Starting phenix.real_space_refine
on Wed Feb  4 02:27:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9u94_63959/02_2026/9u94_63959.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9u94_63959/02_2026/9u94_63959.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9u94_63959/02_2026/9u94_63959.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9u94_63959/02_2026/9u94_63959.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9u94_63959/02_2026/9u94_63959.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9u94_63959/02_2026/9u94_63959.map"
  }
  resolution = 2.11
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.024
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       9      5.16       5
     C    5142      2.51       5
     N    1470      2.21       5
     O    1695      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8316
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "C"
      Number of atoms: 1932
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 263, 1932
          Classifications: {'peptide': 263}
          Link IDs: {'PTRANS': 1, 'TRANS': 261}
    Chain: "F"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 840
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101}
  Restraints were copied for chains:
    A, B, E, D
  Time building chain proxies: 1.13, per 1000 atoms: 0.14
  Number of scatterers: 8316
  At special positions: 0
  Unit cell: (110.2, 115.52, 142.12, 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       9     16.00
     O    1695      8.00
     N    1470      7.00
     C    5142      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: 0.73
  Conformation dependent library (CDL) restraints added in 281.7 milliseconds
  

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1944

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 15 sheets defined
      9.7% alpha, 31.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'C' and resid 244 through 251
      removed outlier: 3.529A  pdb=" N   LEU C 248 " --> pdb=" O   THR C 244 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 255 through 263
    Processing helix  chain 'C' and resid 267 through 273
      removed outlier: 3.606A  pdb=" N   ASP C 273 " --> pdb=" O   ASN C 269 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 278 through 286
    Processing helix  chain 'F' and resid 74 through 76
      No H-bonds generated for 'chain 'F' and resid 74 through 76'
    Processing helix  chain 'A' and resid 244 through 251
      removed outlier: 3.530A  pdb=" N   LEU A 248 " --> pdb=" O   THR A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 263
    Processing helix  chain 'A' and resid 267 through 273
      removed outlier: 3.606A  pdb=" N   ASP A 273 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 286
    Processing helix  chain 'E' and resid 74 through 76
      No H-bonds generated for 'chain 'E' and resid 74 through 76'
    Processing helix  chain 'B' and resid 244 through 251
      removed outlier: 3.530A  pdb=" N   LEU B 248 " --> pdb=" O   THR B 244 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 263
    Processing helix  chain 'B' and resid 267 through 273
      removed outlier: 3.605A  pdb=" N   ASP B 273 " --> pdb=" O   ASN B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 278 through 286
    Processing helix  chain 'D' and resid 74 through 76
      No H-bonds generated for 'chain 'D' and resid 74 through 76'
    Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 30
      removed outlier: 3.550A  pdb=" N   GLY C  40 " --> pdb=" O   VAL C  27 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLN C  29 " --> pdb=" O   VAL C  38 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   VAL C  38 " --> pdb=" O   GLN C  29 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   THR C  37 " --> pdb=" O   ALA C  52 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   GLY C  54 " --> pdb=" O   THR C  37 " (cutoff:3.500A)
      removed outlier: 6.111A  pdb=" N   ALA C  39 " --> pdb=" O   GLY C  54 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   GLY C 149 " --> pdb=" O   MET C 171 " (cutoff:3.500A)
      removed outlier: 8.150A  pdb=" N   GLY C 173 " --> pdb=" O   GLY C 149 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   PHE C 151 " --> pdb=" O   GLY C 173 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   TYR C 170 " --> pdb=" O   ILE C 187 " (cutoff:3.500A)
      removed outlier: 7.817A  pdb=" N   GLY C 189 " --> pdb=" O   TYR C 170 " (cutoff:3.500A)
      removed outlier: 5.592A  pdb=" N   ILE C 172 " --> pdb=" O   GLY C 189 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   PHE C 186 " --> pdb=" O   ALA C 203 " (cutoff:3.500A)
      removed outlier: 8.465A  pdb=" N   GLY C 205 " --> pdb=" O   PHE C 186 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   LEU C 188 " --> pdb=" O   GLY C 205 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   VAL C 202 " --> pdb=" O   SER C 217 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 44 through 45
      removed outlier: 6.635A  pdb=" N   GLU C  44 " --> pdb=" O   ALA C  59 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   LYS C  58 " --> pdb=" O   ALA C  73 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   ILE C  72 " --> pdb=" O   ALA C  87 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   LEU C  86 " --> pdb=" O   ALA C 101 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   VAL C 100 " --> pdb=" O   ALA C 115 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   GLU C 114 " --> pdb=" O   VAL C 129 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   THR C 128 " --> pdb=" O   VAL C 143 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   GLU C 142 " --> pdb=" O   ASN C 164 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 177 through 178
