N   LYS B  13 " --> pdb=" O   GLN A  30 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   VAL A  32 " --> pdb=" O   LYS B  13 " (cutoff:3.500A)
      removed outlier: 9.262A  pdb=" N   GLU B  15 " --> pdb=" O   VAL A  32 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   PHE A 154 " --> pdb=" O   GLY B   7 " (cutoff:3.500A)
      removed outlier: 5.000A  pdb=" N   THR B   9 " --> pdb=" O   ALA A 152 " (cutoff:3.500A)
      removed outlier: 7.099A  pdb=" N   ALA A 152 " --> pdb=" O   THR B   9 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 33
      removed outlier: 6.967A  pdb=" N   GLN A  30 " --> pdb=" O   HIS B  11 " (cutoff:3.500A)
      removed outlier: 8.208A  pdb=" N   LYS B  13 " --> pdb=" O   GLN A  30 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   VAL A  32 " --> pdb=" O   LYS B  13 " (cutoff:3.500A)
      removed outlier: 9.262A  pdb=" N   GLU B  15 " --> pdb=" O   VAL A  32 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA A 148 " --> pdb=" O   GLY B  14 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   VAL B  16 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 22 through 23
      removed outlier: 6.519A  pdb=" N   THR B  48 " --> pdb=" O   ALA B 139 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   ALA B 139 " --> pdb=" O   THR B  48 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   SER B  50 " --> pdb=" O   TYR B 137 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   TYR B 137 " --> pdb=" O   SER B  50 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 33
      removed outlier: 6.970A  pdb=" N   GLN B  30 " --> pdb=" O   HIS C  11 " (cutoff:3.500A)
      removed outlier: 8.179A  pdb=" N   LYS C  13 " --> pdb=" O   GLN B  30 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   VAL B  32 " --> pdb=" O   LYS C  13 " (cutoff:3.500A)
      removed outlier: 9.204A  pdb=" N   GLU C  15 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 5.776A  pdb=" N   PHE B 154 " --> pdb=" O   GLY C   7 " (cutoff:3.500A)
      removed outlier: 5.000A  pdb=" N   THR C   9 " --> pdb=" O   ALA B 152 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   ALA B 152 " --> pdb=" O   THR C   9 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 33
      removed outlier: 6.970A  pdb=" N   GLN B  30 " --> pdb=" O   HIS C  11 " (cutoff:3.500A)
      removed outlier: 8.179A  pdb=" N   LYS C  13 " --> pdb=" O   GLN B  30 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   VAL B  32 " --> pdb=" O   LYS C  13 " (cutoff:3.500A)
      removed outlier: 9.204A  pdb=" N   GLU C  15 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ALA B 148 " --> pdb=" O   GLY C  14 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   VAL C  16 " --> pdb=" O   GLY B 146 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 22 through 23
      removed outlier: 6.519A  pdb=" N   THR C  48 " --> pdb=" O   ALA C 139 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   ALA C 139 " --> pdb=" O   THR C  48 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   SER C  50 " --> pdb=" O   TYR C 137 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   TYR C 137 " --> pdb=" O   SER C  50 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 29 through 35
      removed outlier: 3.788A  pdb=" N   GLN C  30 " --> pdb=" O   THR D   9 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   VAL C  32 " --> pdb=" O   HIS D  11 " (cutoff:3.500A)
      removed outlier: 6.030A  pdb=" N   GLU D  15 " --> pdb=" O   LEU C  34 " (cutoff:3.500A)
      removed outlier: 5.695A  pdb=" N   PHE C 154 " --> pdb=" O   GLY D   7 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   THR D   9 " --> pdb=" O   ALA C 152 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   ALA C 152 " --> pdb=" O   THR D   9 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 35
      removed outlier: 3.788A  pdb=" N   GLN C  30 " --> pdb=" O   THR D   9 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   VAL C  32 " --> pdb=" O   HIS D  11 " (cutoff:3.500A)
