Starting phenix.real_space_refine
on Wed Jul 30 13:23:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d67_27219/07_2025/8d67_27219_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d67_27219/07_2025/8d67_27219.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/8d67_27219/07_2025/8d67_27219.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d67_27219/07_2025/8d67_27219.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d67_27219/07_2025/8d67_27219_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d67_27219/07_2025/8d67_27219_neut.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=   0.012
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      35      5.16       5
     C    8195      2.51       5
     N    2085      2.21       5
     O    2255      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 95 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12570
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2510
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'DHL': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 5.28, per 1000 atoms: 0.42
  Number of scatterers: 12570
  At special positions: 0
  Unit cell: (89.1, 89.1, 125.4, 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      35     16.00
     O    2255      8.00
     N    2085      7.00
     C    8195      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 2.61
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2910

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 20 sheets defined
      31.8% alpha, 32.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 63 through 68
    Processing helix  chain 'A' and resid 201 through 209
      removed outlier: 3.802A  pdb=" N   ILE A 209 " --> pdb=" O   LEU A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 221
    Processing helix  chain 'A' and resid 222 through 225
      removed outlier: 3.579A  pdb=" N   LEU A 225 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 222 through 225'
    Processing helix  chain 'A' and resid 228 through 251
      removed outlier: 3.626A  pdb=" N   TYR A 245 " --> pdb=" O   THR A 241 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ALA A 246 " --> pdb=" O   VAL A 242 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   PHE A 247 " --> pdb=" O   VAL A 243 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   ASN A 251 " --> pdb=" O   PHE A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 285
    Processing helix  chain 'A' and resid 302 through 317
      removed outlier: 3.841A  pdb=" N   LEU A 306 " --> pdb=" O   LEU A 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 63 through 68
    Processing helix  chain 'B' and resid 201 through 209
      removed outlier: 3.802A  pdb=" N   ILE B 209 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 221
    Processing helix  chain 'B' and resid 222 through 225
      removed outlier: 3.580A  pdb=" N   LEU B 225 " --> pdb=" O   VAL B 222 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 222 through 225'
    Processing helix  chain 'B' and resid 228 through 251
      removed outlier: 3.626A  pdb=" N   TYR B 245 " --> pdb=" O   THR B 241 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ALA B 246 " --> pdb=" O   VAL B 242 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   PHE B 247 " --> pdb=" O   VAL B 243 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   ASN B 251 " --> pdb=" O   PHE B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 285
    Processing helix  chain 'B' and resid 302 through 317
      removed outlier: 3.842A  pdb=" N   LEU B 306 " --> pdb=" O   LEU B 302 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 68
    Processing helix  chain 'C' and resid 201 through 209
      removed outlier: 3.802A  pdb=" N   ILE C 209 " --> pdb=" O   LEU C 205 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 221
    Processing helix  chain 'C' and resid 222 through 225
      removed outlier: 3.580A  pdb=" N   LEU C 225 " --> pdb=" O   VAL C 222 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 222 through 225'
    Processing helix  chain 'C' and resid 228 through 251
      removed outlier: 3.626A  pdb=" N   TYR C 245 " --> pdb=" O   THR C 241 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ALA C 246 " --> pdb=" O   VAL C 242 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   PHE C 247 " --> pdb=" O   VAL C 243 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   ASN C 251 " --> pdb=" O   PHE C 247 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 260 through 285
    Processing helix  chain 'C' and resid 302 through 317
      removed outlier: 3.842A  pdb=" N   LEU C 306 " --> pdb=" O   LEU C 302 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 63 through 68
    Processing helix  chain 'D' and resid 201 through 209
      removed outlier: 3.803A  pdb=" N   ILE D 209 " --> pdb=" O   LEU D 205 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 209 through 221
    Processing helix  chain 'D' and resid 222 through 225
      removed outlier: 3.579A  pdb=" N   LEU D 225 " --> pdb=" O   VAL D 222 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 222 through 225'
    Processing helix  chain 'D' and resid 228 through 251
      removed outlier: 3.625A  pdb=" N   TYR D 245 " --> pdb=" O   THR D 241 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ALA D 246 " --> pdb=" O   VAL D 242 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   PHE D 247 " --> pdb=" O   VAL D 243 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   ASN D 251 " --> pdb=" O   PHE D 247 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 260 through 285