      removed outlier: 6.735A  pdb=" N   LYS C 177 " --> pdb=" O   ILE C 194 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 226 through 228
      removed outlier: 6.067A  pdb=" N   LYS C 226 " --> pdb=" O   VAL B 216 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   VAL B 202 " --> pdb=" O   SER B 217 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   PHE B 186 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 8.465A  pdb=" N   GLY B 205 " --> pdb=" O   PHE B 186 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   LEU B 188 " --> pdb=" O   GLY B 205 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   TYR B 170 " --> pdb=" O   ILE B 187 " (cutoff:3.500A)
      removed outlier: 7.818A  pdb=" N   GLY B 189 " --> pdb=" O   TYR B 170 " (cutoff:3.500A)
      removed outlier: 5.591A  pdb=" N   ILE B 172 " --> pdb=" O   GLY B 189 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   GLY B 149 " --> pdb=" O   MET B 171 " (cutoff:3.500A)
      removed outlier: 8.150A  pdb=" N   GLY B 173 " --> pdb=" O   GLY B 149 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   PHE B 151 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   THR B  37 " --> pdb=" O   ALA B  52 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   GLY B  54 " --> pdb=" O   THR B  37 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   ALA B  39 " --> pdb=" O   GLY B  54 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   VAL B  38 " --> pdb=" O   GLN B  29 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLN B  29 " --> pdb=" O   VAL B  38 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLY B  40 " --> pdb=" O   VAL B  27 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'F' and resid 37 through 41
    Processing sheet with id=AA6, first strand: chain 'F' and resid 44 through 45
      removed outlier: 3.902A  pdb=" N   VAL F  45 " --> pdb=" O   HIS F 139 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   THR F 121 " --> pdb=" O   TYR F  68 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLY F  64 " --> pdb=" O   ILE F 125 " (cutoff:3.500A)
      removed outlier: 8.498A  pdb=" N   PHE F  63 " --> pdb=" O   ALA F  83 " (cutoff:3.500A)
      removed outlier: 5.233A  pdb=" N   ALA F  83 " --> pdb=" O   PHE F  63 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   TYR F  65 " --> pdb=" O   GLY F  81 " (cutoff:3.500A)
      removed outlier: 4.912A  pdb=" N   GLY F  81 " --> pdb=" O   TYR F  65 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   TRP F  67 " --> pdb=" O   ILE F  79 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 27 through 30
      removed outlier: 3.550A  pdb=" N   GLY A  40 " --> pdb=" O   VAL A  27 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   GLN A  29 " --> pdb=" O   VAL A  38 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   VAL A  38 " --> pdb=" O   GLN A  29 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   THR A  37 " --> pdb=" O   ALA A  52 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   GLY A  54 " --> pdb=" O   THR A  37 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   ALA A  39 " --> pdb=" O   GLY A  54 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   GLY A 149 " --> pdb=" O   MET A 171 " (cutoff:3.500A)
      removed outlier: 8.149A  pdb=" N   GLY A 173 " --> pdb=" O   GLY A 149 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   PHE A 151 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   TYR A 170 " --> pdb=" O   ILE A 187 " (cutoff:3.500A)
      removed outlier: 7.818A  pdb=" N   GLY A 189 " --> pdb=" O   TYR A 170 " (cutoff:3.500A)
      removed outlier: 5.591A  pdb=" N   ILE A 172 " --> pdb=" O   GLY A 189 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   PHE A 186 " --> pdb=" O   ALA A 203 " (cutoff:3.500A)
      removed outlier: 8.465A  pdb=" N   GLY A 205 " --> pdb=" O   PHE A 186 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   LEU A 188 " --> pdb=" O   GLY A 205 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   VAL A 202 " --> pdb=" O   SER A 217 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 44 through 45
      removed outlier: 6.636A  pdb=" N   GLU A  44 " --> pdb=" O   ALA A  59 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   LYS A  58 " --> pdb=" O   ALA A  73 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   ILE A  72 " --> pdb=" O   ALA A  87 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   LEU A  86 " --> pdb=" O   ALA A 101 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   VAL A 100 " --> pdb=" O   ALA A 115 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   GLU A 114 " --> pdb=" O   VAL A 129 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   THR A 128 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   GLU A 142 " --> pdb=" O   ASN A 164 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 177 through 178
      removed outlier: 6.735A  pdb=" N   LYS A 177 " --> pdb=" O   ILE A 194 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'E' and resid 37 through 41
    Processing sheet with id=AB2, first strand: chain 'E' and resid 44 through 45