      removed outlier: 6.030A  pdb=" N   GLU D  15 " --> pdb=" O   LEU C  34 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ALA C 148 " --> pdb=" O   GLY D  14 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   VAL D  16 " --> pdb=" O   GLY C 146 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 22 through 23
      removed outlier: 6.518A  pdb=" N   THR D  48 " --> pdb=" O   ALA D 139 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   ALA D 139 " --> pdb=" O   THR D  48 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   SER D  50 " --> pdb=" O   TYR D 137 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   TYR D 137 " --> pdb=" O   SER D  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 29 through 33
      removed outlier: 6.940A  pdb=" N   GLN D  30 " --> pdb=" O   HIS E  11 " (cutoff:3.500A)
      removed outlier: 8.187A  pdb=" N   LYS E  13 " --> pdb=" O   GLN D  30 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   VAL D  32 " --> pdb=" O   LYS E  13 " (cutoff:3.500A)
      removed outlier: 9.248A  pdb=" N   GLU E  15 " --> pdb=" O   VAL D  32 " (cutoff:3.500A)
      removed outlier: 5.852A  pdb=" N   PHE D 154 " --> pdb=" O   GLY E   7 " (cutoff:3.500A)
      removed outlier: 5.025A  pdb=" N   THR E   9 " --> pdb=" O   ALA D 152 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   ALA D 152 " --> pdb=" O   THR E   9 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 29 through 33
      removed outlier: 6.940A  pdb=" N   GLN D  30 " --> pdb=" O   HIS E  11 " (cutoff:3.500A)
      removed outlier: 8.187A  pdb=" N   LYS E  13 " --> pdb=" O   GLN D  30 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   VAL D  32 " --> pdb=" O   LYS E  13 " (cutoff:3.500A)
      removed outlier: 9.248A  pdb=" N   GLU E  15 " --> pdb=" O   VAL D  32 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA D 148 " --> pdb=" O   GLY E  14 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   VAL E  16 " --> pdb=" O   GLY D 146 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 22 through 23
      removed outlier: 6.518A  pdb=" N   THR E  48 " --> pdb=" O   ALA E 139 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   ALA E 139 " --> pdb=" O   THR E  48 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   SER E  50 " --> pdb=" O   TYR E 137 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   TYR E 137 " --> pdb=" O   SER E  50 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 29 through 35
      removed outlier: 3.720A  pdb=" N   GLN E  30 " --> pdb=" O   THR F   9 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   VAL E  32 " --> pdb=" O   HIS F  11 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   GLU F  15 " --> pdb=" O   LEU E  34 " (cutoff:3.500A)
      removed outlier: 5.801A  pdb=" N   PHE E 154 " --> pdb=" O   GLY F   7 " (cutoff:3.500A)
      removed outlier: 4.970A  pdb=" N   THR F   9 " --> pdb=" O   ALA E 152 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   ALA E 152 " --> pdb=" O   THR F   9 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 29 through 35
      removed outlier: 3.720A  pdb=" N   GLN E  30 " --> pdb=" O   THR F   9 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   VAL E  32 " --> pdb=" O   HIS F  11 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   GLU F  15 " --> pdb=" O   LEU E  34 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ALA E 148 " --> pdb=" O   GLY F  14 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   VAL F  16 " --> pdb=" O   GLY E 146 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 22 through 23
      removed outlier: 6.519A  pdb=" N   THR F  48 " --> pdb=" O   ALA F 139 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   ALA F 139 " --> pdb=" O   THR F  48 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   SER F  50 " --> pdb=" O   TYR F 137 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   TYR F 137 " --> pdb=" O   SER F  50 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 70 through 74

    145 hydrogen bonds defined for protein.