    Processing helix  chain 'D' and resid 302 through 317
      removed outlier: 3.842A  pdb=" N   LEU D 306 " --> pdb=" O   LEU D 302 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 68
    Processing helix  chain 'E' and resid 201 through 209
      removed outlier: 3.802A  pdb=" N   ILE E 209 " --> pdb=" O   LEU E 205 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 209 through 221
    Processing helix  chain 'E' and resid 222 through 225
      removed outlier: 3.580A  pdb=" N   LEU E 225 " --> pdb=" O   VAL E 222 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 222 through 225'
    Processing helix  chain 'E' and resid 228 through 251
      removed outlier: 3.626A  pdb=" N   TYR E 245 " --> pdb=" O   THR E 241 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ALA E 246 " --> pdb=" O   VAL E 242 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   PHE E 247 " --> pdb=" O   VAL E 243 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   ASN E 251 " --> pdb=" O   PHE E 247 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 260 through 285
    Processing helix  chain 'E' and resid 302 through 317
      removed outlier: 3.842A  pdb=" N   LEU E 306 " --> pdb=" O   LEU E 302 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16
      removed outlier: 5.724A  pdb=" N   VAL A  12 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   SER A 143 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   VAL A  14 " --> pdb=" O   SER A 143 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   ILE A 145 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   VAL A  16 " --> pdb=" O   ILE A 145 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 24
      removed outlier: 5.174A  pdb=" N   ILE A  20 " --> pdb=" O   TYR A  38 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   TYR A  38 " --> pdb=" O   ILE A  20 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.572A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.572A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 12 through 16
      removed outlier: 5.724A  pdb=" N   VAL B  12 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   SER B 143 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   VAL B  14 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   ILE B 145 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 7.183A  pdb=" N   VAL B  16 " --> pdb=" O   ILE B 145 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 19 through 24
      removed outlier: 5.174A  pdb=" N   ILE B  20 " --> pdb=" O   TYR B  38 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   TYR B  38 " --> pdb=" O   ILE B  20 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.572A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.572A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 12 through 16
      removed outlier: 5.724A  pdb=" N   VAL C  12 " --> pdb=" O   ARG C 141 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   SER C 143 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   VAL C  14 " --> pdb=" O   SER C 143 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   ILE C 145 " --> pdb=" O   VAL C  14 " (cutoff:3.500A)
      removed outlier: 7.183A  pdb=" N   VAL C  16 " --> pdb=" O   ILE C 145 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'C' and resid 19 through 24
      removed outlier: 5.174A  pdb=" N   ILE C  20 " --> pdb=" O   TYR C  38 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   TYR C  38 " --> pdb=" O   ILE C  20 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.572A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.572A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 12 through 16
      removed outlier: 5.724A  pdb=" N   VAL D  12 " --> pdb=" O   ARG D 141 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   SER D 143 " --> pdb=" O   VAL D  12 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   VAL D  14 " --> pdb=" O   SER D 143 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   ILE D 145 " --> pdb=" O   VAL D  14 " (cutoff:3.500A)
      removed outlier: 7.183A  pdb=" N   VAL D  16 " --> pdb=" O   ILE D 145 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 24
      removed outlier: 5.174A  pdb=" N   ILE D  20 " --> pdb=" O   TYR D  38 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   TYR D  38 " --> pdb=" O   ILE D  20 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 78
      removed outlier: 6.572A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 76 through 78
      removed outlier: 6.572A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 12 through 16
      removed outlier: 5.724A  pdb=" N   VAL E  12 " --> pdb=" O   ARG E 141 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   SER E 143 " --> pdb=" O   VAL E  12 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   VAL E  14 " --> pdb=" O   SER E 143 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   ILE E 145 " --> pdb=" O   VAL E  14 " (cutoff:3.500A)
      removed outlier: 7.183A  pdb=" N   VAL E  16 " --> pdb=" O   ILE E 145 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'E' and resid 19 through 24
      removed outlier: 5.174A  pdb=" N   ILE E  20 " --> pdb=" O   TYR E  38 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   TYR E  38 " --> pdb=" O   ILE E  20 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 78
      removed outlier: 6.572A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 78
      removed outlier: 6.572A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)