      removed outlier: 3.902A  pdb=" N   VAL E  45 " --> pdb=" O   HIS E 139 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   THR E 121 " --> pdb=" O   TYR E  68 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLY E  64 " --> pdb=" O   ILE E 125 " (cutoff:3.500A)
      removed outlier: 8.498A  pdb=" N   PHE E  63 " --> pdb=" O   ALA E  83 " (cutoff:3.500A)
      removed outlier: 5.232A  pdb=" N   ALA E  83 " --> pdb=" O   PHE E  63 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   TYR E  65 " --> pdb=" O   GLY E  81 " (cutoff:3.500A)
      removed outlier: 4.911A  pdb=" N   GLY E  81 " --> pdb=" O   TYR E  65 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   TRP E  67 " --> pdb=" O   ILE E  79 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 44 through 45
      removed outlier: 6.636A  pdb=" N   GLU B  44 " --> pdb=" O   ALA B  59 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   LYS B  58 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   ILE B  72 " --> pdb=" O   ALA B  87 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   LEU B  86 " --> pdb=" O   ALA B 101 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   VAL B 100 " --> pdb=" O   ALA B 115 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   GLU B 114 " --> pdb=" O   VAL B 129 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   THR B 128 " --> pdb=" O   VAL B 143 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   GLU B 142 " --> pdb=" O   ASN B 164 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'B' and resid 177 through 178
      removed outlier: 6.736A  pdb=" N   LYS B 177 " --> pdb=" O   ILE B 194 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'D' and resid 37 through 41
    Processing sheet with id=AB6, first strand: chain 'D' and resid 44 through 45
      removed outlier: 3.902A  pdb=" N   VAL D  45 " --> pdb=" O   HIS D 139 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   THR D 121 " --> pdb=" O   TYR D  68 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLY D  64 " --> pdb=" O   ILE D 125 " (cutoff:3.500A)
      removed outlier: 8.498A  pdb=" N   PHE D  63 " --> pdb=" O   ALA D  83 " (cutoff:3.500A)
      removed outlier: 5.233A  pdb=" N   ALA D  83 " --> pdb=" O   PHE D  63 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   TYR D  65 " --> pdb=" O   GLY D  81 " (cutoff:3.500A)
      removed outlier: 4.912A  pdb=" N   GLY D  81 " --> pdb=" O   TYR D  65 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   TRP D  67 " --> pdb=" O   ILE D  79 " (cutoff:3.500A)

    223 hydrogen bonds defined for protein.
    624 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: 1.23

  Time building geometry restraints manager: 0.97 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: 2856
        1.34 -     1.46: 1509
        1.46 -     1.57: 4077
        1.57 -     1.69: 0
        1.69 -     1.80: 18
  Bond restraints: 8460
  Sorted by residual:
  bond pdb=" N   ILE E 125 "
       pdb=" CA  ILE E 125 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.27e-02 6.20e+03 9.58e+00
  bond pdb=" N   ILE D 125 "
       pdb=" CA  ILE D 125 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.27e-02 6.20e+03 9.56e+00
  bond pdb=" N   ILE F 125 "
       pdb=" CA  ILE F 125 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.27e-02 6.20e+03 9.29e+00
  bond pdb=" N   ASN F 131 "
       pdb=" CA  ASN F 131 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.037 1.23e-02 6.61e+03 9.05e+00
  bond pdb=" N   ASN D 131 "
       pdb=" CA  ASN D 131 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.037 1.23e-02 6.61e+03 8.94e+00
  ... (remaining 8455 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.01: 10601
        1.01 -     2.02: 643
        2.02 -     3.03: 136
        3.03 -     4.04: 38
        4.04 -     5.05: 6
  Bond angle restraints: 11424
  Sorted by residual:
  angle pdb=" CA  VAL F 130 "
        pdb=" C   VAL F 130 "
        pdb=" O   VAL F 130 "
      ideal   model   delta    sigma   weight residual
     121.93  117.39    4.54 1.12e+00 7.97e-01 1.65e+01
  angle pdb=" CA  VAL E 130 "
        pdb=" C   VAL E 130 "
        pdb=" O   VAL E 130 "
      ideal   model   delta    sigma   weight residual
     121.93  117.42    4.51 1.12e+00 7.97e-01 1.62e+01
  angle pdb=" CA  VAL D 130 "
        pdb=" C   VAL D 130 "
        pdb=" O   VAL D 130 "
      ideal   model   delta    sigma   weight residual
     121.93  117.43    4.50 1.12e+00 7.97e-01 1.61e+01
  angle pdb=" N   GLY B 149 "
        pdb=" CA  GLY B 149 "
        pdb=" C   GLY B 149 "
      ideal   model   delta    sigma   weight residual
     110.87  115.92   -5.05 1.54e+00 4.22e-01 1.08e+01
  angle pdb=" N   GLY C 149 "
        pdb=" CA  GLY C 149 "
        pdb=" C   GLY C 149 "
      ideal   model   delta    sigma   weight residual
     110.87  115.89   -5.02 1.54e+00 4.22e-01 1.06e+01
  ... (remaining 11419 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 4554
       17.73 -    35.45: 306
       35.45 -    53.18: 42
       53.18 -    70.91: 12
       70.91 -    88.63: 9
  Dihedral angle restraints: 4923
    sinusoidal: 1830
      harmonic: 3093
  Sorted by residual:
  dihedral pdb=" CA  GLN A 140 "
           pdb=" C   GLN A 140 "
           pdb=" N   TYR A 141 "
           pdb=" CA  TYR A 141 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.04   15.96     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CA  GLN B 140 "
           pdb=" C   GLN B 140 "
           pdb=" N   TYR B 141 "
           pdb=" CA  TYR B 141 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.10   15.90     0      5.00e+00 4.00e-02 1.01e+01