    312 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: 1.45

  Time building geometry restraints manager: 1.61 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: 2328
        1.34 -     1.46: 1473
        1.46 -     1.58: 2847
        1.58 -     1.70: 0
        1.70 -     1.82: 12
  Bond restraints: 6660
  Sorted by residual:
  bond pdb=" N   GLY A  53 "
       pdb=" CA  GLY A  53 "
    ideal  model  delta    sigma   weight residual
    1.444  1.455 -0.011 1.02e-02 9.61e+03 1.24e+00
  bond pdb=" N   GLY F  53 "
       pdb=" CA  GLY F  53 "
    ideal  model  delta    sigma   weight residual
    1.444  1.455 -0.011 1.02e-02 9.61e+03 1.18e+00
  bond pdb=" N   GLY E  53 "
       pdb=" CA  GLY E  53 "
    ideal  model  delta    sigma   weight residual
    1.444  1.455 -0.011 1.02e-02 9.61e+03 1.16e+00
  bond pdb=" N   GLY D  53 "
       pdb=" CA  GLY D  53 "
    ideal  model  delta    sigma   weight residual
    1.444  1.455 -0.011 1.02e-02 9.61e+03 1.14e+00
  bond pdb=" N   GLY B  53 "
       pdb=" CA  GLY B  53 "
    ideal  model  delta    sigma   weight residual
    1.444  1.455 -0.011 1.02e-02 9.61e+03 1.11e+00
  ... (remaining 6655 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.06: 8012
        1.06 -     2.12: 877
        2.12 -     3.19: 170
        3.19 -     4.25: 32
        4.25 -     5.31: 11
  Bond angle restraints: 9102
  Sorted by residual:
  angle pdb=" N   ASP A 114 "
        pdb=" CA  ASP A 114 "
        pdb=" C   ASP A 114 "
      ideal   model   delta    sigma   weight residual
     114.56  110.82    3.74 1.27e+00 6.20e-01 8.70e+00
  angle pdb=" N   ASP D 114 "
        pdb=" CA  ASP D 114 "
        pdb=" C   ASP D 114 "
      ideal   model   delta    sigma   weight residual
     114.56  110.84    3.72 1.27e+00 6.20e-01 8.59e+00
  angle pdb=" N   ASP C 114 "
        pdb=" CA  ASP C 114 "
        pdb=" C   ASP C 114 "
      ideal   model   delta    sigma   weight residual
     114.56  110.84    3.72 1.27e+00 6.20e-01 8.58e+00
  angle pdb=" N   ASP F 114 "
        pdb=" CA  ASP F 114 "
        pdb=" C   ASP F 114 "
      ideal   model   delta    sigma   weight residual
     114.56  110.86    3.70 1.27e+00 6.20e-01 8.48e+00
  angle pdb=" N   ASP B 114 "
        pdb=" CA  ASP B 114 "
        pdb=" C   ASP B 114 "
      ideal   model   delta    sigma   weight residual
     114.56  110.86    3.70 1.27e+00 6.20e-01 8.47e+00
  ... (remaining 9097 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.28: 3710
       14.28 -    28.57: 136
       28.57 -    42.85: 30
       42.85 -    57.13: 0
       57.13 -    71.42: 6
  Dihedral angle restraints: 3882
    sinusoidal: 1242
      harmonic: 2640
  Sorted by residual:
  dihedral pdb=" CA  PHE E 154 "
           pdb=" C   PHE E 154 "
           pdb=" N   LYS E 155 "
           pdb=" CA  LYS E 155 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.13  -15.87     0      5.00e+00 4.00e-02 1.01e+01
  dihedral pdb=" CA  PHE D 154 "
           pdb=" C   PHE D 154 "
           pdb=" N   LYS D 155 "
           pdb=" CA  LYS D 155 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.14  -15.86     0      5.00e+00 4.00e-02 1.01e+01
  dihedral pdb=" CA  PHE C 154 "
           pdb=" C   PHE C 154 "
           pdb=" N   LYS C 155 "
           pdb=" CA  LYS C 155 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.15  -15.85     0      5.00e+00 4.00e-02 1.00e+01
  ... (remaining 3879 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 614
       0.030 -    0.059: 322
       0.059 -    0.089: 113
       0.089 -    0.119: 60
       0.119 -    0.148: 31
  Chirality restraints: 1140
  Sorted by residual:
  chirality pdb=" CA  VAL E   5 "
            pdb=" N   VAL E   5 "
            pdb=" C   VAL E   5 "
            pdb=" CB  VAL E   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.50e-01
  chirality pdb=" CA  VAL C   5 "
            pdb=" N   VAL C   5 "
            pdb=" C   VAL C   5 "
            pdb=" CB  VAL C   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.49e-01
  chirality pdb=" CA  VAL F   5 "
            pdb=" N   VAL F   5 "
            pdb=" C   VAL F   5 "
            pdb=" CB  VAL F   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.44e-01
  ... (remaining 1137 not shown)

  Planarity restraints: 1218
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D 131 "    0.026 5.00e-02 4.00e+02   3.95e-02 2.49e+00
        pdb=" N   PRO D 132 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO D 132 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO D 132 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 131 "   -0.026 5.00e-02 4.00e+02   3.94e-02 2.49e+00
        pdb=" N   PRO B 132 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO B 132 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 132 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 131 "    0.026 5.00e-02 4.00e+02   3.94e-02 2.49e+00