    590 hydrogen bonds defined for protein.
    1740 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: 3.69

  Time building geometry restraints manager: 3.22 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 2765
        1.33 -     1.45: 3066
        1.45 -     1.57: 7024
        1.57 -     1.69: 0
        1.69 -     1.81: 55
  Bond restraints: 12910
  Sorted by residual:
  bond pdb=" C   GLU C  59 "
       pdb=" O   GLU C  59 "
    ideal  model  delta    sigma   weight residual
    1.234  1.205  0.029 1.07e-02 8.73e+03 7.30e+00
  bond pdb=" CA  GLN A  62 "
       pdb=" C   GLN A  62 "
    ideal  model  delta    sigma   weight residual
    1.521  1.486  0.035 1.31e-02 5.83e+03 7.25e+00
  bond pdb=" CA  GLN E  62 "
       pdb=" C   GLN E  62 "
    ideal  model  delta    sigma   weight residual
    1.521  1.486  0.035 1.31e-02 5.83e+03 7.23e+00
  bond pdb=" CA  GLN C  62 "
       pdb=" C   GLN C  62 "
    ideal  model  delta    sigma   weight residual
    1.521  1.486  0.035 1.31e-02 5.83e+03 7.18e+00
  bond pdb=" C   GLU E  59 "
       pdb=" O   GLU E  59 "
    ideal  model  delta    sigma   weight residual
    1.234  1.206  0.029 1.07e-02 8.73e+03 7.13e+00
  ... (remaining 12905 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.45: 17064
        2.45 -     4.90: 441
        4.90 -     7.35: 65
        7.35 -     9.80: 0
        9.80 -    12.25: 15
  Bond angle restraints: 17585
  Sorted by residual:
  angle pdb=" N   GLN B  62 "
        pdb=" CA  GLN B  62 "
        pdb=" C   GLN B  62 "
      ideal   model   delta    sigma   weight residual
     113.61  101.36   12.25 1.50e+00 4.44e-01 6.67e+01
  angle pdb=" N   GLN D  62 "
        pdb=" CA  GLN D  62 "
        pdb=" C   GLN D  62 "
      ideal   model   delta    sigma   weight residual
     113.61  101.36   12.25 1.50e+00 4.44e-01 6.67e+01
  angle pdb=" N   GLN A  62 "
        pdb=" CA  GLN A  62 "
        pdb=" C   GLN A  62 "
      ideal   model   delta    sigma   weight residual
     113.61  101.40   12.21 1.50e+00 4.44e-01 6.63e+01
  angle pdb=" N   GLN C  62 "
        pdb=" CA  GLN C  62 "
        pdb=" C   GLN C  62 "
      ideal   model   delta    sigma   weight residual
     113.61  101.40   12.21 1.50e+00 4.44e-01 6.63e+01
  angle pdb=" N   GLN E  62 "
        pdb=" CA  GLN E  62 "
        pdb=" C   GLN E  62 "
      ideal   model   delta    sigma   weight residual
     113.61  101.40   12.21 1.50e+00 4.44e-01 6.62e+01
  ... (remaining 17580 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 6784
       17.66 -    35.33: 631
       35.33 -    52.99: 105
       52.99 -    70.66: 10
       70.66 -    88.32: 10
  Dihedral angle restraints: 7540
    sinusoidal: 3030
      harmonic: 4510
  Sorted by residual:
  dihedral pdb=" CA  SER A 250 "
           pdb=" C   SER A 250 "
           pdb=" N   ASN A 251 "
           pdb=" CA  ASN A 251 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.02  -20.98     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" CA  SER C 250 "
           pdb=" C   SER C 250 "
           pdb=" N   ASN C 251 "
           pdb=" CA  ASN C 251 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.04  -20.96     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" CA  SER E 250 "
           pdb=" C   SER E 250 "
           pdb=" N   ASN E 251 "
           pdb=" CA  ASN E 251 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.05  -20.95     0      5.00e+00 4.00e-02 1.76e+01
  ... (remaining 7537 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.087: 1654
       0.087 -    0.175: 251
       0.175 -    0.262: 20
       0.262 -    0.350: 15
       0.350 -    0.437: 5
  Chirality restraints: 1945
  Sorted by residual:
  chirality pdb=" CA  PHE A 119 "
            pdb=" N   PHE A 119 "
            pdb=" C   PHE A 119 "
            pdb=" CB  PHE A 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.78e+00
  chirality pdb=" CA  PHE C 119 "
            pdb=" N   PHE C 119 "
            pdb=" C   PHE C 119 "
            pdb=" CB  PHE C 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.68e+00
  chirality pdb=" CA  PHE D 119 "
            pdb=" N   PHE D 119 "
            pdb=" C   PHE D 119 "
            pdb=" CB  PHE D 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.68e+00
  ... (remaining 1942 not shown)