  dihedral pdb=" CA  GLN C 140 "
           pdb=" C   GLN C 140 "
           pdb=" N   TYR C 141 "
           pdb=" CA  TYR C 141 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.13   15.87     0      5.00e+00 4.00e-02 1.01e+01
  ... (remaining 4920 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 754
       0.035 -    0.070: 310
       0.070 -    0.104: 105
       0.104 -    0.139: 40
       0.139 -    0.174: 3
  Chirality restraints: 1212
  Sorted by residual:
  chirality pdb=" CA  ILE F 125 "
            pdb=" N   ILE F 125 "
            pdb=" C   ILE F 125 "
            pdb=" CB  ILE F 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.58e-01
  chirality pdb=" CA  ILE E 125 "
            pdb=" N   ILE E 125 "
            pdb=" C   ILE E 125 "
            pdb=" CB  ILE E 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.38e-01
  chirality pdb=" CA  ILE D 125 "
            pdb=" N   ILE D 125 "
            pdb=" C   ILE D 125 "
            pdb=" CB  ILE D 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.32e-01
  ... (remaining 1209 not shown)

  Planarity restraints: 1545
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D 124 "    0.007 2.00e-02 2.50e+03   1.38e-02 1.92e+00
        pdb=" C   VAL D 124 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   VAL D 124 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ILE D 125 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL E 124 "   -0.007 2.00e-02 2.50e+03   1.38e-02 1.89e+00
        pdb=" C   VAL E 124 "    0.024 2.00e-02 2.50e+03
        pdb=" O   VAL E 124 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ILE E 125 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL F 124 "    0.007 2.00e-02 2.50e+03   1.37e-02 1.87e+00
        pdb=" C   VAL F 124 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   VAL F 124 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ILE F 125 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1542 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1225
        2.77 -     3.30: 6975
        3.30 -     3.84: 13341
        3.84 -     4.37: 16363
        4.37 -     4.90: 29238
  Nonbonded interactions: 67142
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS E 126 "
            pdb=" OE2 GLU E 132 "
     model   vdw
     2.240 3.120
  nonbonded pdb=" NZ  LYS D 126 "
            pdb=" OE2 GLU D 132 "
     model   vdw
     2.240 3.120
  nonbonded pdb=" NZ  LYS F 126 "
            pdb=" OE2 GLU F 132 "
     model   vdw
     2.240 3.120
  nonbonded pdb=" CE  LYS D 126 "
            pdb=" OE2 GLU D 132 "
     model   vdw
     2.245 3.440
  nonbonded pdb=" CE  LYS E 126 "
            pdb=" OE2 GLU E 132 "
     model   vdw
     2.245 3.440
  ... (remaining 67137 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'F'
  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:             2.190
  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:          0.190
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.290
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
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   0.053   8460  Z= 0.210
  Angle     :  0.581   5.051  11424  Z= 0.365
  Chirality :  0.046   0.174   1212
  Planarity :  0.002   0.033   1545
  Dihedral  : 12.714  88.633   2979
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.23 (0.22), residues: 1098
  helix: -1.01 (0.51), residues: 93
  sheet: -0.09 (0.28), residues: 345
  loop : -2.48 (0.19), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  98 
 TYR   0.016   0.002   TYR B 141 
 PHE   0.013   0.001   PHE E 138 
 TRP   0.005   0.001   TRP B 259 
 HIS   0.002   0.001   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8460)
  covalent geometry    : angle       0.58086 (11424)
  hydrogen bonds       : bond        0.14853 (  223)
  hydrogen bonds       : angle       7.04943 (  624)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A   86 LEU cc_start: 0.8917 (tp) cc_final: 0.8715 (tp)
REVERT: A  116 ASN cc_start: 0.8046 (m-40) cc_final: 0.7795 (m-40)
REVERT: B  116 ASN cc_start: 0.8088 (m-40) cc_final: 0.7819 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.4872
  time to fit residues: 79.9269
Evaluate side-chains
  126 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
C 174 ASN
C 199 ASN
C 275 ASN
F 137 GLN
A 159 GLN
A 199 ASN
A 200 ASN
A 275 ASN
E 137 GLN
B 161 GLN
B 199 ASN
B 200 ASN
B 275 ASN
D 137 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.123741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.105851 restraints weight = 10547.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.3750 rms_B_bonded: 1.14
r_work: 0.3677 rms_B_bonded: 1.43 restraints_weight: 0.5000
r_work: 0.3580 rms_B_bonded: 2.55 restraints_weight: 0.2500
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.050   8460  Z= 0.316
  Angle     :  0.669   5.955  11424  Z= 0.381
  Chirality :  0.051   0.169   1212
  Planarity :  0.004   0.037   1545
  Dihedral  :  4.762  15.082   1173
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 2.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  :  7.10 %
    Favored  : 90.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.42 (0.21), residues: 1098
  helix: -1.51 (0.44), residues: 99
  sheet: -0.02 (0.27), residues: 345
  loop : -2.68 (0.17), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 225 
 TYR   0.016   0.002   TYR F  65 
 PHE   0.016   0.002   PHE E 138 
 TRP   0.016   0.002   TRP A 259 