        pdb=" N   PRO C 132 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO C 132 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO C 132 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1215 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2071
        2.82 -     3.34: 4982
        3.34 -     3.86: 10156
        3.86 -     4.38: 10347
        4.38 -     4.90: 19483
  Nonbonded interactions: 47039
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A  98 "
            pdb=" OG1 THR A 140 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" OD1 ASN D  98 "
            pdb=" OG1 THR D 140 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OD1 ASN E  98 "
            pdb=" OG1 THR E 140 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OD1 ASN B  98 "
            pdb=" OG1 THR B 140 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OD1 ASN C  98 "
            pdb=" OG1 THR C 140 "
     model   vdw
     2.296 3.040
  ... (remaining 47034 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             73.160
  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:          0.250
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     16.380
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  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:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   93.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6666  Z= 0.177
  Angle     :  0.751   5.312   9114  Z= 0.463
  Chirality :  0.047   0.148   1140
  Planarity :  0.004   0.039   1218
  Dihedral  :  8.942  71.416   2172
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.74 (0.24), residues: 930
  helix:  None (None), residues: 0
  sheet: -1.38 (0.38), residues: 216
  loop : -3.13 (0.19), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS B  11 
 PHE   0.020   0.002   PHE E 154 
 TYR   0.002   0.001   TYR F 158 
 ARG   0.001   0.000   ARG A 106 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.29446 (  139)
  hydrogen bonds       : angle       9.52740 (  312)
  SS BOND              : bond        0.00191 (    6)
  SS BOND              : angle       1.41601 (   12)
  covalent geometry    : bond        0.00318 ( 6660)
  covalent geometry    : angle       0.75011 ( 9102)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.661 
Fit side-chains
REVERT: F   29 ASP cc_start: 0.8339 (t70) cc_final: 0.8054 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.2960
  time to fit residues: 31.5667
Evaluate side-chains
  23 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    9.9990
   chunk 68 optimal weight:    0.7980
   chunk 37 optimal weight:    6.9990
   chunk 23 optimal weight:    9.9990
   chunk 46 optimal weight:    7.9990
   chunk 36 optimal weight:    2.9990
   chunk 70 optimal weight:    7.9990
   chunk 27 optimal weight:    0.8980
   chunk 42 optimal weight:   10.0000
   chunk 52 optimal weight:    0.2980
   chunk 81 optimal weight:   20.0000
   overall best weight:    2.3984

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 125 ASN
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  33 GLN
** E  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  89 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 = 0.2747 r_free = 0.2747 target = 0.043550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2572 r_free = 0.2572 target = 0.037947 restraints weight = 38242.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2609 r_free = 0.2609 target = 0.039081 restraints weight = 21989.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2634 r_free = 0.2634 target = 0.039878 restraints weight = 14526.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.2634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6666  Z= 0.157
  Angle     :  0.497   4.731   9114  Z= 0.274
  Chirality :  0.038   0.122   1140
  Planarity :  0.003   0.031   1218
  Dihedral  :  4.155  12.339    966
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.03 (0.25), residues: 930
  helix:  None (None), residues: 0
  sheet: -1.00 (0.35), residues: 240
  loop : -2.61 (0.21), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B  11 
 PHE   0.008   0.001   PHE F 118 
 TYR   0.005   0.001   TYR E 158 
 ARG   0.002   0.000   ARG A 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03710 (  139)
  hydrogen bonds       : angle       6.28746 (  312)
  SS BOND              : bond        0.00060 (    6)
  SS BOND              : angle       1.06236 (   12)
  covalent geometry    : bond        0.00338 ( 6660)
  covalent geometry    : angle       0.49618 ( 9102)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 1.124 
Fit side-chains
REVERT: B   15 GLU cc_start: 0.8369 (tp30) cc_final: 0.8017 (tp30)