  Planarity restraints: 2240
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 206 "    0.014 2.00e-02 2.50e+03   1.50e-02 5.63e+00
        pdb=" CG  TRP A 206 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 206 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 206 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 206 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 206 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 206 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 206 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 206 "    0.017 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 206 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 206 "   -0.014 2.00e-02 2.50e+03   1.49e-02 5.58e+00
        pdb=" CG  TRP D 206 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 206 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 206 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 206 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 206 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 206 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 206 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 206 "   -0.017 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 206 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 206 "   -0.013 2.00e-02 2.50e+03   1.49e-02 5.57e+00
        pdb=" CG  TRP C 206 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 206 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 206 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 206 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 206 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 206 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 206 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 206 "   -0.017 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 206 "    0.003 2.00e-02 2.50e+03
  ... (remaining 2237 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2999
        2.79 -     3.32: 10644
        3.32 -     3.84: 19850
        3.84 -     4.37: 23606
        4.37 -     4.90: 41997
  Nonbonded interactions: 99096
  Sorted by model distance:
  nonbonded pdb=" OG  SER A  84 "
            pdb=" OD2 ASP B  86 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O   SER B 221 "
            pdb=" OG  SER B 221 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   SER A 221 "
            pdb=" OG  SER A 221 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   SER C 221 "
            pdb=" OG  SER C 221 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   SER E 221 "
            pdb=" OG  SER E 221 "
     model   vdw
     2.290 3.040
  ... (remaining 99091 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: 0.09
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:             0.360
  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:          0.430
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     27.000
  Find NCS groups from input model:        0.240
  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:             0.010
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
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      :  0.009   0.063  12910  Z= 0.397
  Angle     :  0.968  12.253  17585  Z= 0.560
  Chirality :  0.070   0.437   1945
  Planarity :  0.006   0.057   2240
  Dihedral  : 13.901  88.320   4630
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  0.73 %
    Favored  : 98.91 %
  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: -1.52 (0.21), residues: 1525
  helix: -0.17 (0.24), residues: 460
  sheet: -0.05 (0.25), residues: 480
  loop : -2.52 (0.22), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP A 206 
 HIS   0.005   0.001   HIS D 177 
 PHE   0.021   0.003   PHE A 208 
 TYR   0.022   0.003   TYR C 248 
 ARG   0.004   0.001   ARG B 141 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07198 (  540)
  hydrogen bonds       : angle       5.29909 ( 1740)
  covalent geometry    : bond        0.00932 (12910)
  covalent geometry    : angle       0.96773 (17585)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 150
  time to evaluate  : 1.291 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8876 (pttm) cc_final: 0.8515 (pttm)
REVERT: A  123 ARG cc_start: 0.7668 (ttm110) cc_final: 0.7360 (ttm-80)
REVERT: A  176 ASP cc_start: 0.7592 (m-30) cc_final: 0.7245 (m-30)
REVERT: B   86 ASP cc_start: 0.8073 (t70) cc_final: 0.7643 (t70)
REVERT: B   90 LYS cc_start: 0.8862 (pttm) cc_final: 0.8647 (pttm)
REVERT: C  124 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7748 (mm110)
REVERT: D   86 ASP cc_start: 0.8197 (t70) cc_final: 0.7983 (t70)
REVERT: D  124 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7495 (mm-40)
REVERT: E   86 ASP cc_start: 0.8117 (t70) cc_final: 0.7556 (t70)
REVERT: E   90 LYS cc_start: 0.8788 (pttm) cc_final: 0.8533 (pttm)
REVERT: E  123 ARG cc_start: 0.7583 (ttm110) cc_final: 0.7369 (ttm-80)
REVERT: E  208 PHE cc_start: 0.8357 (m-10) cc_final: 0.8097 (m-80)
  outliers start: 5
  outliers final: 5
  residues processed: 155
  average time/residue: 0.3561
  time to fit residues: 73.5726
Evaluate side-chains
  117 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 112
  time to evaluate  : 1.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain E residue  118 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    3.9990
   chunk 113 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 38 optimal weight:    0.5980
   chunk 76 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 117 optimal weight:    9.9990
   chunk 45 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 87 optimal weight:   20.0000
   chunk 136 optimal weight:    4.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 124 GLN
B 124 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.175484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.133270 restraints weight = 12881.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 1.63
r_work: 0.3176 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3015 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.1064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12910  Z= 0.137
  Angle     :  0.556   6.283  17585  Z= 0.285
  Chirality :  0.047   0.150   1945
  Planarity :  0.004   0.040   2240
  Dihedral  :  4.791  17.580   1705
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  5.96 %
    Favored  : 93.31 %
  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: -0.88 (0.21), residues: 1525
  helix:  0.86 (0.25), residues: 460
  sheet:  0.33 (0.25), residues: 455
  loop : -2.52 (0.21), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 206 
 HIS   0.002   0.001   HIS C 177 
 PHE   0.015   0.001   PHE E 119 
 TYR   0.011   0.001   TYR D 245 
 ARG   0.002   0.000   ARG C  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03740 (  540)
  hydrogen bonds       : angle       4.28669 ( 1740)
  covalent geometry    : bond        0.00323 (12910)
  covalent geometry    : angle       0.55594 (17585)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 1.491 
Fit side-chains
REVERT: A   86 ASP cc_start: 0.8742 (t70) cc_final: 0.8511 (t70)
REVERT: A  252 ILE cc_start: 0.8093 (mt) cc_final: 0.7726 (pt)
REVERT: B   86 ASP cc_start: 0.8604 (t70) cc_final: 0.8401 (t70)
REVERT: B  114 MET cc_start: 0.8038 (mtt) cc_final: 0.7768 (mtt)
REVERT: C   86 ASP cc_start: 0.8538 (t70) cc_final: 0.8318 (t70)
REVERT: D  115 ASP cc_start: 0.8449 (t70) cc_final: 0.8134 (t70)
REVERT: E   86 ASP cc_start: 0.8375 (t70) cc_final: 0.8162 (t70)
REVERT: E  123 ARG cc_start: 0.8099 (ttm110) cc_final: 0.7874 (ttm-80)
  outliers start: 10
  outliers final: 8
  residues processed: 112
  average time/residue: 0.3696
  time to fit residues: 55.0481
Evaluate side-chains
  104 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 1.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue  265 MET
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue  265 MET
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain D residue  278 LEU
Chi-restraints excluded: chain E residue  113 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 88 optimal weight:   20.0000
   chunk 45 optimal weight:    0.1980
   chunk 116 optimal weight:    9.9990
   chunk 115 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 109 optimal weight:    0.0770
   chunk 49 optimal weight:    2.9990
   chunk 69 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9990
   chunk 67 optimal weight:    6.9990
   overall best weight:    1.4544