 HIS   0.007   0.002   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00771 ( 8460)
  covalent geometry    : angle       0.66870 (11424)
  hydrogen bonds       : bond        0.08429 (  223)
  hydrogen bonds       : angle       6.14395 (  624)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 0.341 
Fit side-chains
  outliers start: 19
  outliers final: 12
  residues processed: 141
  average time/residue: 0.3981
  time to fit residues: 60.5784
Evaluate side-chains
  135 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   32 THR
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  222 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  141 TYR
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   56 GLU
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  141 TYR
Chi-restraints excluded: chain D residue   65 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0870
   chunk 14 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 85 optimal weight:    0.6980
   chunk 32 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 16 optimal weight:    0.3980
   chunk 102 optimal weight:    1.9990
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
C 133 ASN
C 161 GLN
C 199 ASN
F 137 GLN
A 159 GLN
B 199 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.126727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.108798 restraints weight = 10553.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3792 rms_B_bonded: 1.15
r_work: 0.3717 rms_B_bonded: 1.45 restraints_weight: 0.5000
r_work: 0.3621 rms_B_bonded: 2.60 restraints_weight: 0.2500
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   8460  Z= 0.124
  Angle     :  0.476   3.987  11424  Z= 0.274
  Chirality :  0.045   0.138   1212
  Planarity :  0.003   0.034   1545
  Dihedral  :  4.314  13.478   1173
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 1.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  :  7.79 %
    Favored  : 90.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.30 (0.21), residues: 1098
  helix: -1.40 (0.43), residues: 99
  sheet: -0.18 (0.26), residues: 375
  loop : -2.54 (0.18), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 225 
 TYR   0.009   0.001   TYR F  65 
 PHE   0.012   0.001   PHE D 138 
 TRP   0.010   0.001   TRP B 282 
 HIS   0.003   0.001   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 8460)
  covalent geometry    : angle       0.47617 (11424)
  hydrogen bonds       : bond        0.05487 (  223)
  hydrogen bonds       : angle       5.68583 (  624)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 0.308 
Fit side-chains
  outliers start: 15
  outliers final: 9
  residues processed: 129
  average time/residue: 0.4071
  time to fit residues: 56.6051
Evaluate side-chains
  128 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 119
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  141 TYR
Chi-restraints excluded: chain C residue  279 VAL
Chi-restraints excluded: chain F residue   65 TYR
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain E residue   65 TYR
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue  135 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 0 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
C  74 ASN
C 174 ASN
C 199 ASN
A 159 GLN
A 200 ASN
B 116 ASN
B 200 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.122808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.104959 restraints weight = 10712.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 1.14
r_work: 0.3663 rms_B_bonded: 1.43 restraints_weight: 0.5000
r_work: 0.3567 rms_B_bonded: 2.53 restraints_weight: 0.2500
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.057   8460  Z= 0.349
  Angle     :  0.675   5.402  11424  Z= 0.387
  Chirality :  0.051   0.174   1212
  Planarity :  0.004   0.035   1545
  Dihedral  :  4.844  15.396   1173
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 1.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  :  7.79 %
    Favored  : 89.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.47 (0.21), residues: 1098
  helix: -1.52 (0.43), residues: 99
  sheet:  0.12 (0.28), residues: 324
  loop : -2.75 (0.17), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 225 
 TYR   0.017   0.003   TYR F  65 
 PHE   0.016   0.002   PHE E 138 
 TRP   0.013   0.002   TRP A 259 
 HIS   0.007   0.002   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00858 ( 8460)
  covalent geometry    : angle       0.67467 (11424)
  hydrogen bonds       : bond        0.08701 (  223)
  hydrogen bonds       : angle       6.01548 (  624)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 0.197 
Fit side-chains
  outliers start: 25
  outliers final: 20
  residues processed: 135
  average time/residue: 0.3964
  time to fit residues: 57.6071
Evaluate side-chains
  142 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 122
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   32 THR
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  141 TYR
Chi-restraints excluded: chain C residue  200 ASN
Chi-restraints excluded: chain C residue  222 THR
Chi-restraints excluded: chain C residue  279 VAL
Chi-restraints excluded: chain F residue   65 TYR
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain E residue   41 MET
Chi-restraints excluded: chain E residue   65 TYR
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  141 TYR
Chi-restraints excluded: chain B residue  261 ASN
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain D residue   65 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0000