REVERT: C   33 GLN cc_start: 0.8801 (mp10) cc_final: 0.8569 (mp10)
REVERT: C  105 ASP cc_start: 0.8028 (t70) cc_final: 0.7699 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.1959
  time to fit residues: 10.4920
Evaluate side-chains
  19 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 1.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 56 optimal weight:    0.0040
   chunk 36 optimal weight:   10.0000
   chunk 53 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   chunk 14 optimal weight:   20.0000
   chunk 57 optimal weight:    9.9990
   chunk 15 optimal weight:    0.9980
   chunk 76 optimal weight:    8.9990
   chunk 69 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 66 optimal weight:    9.9990
   overall best weight:    3.3998

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2692 r_free = 0.2692 target = 0.042222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2518 r_free = 0.2518 target = 0.036698 restraints weight = 39776.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2550 r_free = 0.2550 target = 0.037726 restraints weight = 23054.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2575 r_free = 0.2575 target = 0.038483 restraints weight = 15504.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.2572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.2997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   6666  Z= 0.206
  Angle     :  0.538   6.694   9114  Z= 0.292
  Chirality :  0.038   0.115   1140
  Planarity :  0.003   0.026   1218
  Dihedral  :  4.431  14.071    966
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.83 (0.26), residues: 930
  helix:  None (None), residues: 0
  sheet: -0.33 (0.38), residues: 216
  loop : -2.62 (0.21), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A  11 
 PHE   0.008   0.001   PHE A  73 
 TYR   0.005   0.001   TYR F 158 
 ARG   0.003   0.001   ARG A 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03528 (  139)
  hydrogen bonds       : angle       5.66104 (  312)
  SS BOND              : bond        0.00114 (    6)
  SS BOND              : angle       1.09137 (   12)
  covalent geometry    : bond        0.00450 ( 6660)
  covalent geometry    : angle       0.53732 ( 9102)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.721 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.1443
  time to fit residues: 6.7505
Evaluate side-chains
  17 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 18 optimal weight:    8.9990
   chunk 61 optimal weight:    1.9990
   chunk 54 optimal weight:   10.0000
   chunk 36 optimal weight:    8.9990
   chunk 79 optimal weight:   10.0000
   chunk 28 optimal weight:    3.9990
   chunk 89 optimal weight:    5.9990
   chunk 52 optimal weight:    7.9990
   chunk 81 optimal weight:   20.0000
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 125 ASN
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2685 r_free = 0.2685 target = 0.041891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2509 r_free = 0.2509 target = 0.036408 restraints weight = 40188.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.2544 r_free = 0.2544 target = 0.037459 restraints weight = 23425.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2567 r_free = 0.2567 target = 0.038185 restraints weight = 15766.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.2566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.3494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   6666  Z= 0.247
  Angle     :  0.577   7.247   9114  Z= 0.309
  Chirality :  0.039   0.115   1140
  Planarity :  0.003   0.024   1218
  Dihedral  :  4.748  16.130    966
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.69 (0.26), residues: 930
  helix:  None (None), residues: 0
  sheet: -0.33 (0.36), residues: 222
  loop : -2.50 (0.21), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A  11 
 PHE   0.009   0.001   PHE A  73 
 TYR   0.007   0.001   TYR F 158 
 ARG   0.003   0.001   ARG A 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03552 (  139)
  hydrogen bonds       : angle       5.66841 (  312)
  SS BOND              : bond        0.00123 (    6)
  SS BOND              : angle       1.81287 (   12)
  covalent geometry    : bond        0.00543 ( 6660)
  covalent geometry    : angle       0.57320 ( 9102)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.726 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.1291
  time to fit residues: 5.2896
Evaluate side-chains
  16 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 74 optimal weight:    9.9990
   chunk 73 optimal weight:    8.9990
   chunk 60 optimal weight:    9.9990
   chunk 2 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 62 optimal weight:    7.9990
   chunk 56 optimal weight:    4.9990
   chunk 24 optimal weight:    9.9990