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

Flipped N/Q/H residues before XYZ refinement:
B  89 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.175081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.133024 restraints weight = 13060.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 1.62
r_work: 0.3249 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.1409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12910  Z= 0.132
  Angle     :  0.524   5.539  17585  Z= 0.267
  Chirality :  0.046   0.143   1945
  Planarity :  0.003   0.032   2240
  Dihedral  :  4.499  18.946   1695
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  :  8.00 %
    Favored  : 90.40 %
  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: -0.58 (0.22), residues: 1525
  helix:  1.41 (0.25), residues: 460
  sheet:  0.29 (0.25), residues: 460
  loop : -2.45 (0.22), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E 206 
 HIS   0.003   0.001   HIS D 177 
 PHE   0.013   0.001   PHE A 247 
 TYR   0.011   0.001   TYR C 245 
 ARG   0.002   0.000   ARG C 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03506 (  540)
  hydrogen bonds       : angle       4.08359 ( 1740)
  covalent geometry    : bond        0.00318 (12910)
  covalent geometry    : angle       0.52350 (17585)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 1.268 
Fit side-chains
REVERT: A   86 ASP cc_start: 0.8578 (t70) cc_final: 0.8280 (t70)
REVERT: A  174 ARG cc_start: 0.8579 (tpp80) cc_final: 0.8305 (tpp80)
REVERT: A  252 ILE cc_start: 0.8136 (mt) cc_final: 0.7796 (pt)
REVERT: B   86 ASP cc_start: 0.8486 (t70) cc_final: 0.8281 (t70)
REVERT: C   86 ASP cc_start: 0.8363 (t70) cc_final: 0.8118 (t70)
REVERT: C  114 MET cc_start: 0.8402 (mtt) cc_final: 0.8005 (mtt)
REVERT: E   44 THR cc_start: 0.8944 (t) cc_final: 0.8737 (m)
REVERT: E   86 ASP cc_start: 0.8388 (t70) cc_final: 0.7787 (t70)
  outliers start: 22
  outliers final: 13
  residues processed: 118
  average time/residue: 0.3615
  time to fit residues: 56.0867
Evaluate side-chains
  117 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 1.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  265 MET
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  265 MET
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue  265 MET
Chi-restraints excluded: chain D residue  265 MET
Chi-restraints excluded: chain E residue   60 ASN
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain E residue  278 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 139 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 105 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 75 optimal weight:    5.9990
   chunk 93 optimal weight:    0.9980
   chunk 137 optimal weight:    7.9990
   chunk 24 optimal weight:    0.5980
   chunk 100 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 15 optimal weight:    7.9990
   overall best weight:    1.7186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.174463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.132371 restraints weight = 12922.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 1.61
r_work: 0.3213 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.1581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12910  Z= 0.145
  Angle     :  0.522   5.321  17585  Z= 0.268
  Chirality :  0.047   0.160   1945
  Planarity :  0.003   0.028   2240
  Dihedral  :  4.457  17.452   1695
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  9.75 %
    Favored  : 88.80 %
  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: -0.53 (0.22), residues: 1525
  helix:  1.47 (0.24), residues: 490
  sheet:  0.34 (0.25), residues: 460
  loop : -2.69 (0.22), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP E 206 
 HIS   0.003   0.001   HIS E 177 
 PHE   0.013   0.001   PHE A 247 
 TYR   0.011   0.001   TYR D 245 
 ARG   0.002   0.000   ARG C 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03578 (  540)
  hydrogen bonds       : angle       4.06750 ( 1740)
  covalent geometry    : bond        0.00351 (12910)
  covalent geometry    : angle       0.52171 (17585)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 1.353 
Fit side-chains
REVERT: A   86 ASP cc_start: 0.8579 (t70) cc_final: 0.8234 (t70)
REVERT: A  174 ARG cc_start: 0.8619 (tpp80) cc_final: 0.8305 (tpp80)
REVERT: B   86 ASP cc_start: 0.8531 (t70) cc_final: 0.8325 (t70)
REVERT: C  114 MET cc_start: 0.8475 (mtt) cc_final: 0.8072 (mtt)
REVERT: E   44 THR cc_start: 0.8966 (t) cc_final: 0.8765 (m)
REVERT: E   86 ASP cc_start: 0.8479 (t70) cc_final: 0.7966 (t70)
  outliers start: 20
  outliers final: 14
  residues processed: 125
  average time/residue: 0.3463
  time to fit residues: 57.6917
Evaluate side-chains
  114 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 1.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  265 MET
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  265 MET
Chi-restraints excluded: chain D residue  265 MET
Chi-restraints excluded: chain E residue   60 ASN
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain E residue  265 MET
Chi-restraints excluded: chain E residue  278 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 123 optimal weight:    2.9990
   chunk 9 optimal weight:    6.9990
   chunk 1 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 73 optimal weight:    0.8980
   chunk 43 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   chunk 27 optimal weight:    0.3980
   chunk 144 optimal weight:    0.0980
   chunk 20 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.177582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.135878 restraints weight = 12993.607|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 1.62
r_work: 0.3283 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.1834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  12910  Z= 0.092
  Angle     :  0.472   5.084  17585  Z= 0.241
  Chirality :  0.045   0.154   1945
  Planarity :  0.003   0.025   2240
  Dihedral  :  4.146  17.148   1695
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 11.20 %
    Favored  : 87.85 %
  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: -0.34 (0.22), residues: 1525
  helix:  1.53 (0.24), residues: 495
  sheet:  0.51 (0.26), residues: 455
  loop : -2.55 (0.23), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP E 206 
 HIS   0.002   0.000   HIS E 177 
 PHE   0.012   0.001   PHE A 247 
 TYR   0.012   0.001   TYR C 245 
 ARG   0.002   0.000   ARG A 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03058 (  540)
  hydrogen bonds       : angle       3.83544 ( 1740)
  covalent geometry    : bond        0.00203 (12910)
  covalent geometry    : angle       0.47242 (17585)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 1.266 
Fit side-chains
REVERT: A   86 ASP cc_start: 0.8613 (t70) cc_final: 0.8333 (t70)
REVERT: A  174 ARG cc_start: 0.8518 (tpp80) cc_final: 0.8161 (tpp80)
REVERT: A  265 MET cc_start: 0.7863 (ttp) cc_final: 0.7304 (ttt)
REVERT: B   86 ASP cc_start: 0.8405 (t70) cc_final: 0.7989 (t70)
REVERT: C   86 ASP cc_start: 0.8364 (t70) cc_final: 0.8086 (t70)
REVERT: C  114 MET cc_start: 0.8415 (mtt) cc_final: 0.8011 (mtt)
REVERT: D   44 THR cc_start: 0.8926 (t) cc_final: 0.8721 (m)
REVERT: E   86 ASP cc_start: 0.8267 (t70) cc_final: 0.7837 (t70)
  outliers start: 13
  outliers final: 9
  residues processed: 113
  average time/residue: 0.3522
  time to fit residues: 52.5611
Evaluate side-chains
  105 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 1.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue  265 MET
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  265 MET
Chi-restraints excluded: chain D residue  265 MET
Chi-restraints excluded: chain E residue  265 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 34 optimal weight:   20.0000
   chunk 29 optimal weight:   20.0000
   chunk 112 optimal weight:    9.9990
   chunk 131 optimal weight:    0.8980
   chunk 62 optimal weight:    5.9990
   chunk 27 optimal weight:    0.0570
   chunk 67 optimal weight:    0.0570
   chunk 16 optimal weight:    6.9990
   chunk 103 optimal weight:    6.9990
   chunk 135 optimal weight:    2.9990
   chunk 108 optimal weight:    1.9990
   overall best weight:    1.2020