   chunk 21 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 59 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   chunk 90 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   overall best weight:    0.6184

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

Flipped N/Q/H residues before XYZ refinement:
C 159 GLN
C 199 ASN
F 137 GLN
A 116 ASN
A 159 GLN
B 116 ASN
B 199 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.127753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.110182 restraints weight = 10549.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3797 rms_B_bonded: 1.07
r_work: 0.3728 rms_B_bonded: 1.34 restraints_weight: 0.5000
r_work: 0.3639 rms_B_bonded: 2.37 restraints_weight: 0.2500
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8460  Z= 0.122
  Angle     :  0.474   4.055  11424  Z= 0.273
  Chirality :  0.045   0.141   1212
  Planarity :  0.003   0.033   1545
  Dihedral  :  4.349  17.025   1173
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 1.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  :  8.25 %
    Favored  : 89.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.18 (0.21), residues: 1098
  helix: -1.20 (0.44), residues: 99
  sheet:  0.05 (0.26), residues: 369
  loop : -2.57 (0.18), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 225 
 TYR   0.013   0.001   TYR A 141 
 PHE   0.012   0.001   PHE F 138 
 TRP   0.009   0.001   TRP A 282 
 HIS   0.002   0.001   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 8460)
  covalent geometry    : angle       0.47396 (11424)
  hydrogen bonds       : bond        0.05439 (  223)
  hydrogen bonds       : angle       5.61522 (  624)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 0.204 
Fit side-chains
  outliers start: 19
  outliers final: 16
  residues processed: 126
  average time/residue: 0.4312
  time to fit residues: 58.3230
Evaluate side-chains
  134 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  141 TYR
Chi-restraints excluded: chain C residue  279 VAL
Chi-restraints excluded: chain F residue   65 TYR
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain E residue   65 TYR
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  141 TYR
Chi-restraints excluded: chain B residue  261 ASN
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain D residue   65 TYR
Chi-restraints excluded: chain D residue   66 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 100 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
C 199 ASN
F 137 GLN
A 116 ASN
A 159 GLN
A 200 ASN
B 200 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.122342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.104534 restraints weight = 10553.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3731 rms_B_bonded: 1.13
r_work: 0.3658 rms_B_bonded: 1.40 restraints_weight: 0.5000
r_work: 0.3563 rms_B_bonded: 2.49 restraints_weight: 0.2500
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.2055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.062   8460  Z= 0.376
  Angle     :  0.698   5.578  11424  Z= 0.400
  Chirality :  0.052   0.183   1212
  Planarity :  0.004   0.034   1545
  Dihedral  :  4.920  19.738   1173
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 1.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  :  8.59 %
    Favored  : 88.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.48 (0.21), residues: 1098
  helix: -1.48 (0.43), residues: 99
  sheet:  0.16 (0.28), residues: 324
  loop : -2.80 (0.17), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 225 
 TYR   0.023   0.003   TYR A 141 
 PHE   0.017   0.003   PHE E 138 
 TRP   0.014   0.002   TRP C 259 
 HIS   0.006   0.002   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00926 ( 8460)
  covalent geometry    : angle       0.69843 (11424)
  hydrogen bonds       : bond        0.08948 (  223)
  hydrogen bonds       : angle       5.99482 (  624)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 123
  time to evaluate  : 0.314 
Fit side-chains
  outliers start: 23
  outliers final: 18
  residues processed: 133
  average time/residue: 0.4129
  time to fit residues: 59.1647
Evaluate side-chains
  143 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  141 TYR
Chi-restraints excluded: chain C residue  279 VAL
Chi-restraints excluded: chain F residue   65 TYR
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain E residue   41 MET
Chi-restraints excluded: chain E residue   65 TYR
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  141 TYR
Chi-restraints excluded: chain B residue  261 ASN
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain D residue   65 TYR
Chi-restraints excluded: chain D residue   66 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 85 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 87 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 40 optimal weight:    0.5980
   chunk 71 optimal weight:    0.3980
   chunk 69 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
C 159 GLN
C 199 ASN
F 137 GLN
A 116 ASN
A 159 GLN
B 199 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.126207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.108445 restraints weight = 10614.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.3791 rms_B_bonded: 1.10
r_work: 0.3719 rms_B_bonded: 1.41 restraints_weight: 0.5000
r_work: 0.3625 rms_B_bonded: 2.52 restraints_weight: 0.2500
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.1908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8460  Z= 0.119