   chunk 36 optimal weight:   10.0000
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.042291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2523 r_free = 0.2523 target = 0.036767 restraints weight = 39983.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2557 r_free = 0.2557 target = 0.037830 restraints weight = 23328.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2580 r_free = 0.2580 target = 0.038565 restraints weight = 15734.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.2578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.3660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   6666  Z= 0.214
  Angle     :  0.541   6.770   9114  Z= 0.292
  Chirality :  0.038   0.119   1140
  Planarity :  0.002   0.022   1218
  Dihedral  :  4.574  15.572    966
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  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: -2.57 (0.26), residues: 930
  helix:  None (None), residues: 0
  sheet: -0.13 (0.36), residues: 216
  loop : -2.44 (0.21), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A  11 
 PHE   0.007   0.001   PHE C 133 
 TYR   0.005   0.001   TYR C 158 
 ARG   0.003   0.000   ARG A 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03269 (  139)
  hydrogen bonds       : angle       5.50161 (  312)
  SS BOND              : bond        0.00092 (    6)
  SS BOND              : angle       1.56327 (   12)
  covalent geometry    : bond        0.00471 ( 6660)
  covalent geometry    : angle       0.53878 ( 9102)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.670 
Fit side-chains
REVERT: E   24 ASP cc_start: 0.8843 (t0) cc_final: 0.8614 (t70)
REVERT: F   74 LEU cc_start: 0.9344 (tp) cc_final: 0.9144 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.1540
  time to fit residues: 6.5829
Evaluate side-chains
  17 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 10 optimal weight:    6.9990
   chunk 20 optimal weight:    5.9990
   chunk 14 optimal weight:    9.9990
   chunk 60 optimal weight:    1.9990
   chunk 71 optimal weight:   10.0000
   chunk 3 optimal weight:    7.9990
   chunk 74 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0770
   chunk 34 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    3.0146

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.042562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2532 r_free = 0.2532 target = 0.037085 restraints weight = 39950.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2566 r_free = 0.2566 target = 0.038158 restraints weight = 23195.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.2590 r_free = 0.2590 target = 0.038900 restraints weight = 15545.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.2589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          0.3803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6666  Z= 0.181
  Angle     :  0.499   6.074   9114  Z= 0.272
  Chirality :  0.038   0.118   1140
  Planarity :  0.002   0.021   1218
  Dihedral  :  4.287  14.128    966
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  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: -2.45 (0.26), residues: 930
  helix:  None (None), residues: 0
  sheet: -0.04 (0.35), residues: 216
  loop : -2.36 (0.21), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  11 
 PHE   0.007   0.001   PHE C 133 
 TYR   0.005   0.001   TYR C 158 
 ARG   0.002   0.000   ARG A 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02980 (  139)
  hydrogen bonds       : angle       5.31411 (  312)
  SS BOND              : bond        0.00052 (    6)
  SS BOND              : angle       1.39405 (   12)
  covalent geometry    : bond        0.00398 ( 6660)
  covalent geometry    : angle       0.49724 ( 9102)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.971 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.1429
  time to fit residues: 6.0292
Evaluate side-chains
  16 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 15 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 71 optimal weight:    9.9990
   chunk 60 optimal weight:    8.9990
   chunk 59 optimal weight:    5.9990
   chunk 87 optimal weight:    4.9990
   chunk 3 optimal weight:    0.0970
   chunk 47 optimal weight:    9.9990
   chunk 25 optimal weight:    0.4980
   overall best weight:    1.4582

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.043603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.2558 r_free = 0.2558 target = 0.038000 restraints weight = 38490.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2593 r_free = 0.2593 target = 0.039106 restraints weight = 22311.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2616 r_free = 0.2616 target = 0.039885 restraints weight = 14915.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.2617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.3811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6666  Z= 0.099