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.175818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.134024 restraints weight = 13142.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 1.61
r_work: 0.3231 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.1887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12910  Z= 0.116
  Angle     :  0.485   5.024  17585  Z= 0.249
  Chirality :  0.046   0.151   1945
  Planarity :  0.003   0.025   2240
  Dihedral  :  4.173  18.102   1695
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 11.56 %
    Favored  : 87.56 %
  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: -0.28 (0.22), residues: 1525
  helix:  1.60 (0.24), residues: 495
  sheet:  0.55 (0.26), residues: 455
  loop : -2.53 (0.23), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C 206 
 HIS   0.002   0.001   HIS B 177 
 PHE   0.013   0.001   PHE A 247 
 TYR   0.011   0.001   TYR E 245 
 ARG   0.002   0.000   ARG A  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03216 (  540)
  hydrogen bonds       : angle       3.80218 ( 1740)
  covalent geometry    : bond        0.00274 (12910)
  covalent geometry    : angle       0.48537 (17585)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 1.280 
Fit side-chains
REVERT: A   86 ASP cc_start: 0.8748 (t70) cc_final: 0.8480 (t70)
REVERT: A  174 ARG cc_start: 0.8658 (tpp80) cc_final: 0.8427 (tpp80)
REVERT: B   86 ASP cc_start: 0.8563 (t70) cc_final: 0.8325 (t70)
REVERT: C   86 ASP cc_start: 0.8562 (t70) cc_final: 0.7948 (t70)
REVERT: C  114 MET cc_start: 0.8495 (mtt) cc_final: 0.8121 (mtt)
REVERT: D   44 THR cc_start: 0.9018 (t) cc_final: 0.8797 (m)
REVERT: E   86 ASP cc_start: 0.8465 (t70) cc_final: 0.7937 (t70)
  outliers start: 12
  outliers final: 11
  residues processed: 98
  average time/residue: 0.3832
  time to fit residues: 49.1571
Evaluate side-chains
  107 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 1.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue  265 MET
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  265 MET
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  265 MET
Chi-restraints excluded: chain E residue  265 MET
Chi-restraints excluded: chain E residue  278 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 134 optimal weight:    5.9990
   chunk 132 optimal weight:    0.3980
   chunk 54 optimal weight:    0.0670
   chunk 80 optimal weight:    3.9990
   chunk 130 optimal weight:    4.9990
   chunk 100 optimal weight:    5.9990
   chunk 24 optimal weight:    5.9990
   chunk 94 optimal weight:    0.0170
   chunk 140 optimal weight:    3.9990
   chunk 131 optimal weight:    2.9990
   overall best weight:    0.8758