  Angle     :  0.475   4.076  11424  Z= 0.273
  Chirality :  0.044   0.145   1212
  Planarity :  0.003   0.032   1545
  Dihedral  :  4.399  22.007   1173
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 1.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  9.74 %
    Favored  : 88.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.24 (0.21), residues: 1098
  helix: -1.15 (0.44), residues: 99
  sheet: -0.06 (0.26), residues: 372
  loop : -2.58 (0.18), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 225 
 TYR   0.012   0.001   TYR A 141 
 PHE   0.015   0.001   PHE F 138 
 TRP   0.009   0.001   TRP B 282 
 HIS   0.003   0.001   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8460)
  covalent geometry    : angle       0.47508 (11424)
  hydrogen bonds       : bond        0.05385 (  223)
  hydrogen bonds       : angle       5.58627 (  624)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.259 
Fit side-chains
REVERT: E   62 LEU cc_start: 0.8628 (mt) cc_final: 0.8308 (mm)
  outliers start: 18
  outliers final: 18
  residues processed: 129
  average time/residue: 0.4450
  time to fit residues: 61.8515
Evaluate side-chains
  137 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   32 THR
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  141 TYR
Chi-restraints excluded: chain C residue  279 VAL
Chi-restraints excluded: chain F residue   65 TYR
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain E residue   65 TYR
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  141 TYR
Chi-restraints excluded: chain B residue  261 ASN
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain D residue   65 TYR
Chi-restraints excluded: chain D residue   66 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 101 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 74 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9980
   chunk 83 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 87 optimal weight:    0.9990
   overall best weight:    1.1988

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

Flipped N/Q/H residues before XYZ refinement:
C  74 ASN
C 199 ASN
A 116 ASN
A 159 GLN
A 200 ASN
B 161 GLN
B 200 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.124377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.106510 restraints weight = 10532.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3759 rms_B_bonded: 1.14
r_work: 0.3686 rms_B_bonded: 1.43 restraints_weight: 0.5000
r_work: 0.3590 rms_B_bonded: 2.55 restraints_weight: 0.2500
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8460  Z= 0.204
  Angle     :  0.553   4.920  11424  Z= 0.316
  Chirality :  0.046   0.153   1212
  Planarity :  0.003   0.033   1545
  Dihedral  :  4.583  23.326   1173
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 2.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  :  9.05 %
    Favored  : 88.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.26 (0.21), residues: 1098
  helix: -1.19 (0.44), residues: 99
  sheet: -0.04 (0.26), residues: 372
  loop : -2.62 (0.18), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 225 
 TYR   0.016   0.002   TYR A 141 
 PHE   0.016   0.002   PHE F 138 
 TRP   0.008   0.002   TRP A 282 
 HIS   0.004   0.001   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 ( 8460)
  covalent geometry    : angle       0.55303 (11424)
  hydrogen bonds       : bond        0.07004 (  223)
  hydrogen bonds       : angle       5.76208 (  624)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.230 
Fit side-chains
  outliers start: 20
  outliers final: 18
  residues processed: 128
  average time/residue: 0.3994
  time to fit residues: 55.1395
Evaluate side-chains
  137 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   32 THR
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  141 TYR
Chi-restraints excluded: chain C residue  279 VAL
Chi-restraints excluded: chain F residue   65 TYR
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain E residue   65 TYR
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  141 TYR
Chi-restraints excluded: chain B residue  261 ASN
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain D residue   65 TYR
Chi-restraints excluded: chain D residue   66 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 105 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0980
   chunk 72 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 96 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
C 199 ASN
F 137 GLN
A 159 GLN
B 206 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.124896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.106952 restraints weight = 10663.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 1.15
r_work: 0.3692 rms_B_bonded: 1.44 restraints_weight: 0.5000
r_work: 0.3596 rms_B_bonded: 2.58 restraints_weight: 0.2500
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.1967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8460  Z= 0.174
  Angle     :  0.529   5.265  11424  Z= 0.302
  Chirality :  0.046   0.138   1212
  Planarity :  0.003   0.032   1545
  Dihedral  :  4.553  25.131   1173
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 1.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  :  9.97 %
    Favored  : 87.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.23 (0.21), residues: 1098
  helix: -1.14 (0.44), residues: 99
  sheet: -0.04 (0.26), residues: 372
  loop : -2.59 (0.18), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 246 