  Angle     :  0.434   4.765   9114  Z= 0.238
  Chirality :  0.038   0.122   1140
  Planarity :  0.002   0.019   1218
  Dihedral  :  3.682  11.875    966
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.27 (0.26), residues: 930
  helix:  None (None), residues: 0
  sheet:  0.10 (0.35), residues: 216
  loop : -2.23 (0.22), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS E  11 
 PHE   0.005   0.001   PHE F  54 
 TYR   0.002   0.000   TYR A 137 
 ARG   0.001   0.000   ARG A 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02256 (  139)
  hydrogen bonds       : angle       4.95177 (  312)
  SS BOND              : bond        0.00055 (    6)
  SS BOND              : angle       1.30685 (   12)
  covalent geometry    : bond        0.00220 ( 6660)
  covalent geometry    : angle       0.43168 ( 9102)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.922 
Fit side-chains
REVERT: F   74 LEU cc_start: 0.9304 (tp) cc_final: 0.9087 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 27
  average time/residue: 0.1421
  time to fit residues: 7.5337
Evaluate side-chains
  19 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 40 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   chunk 46 optimal weight:    7.9990
   chunk 43 optimal weight:    2.9990
   chunk 37 optimal weight:    9.9990
   chunk 19 optimal weight:    0.7980
   chunk 67 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.043120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2544 r_free = 0.2544 target = 0.037467 restraints weight = 38927.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2580 r_free = 0.2580 target = 0.038591 restraints weight = 22263.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2605 r_free = 0.2605 target = 0.039384 restraints weight = 14771.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.2603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.3889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6666  Z= 0.134
  Angle     :  0.458   4.617   9114  Z= 0.250
  Chirality :  0.038   0.121   1140
  Planarity :  0.002   0.019   1218
  Dihedral  :  3.843  13.115    966
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  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: -2.16 (0.26), residues: 930
  helix:  None (None), residues: 0
  sheet:  0.16 (0.35), residues: 216
  loop : -2.15 (0.22), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS B  11 
 PHE   0.006   0.001   PHE C 133 
 TYR   0.004   0.000   TYR C 158 
 ARG   0.002   0.000   ARG A 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02545 (  139)
  hydrogen bonds       : angle       4.97138 (  312)
  SS BOND              : bond        0.00161 (    6)
  SS BOND              : angle       1.33004 (   12)
  covalent geometry    : bond        0.00296 ( 6660)
  covalent geometry    : angle       0.45544 ( 9102)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.707 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.1805
  time to fit residues: 8.3866
Evaluate side-chains
  19 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 58 optimal weight:    7.9990
   chunk 2 optimal weight:    7.9990
   chunk 23 optimal weight:    9.9990
   chunk 1 optimal weight:    4.9990
   chunk 79 optimal weight:    0.0980
   chunk 66 optimal weight:    8.9990
   chunk 41 optimal weight:    8.9990
   chunk 73 optimal weight:    5.9990
   chunk 17 optimal weight:    8.9990
   chunk 67 optimal weight:    0.9990
   overall best weight:    3.4188

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.042518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2525 r_free = 0.2525 target = 0.036989 restraints weight = 40171.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2560 r_free = 0.2560 target = 0.038071 restraints weight = 23381.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2585 r_free = 0.2585 target = 0.038836 restraints weight = 15677.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.2583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8613
moved from start:          0.4004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6666  Z= 0.202
  Angle     :  0.518   5.951   9114  Z= 0.280
  Chirality :  0.038   0.118   1140
  Planarity :  0.002   0.021   1218
  Dihedral  :  4.294  15.071    966
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  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: -2.23 (0.26), residues: 930
  helix:  None (None), residues: 0
  sheet:  0.05 (0.34), residues: 216
  loop : -2.17 (0.22), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS B  11 
 PHE   0.007   0.001   PHE C 133 
 TYR   0.007   0.001   TYR C 158 