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

Flipped N/Q/H residues before XYZ refinement:
** C 124 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 = 0.3969 r_free = 0.3969 target = 0.177368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.135865 restraints weight = 12973.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 1.59
r_work: 0.3296 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3134 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  12910  Z= 0.100
  Angle     :  0.468   5.026  17585  Z= 0.239
  Chirality :  0.045   0.147   1945
  Planarity :  0.003   0.028   2240
  Dihedral  :  4.042  18.519   1695
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 11.35 %
    Favored  : 87.20 %
  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: -0.18 (0.22), residues: 1525
  helix:  1.63 (0.24), residues: 495
  sheet:  0.65 (0.26), residues: 455
  loop : -2.46 (0.23), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 206 
 HIS   0.002   0.000   HIS C 177 
 PHE   0.012   0.001   PHE A 247 
 TYR   0.011   0.001   TYR C 245 
 ARG   0.007   0.000   ARG B 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03010 (  540)
  hydrogen bonds       : angle       3.71748 ( 1740)
  covalent geometry    : bond        0.00228 (12910)
  covalent geometry    : angle       0.46810 (17585)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 1.400 
Fit side-chains
REVERT: A   86 ASP cc_start: 0.8713 (t70) cc_final: 0.8388 (t70)
REVERT: A  174 ARG cc_start: 0.8632 (tpp80) cc_final: 0.8390 (tpp80)
REVERT: A  176 ASP cc_start: 0.8245 (m-30) cc_final: 0.7941 (m-30)
REVERT: B   86 ASP cc_start: 0.8555 (t70) cc_final: 0.8332 (t70)
REVERT: B  144 ASP cc_start: 0.8681 (p0) cc_final: 0.8461 (p0)
REVERT: C   86 ASP cc_start: 0.8562 (t70) cc_final: 0.8067 (t70)
REVERT: C  114 MET cc_start: 0.8481 (mtt) cc_final: 0.8107 (mtt)
REVERT: D   44 THR cc_start: 0.8990 (t) cc_final: 0.8777 (m)
REVERT: E   86 ASP cc_start: 0.8407 (t70) cc_final: 0.7887 (t70)
REVERT: E  252 ILE cc_start: 0.7961 (pt) cc_final: 0.7751 (mt)
  outliers start: 20
  outliers final: 14
  residues processed: 121
  average time/residue: 0.3524
  time to fit residues: 57.2771
Evaluate side-chains
  112 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 1.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  265 MET
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  265 MET
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain D residue  265 MET
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  265 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 145 optimal weight:    9.9990
   chunk 118 optimal weight:   20.0000
   chunk 67 optimal weight:    8.9990
   chunk 129 optimal weight:    7.9990
   chunk 57 optimal weight:   10.0000
   chunk 91 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 143 optimal weight:    7.9990
   chunk 130 optimal weight:    4.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  89 ASN
** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  89 ASN
** E 103 ASN ** 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 = 0.3890 r_free = 0.3890 target = 0.169343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.127197 restraints weight = 13244.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 1.61
r_work: 0.3145 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.1884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050  12910  Z= 0.281
  Angle     :  0.624   6.848  17585  Z= 0.323
  Chirality :  0.052   0.164   1945
  Planarity :  0.004   0.025   2240
  Dihedral  :  4.905  26.617   1695
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 11.78 %
    Favored  : 86.25 %
  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: -0.54 (0.22), residues: 1525
  helix:  1.55 (0.25), residues: 490
  sheet:  0.25 (0.26), residues: 460
  loop : -2.69 (0.23), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP E 206 
 HIS   0.005   0.001   HIS A 177 
 PHE   0.017   0.002   PHE C  19 
 TYR   0.015   0.002   TYR E 261 
 ARG   0.009   0.001   ARG B 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04554 (  540)
  hydrogen bonds       : angle       4.17124 ( 1740)
  covalent geometry    : bond        0.00709 (12910)
  covalent geometry    : angle       0.62368 (17585)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 1.357 
Fit side-chains
REVERT: A   86 ASP cc_start: 0.8474 (t70) cc_final: 0.8146 (t70)
REVERT: A  263 ASP cc_start: 0.8071 (t70) cc_final: 0.7864 (t0)
REVERT: B   86 ASP cc_start: 0.8393 (t70) cc_final: 0.7886 (t70)
REVERT: C   86 ASP cc_start: 0.8453 (t70) cc_final: 0.8182 (t70)
REVERT: C  114 MET cc_start: 0.8505 (mtt) cc_final: 0.8107 (mtt)
REVERT: E   86 ASP cc_start: 0.8315 (t70) cc_final: 0.8089 (t70)
  outliers start: 27
  outliers final: 21
  residues processed: 126
  average time/residue: 0.3480
  time to fit residues: 59.1924
Evaluate side-chains
  122 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 1.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  265 MET
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  265 MET
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  265 MET
Chi-restraints excluded: chain D residue  278 LEU
Chi-restraints excluded: chain E residue   60 ASN
Chi-restraints excluded: chain E residue  113 ASP
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain E residue  265 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 59 optimal weight:    7.9990
   chunk 109 optimal weight:    0.3980
   chunk 76 optimal weight:    5.9990
   chunk 126 optimal weight:    0.7980
   chunk 144 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 112 optimal weight:    2.9990
   chunk 149 optimal weight:    4.9990
   chunk 74 optimal weight:    9.9990
   chunk 75 optimal weight:    9.9990
   overall best weight:    1.8386