 TYR   0.014   0.002   TYR A 141 
 PHE   0.016   0.001   PHE F 138 
 TRP   0.009   0.001   TRP A 282 
 HIS   0.003   0.001   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 8460)
  covalent geometry    : angle       0.52875 (11424)
  hydrogen bonds       : bond        0.06477 (  223)
  hydrogen bonds       : angle       5.70098 (  624)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 0.310 
Fit side-chains
  outliers start: 19
  outliers final: 19
  residues processed: 123
  average time/residue: 0.4335
  time to fit residues: 57.1683
Evaluate side-chains
  137 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   32 THR
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  141 TYR
Chi-restraints excluded: chain C residue  279 VAL
Chi-restraints excluded: chain F residue   65 TYR
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain E residue   65 TYR
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  141 TYR
Chi-restraints excluded: chain B residue  200 ASN
Chi-restraints excluded: chain B residue  261 ASN
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain D residue   65 TYR
Chi-restraints excluded: chain D residue   66 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 59 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 72 optimal weight:    0.0970
   chunk 91 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 90 optimal weight:    0.8980
   chunk 103 optimal weight:    2.9990
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
C 199 ASN
A 116 ASN
A 159 GLN
A 200 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.125723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.107706 restraints weight = 10455.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3778 rms_B_bonded: 1.14
r_work: 0.3707 rms_B_bonded: 1.44 restraints_weight: 0.5000
r_work: 0.3614 rms_B_bonded: 2.55 restraints_weight: 0.2500
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.1943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8460  Z= 0.138
  Angle     :  0.493   5.047  11424  Z= 0.282
  Chirality :  0.045   0.130   1212
  Planarity :  0.003   0.032   1545
  Dihedral  :  4.441  25.551   1173
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 1.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 10.31 %
    Favored  : 87.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.17 (0.22), residues: 1098
  helix: -1.11 (0.44), residues: 99
  sheet: -0.00 (0.26), residues: 372
  loop : -2.54 (0.18), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 225 
 TYR   0.011   0.001   TYR A 141 
 PHE   0.016   0.001   PHE F 138 
 TRP   0.009   0.001   TRP A 282 
 HIS   0.003   0.001   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8460)
  covalent geometry    : angle       0.49335 (11424)
  hydrogen bonds       : bond        0.05846 (  223)
  hydrogen bonds       : angle       5.60325 (  624)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.319 
Fit side-chains
REVERT: E   62 LEU cc_start: 0.8639 (mt) cc_final: 0.8341 (mm)
  outliers start: 17
  outliers final: 18
  residues processed: 123
  average time/residue: 0.4053
  time to fit residues: 53.8130
Evaluate side-chains
  132 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   32 THR
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  141 TYR
Chi-restraints excluded: chain C residue  279 VAL
Chi-restraints excluded: chain F residue   65 TYR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain E residue   65 TYR
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  141 TYR
Chi-restraints excluded: chain B residue  200 ASN
Chi-restraints excluded: chain B residue  261 ASN
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain D residue   65 TYR
Chi-restraints excluded: chain D residue   66 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 103 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 25 optimal weight:    0.7980
   chunk 77 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
C  74 ASN
C 199 ASN
A 159 GLN
A 252 ASN
B 199 ASN
B 206 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.123200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.105256 restraints weight = 10556.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 1.15
r_work: 0.3667 rms_B_bonded: 1.43 restraints_weight: 0.5000
r_work: 0.3571 rms_B_bonded: 2.55 restraints_weight: 0.2500
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.2078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.047   8460  Z= 0.285
  Angle     :  0.628   4.869  11424  Z= 0.360
  Chirality :  0.049   0.155   1212
  Planarity :  0.003   0.033   1545
  Dihedral  :  4.792  25.327   1173
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 1.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 10.31 %
    Favored  : 87.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.43 (0.21), residues: 1098
  helix: -1.31 (0.43), residues: 99
  sheet:  0.06 (0.27), residues: 342
  loop : -2.77 (0.17), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 225 
 TYR   0.020   0.002   TYR A 141 
 PHE   0.017   0.002   PHE F 138 
 TRP   0.010   0.002   TRP C 259 
 HIS   0.005   0.001   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00693 ( 8460)
  covalent geometry    : angle       0.62826 (11424)
  hydrogen bonds       : bond        0.08129 (  223)
  hydrogen bonds       : angle       5.87723 (  624)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4083.60 seconds
wall clock time: 69 minutes 51.05 seconds (4191.05 seconds total)