 ARG   0.003   0.000   ARG A 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03116 (  139)
  hydrogen bonds       : angle       5.22288 (  312)
  SS BOND              : bond        0.00194 (    6)
  SS BOND              : angle       1.78036 (   12)
  covalent geometry    : bond        0.00447 ( 6660)
  covalent geometry    : angle       0.51445 ( 9102)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.754 
Fit side-chains
REVERT: F   74 LEU cc_start: 0.9346 (tp) cc_final: 0.9133 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.1260
  time to fit residues: 5.5849
Evaluate side-chains
  18 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 40 optimal weight:    7.9990
   chunk 51 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 11 optimal weight:   10.0000
   chunk 54 optimal weight:    6.9990
   chunk 34 optimal weight:    0.0470
   chunk 82 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   chunk 64 optimal weight:    7.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    3.2086

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.042550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2529 r_free = 0.2529 target = 0.037052 restraints weight = 40508.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2564 r_free = 0.2564 target = 0.038141 restraints weight = 23369.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2589 r_free = 0.2589 target = 0.038899 restraints weight = 15586.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.2588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.4060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6666  Z= 0.190
  Angle     :  0.512   5.523   9114  Z= 0.277
  Chirality :  0.038   0.117   1140
  Planarity :  0.002   0.020   1218
  Dihedral  :  4.292  15.637    966
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  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: -2.24 (0.26), residues: 930
  helix:  None (None), residues: 0
  sheet: -0.09 (0.33), residues: 222
  loop : -2.15 (0.22), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS A  11 
 PHE   0.007   0.001   PHE F 154 
 TYR   0.006   0.001   TYR C 158 
 ARG   0.003   0.000   ARG A 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03013 (  139)
  hydrogen bonds       : angle       5.27221 (  312)
  SS BOND              : bond        0.00216 (    6)
  SS BOND              : angle       1.63633 (   12)
  covalent geometry    : bond        0.00419 ( 6660)
  covalent geometry    : angle       0.50870 ( 9102)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.700 
Fit side-chains
REVERT: F   74 LEU cc_start: 0.9341 (tp) cc_final: 0.9138 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.1537
  time to fit residues: 7.3383
Evaluate side-chains
  19 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 9 optimal weight:    0.5980
   chunk 5 optimal weight:    5.9990
   chunk 41 optimal weight:    7.9990
   chunk 37 optimal weight:    0.8980
   chunk 71 optimal weight:   10.0000
   chunk 12 optimal weight:    8.9990
   chunk 86 optimal weight:    1.9990
   chunk 74 optimal weight:    7.9990
   chunk 0 optimal weight:    8.9990
   chunk 77 optimal weight:    9.9990
   overall best weight:    3.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.042441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2525 r_free = 0.2525 target = 0.036948 restraints weight = 40604.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2560 r_free = 0.2560 target = 0.038036 restraints weight = 23448.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2584 r_free = 0.2584 target = 0.038783 restraints weight = 15676.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.2584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start:          0.4124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   6666  Z= 0.206
  Angle     :  0.530   6.080   9114  Z= 0.286
  Chirality :  0.039   0.119   1140
  Planarity :  0.002   0.021   1218
  Dihedral  :  4.413  15.768    966
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  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: -2.27 (0.26), residues: 930
  helix:  None (None), residues: 0
  sheet: -0.16 (0.33), residues: 222
  loop : -2.15 (0.22), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS A  11 
 PHE   0.007   0.001   PHE F 154 
 TYR   0.006   0.001   TYR C 158 
 ARG   0.003   0.000   ARG A 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03144 (  139)
  hydrogen bonds       : angle       5.29549 (  312)
  SS BOND              : bond        0.00214 (    6)
  SS BOND              : angle       1.72141 (   12)
  covalent geometry    : bond        0.00456 ( 6660)
  covalent geometry    : angle       0.52706 ( 9102)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2254.79 seconds
wall clock time: 42 minutes 32.35 seconds (2552.35 seconds total)