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

Flipped N/Q/H residues before XYZ refinement:
** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 103 ASN ** 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 = 0.3922 r_free = 0.3922 target = 0.172604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.131064 restraints weight = 13038.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 1.60
r_work: 0.3272 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3115 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.1989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  12910  Z= 0.152
  Angle     :  0.523   5.038  17585  Z= 0.269
  Chirality :  0.047   0.154   1945
  Planarity :  0.003   0.023   2240
  Dihedral  :  4.528  26.559   1695
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.51 %
    Favored  : 85.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.22), residues: 1525
  helix:  1.63 (0.25), residues: 490
  sheet:  0.35 (0.26), residues: 455
  loop : -2.60 (0.23), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C 206 
 HIS   0.003   0.001   HIS A 177 
 PHE   0.013   0.001   PHE A 247 
 TYR   0.013   0.001   TYR A 245 
 ARG   0.007   0.000   ARG B 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03686 (  540)
  hydrogen bonds       : angle       4.00713 ( 1740)
  covalent geometry    : bond        0.00368 (12910)
  covalent geometry    : angle       0.52346 (17585)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 1.257 
Fit side-chains
REVERT: A   86 ASP cc_start: 0.8542 (t70) cc_final: 0.8201 (t70)
REVERT: B   86 ASP cc_start: 0.8576 (t70) cc_final: 0.8166 (t70)
REVERT: C   86 ASP cc_start: 0.8482 (t70) cc_final: 0.8220 (t70)
REVERT: C  114 MET cc_start: 0.8495 (mtt) cc_final: 0.8096 (mtt)
REVERT: E   86 ASP cc_start: 0.8350 (t70) cc_final: 0.8134 (t70)
  outliers start: 22
  outliers final: 20
  residues processed: 122
  average time/residue: 0.4016
  time to fit residues: 66.3503
Evaluate side-chains
  116 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 1.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  265 MET
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  265 MET
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  265 MET
Chi-restraints excluded: chain E residue   60 ASN
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  265 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 75 optimal weight:    9.9990
   chunk 0 optimal weight:    6.9990
   chunk 128 optimal weight:   20.0000
   chunk 123 optimal weight:    7.9990
   chunk 132 optimal weight:    0.9980
   chunk 116 optimal weight:    6.9990
   chunk 29 optimal weight:   20.0000
   chunk 97 optimal weight:    8.9990
   chunk 48 optimal weight:    6.9990
   chunk 106 optimal weight:    5.9990
   overall best weight:    4.7988

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

Flipped N/Q/H residues before XYZ refinement:
** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 103 ASN ** 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 = 0.3874 r_free = 0.3874 target = 0.167571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.125882 restraints weight = 13054.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 1.57
r_work: 0.3163 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.2019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.053  12910  Z= 0.333
  Angle     :  0.672   7.352  17585  Z= 0.349
  Chirality :  0.054   0.182   1945
  Planarity :  0.004   0.030   2240
  Dihedral  :  5.204  33.622   1695
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 12.80 %
    Favored  : 85.31 %
  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: -0.78 (0.22), residues: 1525
  helix:  1.37 (0.25), residues: 490
  sheet:  0.03 (0.26), residues: 460
  loop : -2.75 (0.22), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP C 206 
 HIS   0.005   0.002   HIS A 177 
 PHE   0.018   0.002   PHE C  19 
 TYR   0.017   0.002   TYR E 261 
 ARG   0.007   0.001   ARG B 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04966 (  540)
  hydrogen bonds       : angle       4.33337 ( 1740)
  covalent geometry    : bond        0.00842 (12910)
  covalent geometry    : angle       0.67165 (17585)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 106
  time to evaluate  : 1.419 
Fit side-chains
REVERT: A  263 ASP cc_start: 0.8100 (t70) cc_final: 0.7866 (t0)
REVERT: B   86 ASP cc_start: 0.8347 (t70) cc_final: 0.8107 (t70)
REVERT: B  263 ASP cc_start: 0.8215 (t70) cc_final: 0.7912 (t0)
REVERT: C  114 MET cc_start: 0.8528 (mtt) cc_final: 0.8130 (mtt)
REVERT: E   86 ASP cc_start: 0.8257 (t70) cc_final: 0.7995 (t70)
  outliers start: 26
  outliers final: 22
  residues processed: 123
  average time/residue: 0.3372
  time to fit residues: 56.3141
Evaluate side-chains
  123 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 1.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  146 GLN
Chi-restraints excluded: chain B residue  265 MET
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  265 MET
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  265 MET
Chi-restraints excluded: chain D residue  278 LEU
Chi-restraints excluded: chain E residue   60 ASN
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain E residue  265 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 92 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0270
   chunk 116 optimal weight:    4.9990
   chunk 123 optimal weight:    5.9990
   chunk 53 optimal weight:    6.9990
   chunk 112 optimal weight:    5.9990
   chunk 0 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.4044

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

Flipped N/Q/H residues before XYZ refinement:
A  89 ASN
** E 103 ASN ** 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 = 0.3926 r_free = 0.3926 target = 0.172931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.131578 restraints weight = 13081.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 1.59
r_work: 0.3173 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  12910  Z= 0.131
  Angle     :  0.517   5.046  17585  Z= 0.267
  Chirality :  0.047   0.158   1945
  Planarity :  0.003   0.024   2240
  Dihedral  :  4.569  31.336   1695
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 13.38 %
    Favored  : 85.02 %
  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: -0.50 (0.22), residues: 1525
  helix:  1.61 (0.25), residues: 490
  sheet:  0.25 (0.26), residues: 455
  loop : -2.63 (0.23), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 206 
 HIS   0.003   0.001   HIS E 177 
 PHE   0.012   0.001   PHE A 247 
 TYR   0.013   0.001   TYR A 245 
 ARG   0.007   0.000   ARG B 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03621 (  540)
  hydrogen bonds       : angle       4.04968 ( 1740)
  covalent geometry    : bond        0.00306 (12910)
  covalent geometry    : angle       0.51681 (17585)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5884.02 seconds
wall clock time: 103 minutes 20.93 seconds (6200.93 seconds total)