Starting phenix.real_space_refine
on Tue Aug  4 18:21:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xbx_38232/08_2026/8xbx_38232.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xbx_38232/08_2026/8xbx_38232.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xbx_38232/08_2026/8xbx_38232.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xbx_38232/08_2026/8xbx_38232.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xbx_38232/08_2026/8xbx_38232.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xbx_38232/08_2026/8xbx_38232.cif"
  }
  resolution = 4.36
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      38      5.49       5
     S      33      5.16       5
     C    3543      2.51       5
     N    1047      2.21       5
     O    1212      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 5873
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "I"
      Number of atoms: 389
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 389
          Classifications: {'DNA': 19}
          Link IDs: {'rna3p': 18}
    Chain: "J"
      Number of atoms: 390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 390
          Classifications: {'DNA': 19}
          Link IDs: {'rna3p': 18}
    Chain: "K"
      Number of atoms: 1698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1698
          Classifications: {'peptide': 221}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 216}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 1698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1698
          Classifications: {'peptide': 221}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 216}
          Chain breaks: 1
    Chain: "M"
      Number of atoms: 1698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1698
          Classifications: {'peptide': 221}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 216}
          Chain breaks: 1
  Time building chain proxies: 1.36, per 1000 atoms: 0.23
  Number of scatterers: 5873
  At special positions: 0
  Unit cell: (109.18, 109.18, 85.86, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      33     16.00
     P      38     15.00
     O    1212      8.00
     N    1047      7.00
     C    3543      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: 0.30
  Conformation dependent library (CDL) restraints added in 164.0 milliseconds
  

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1200

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 3 sheets defined
      47.1% alpha, 20.8% beta
      19 base pairs and 36 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'K' and resid 106 through 113
    Processing helix  chain 'K' and resid 132 through 144
      removed outlier: 3.675A  pdb=" N   VAL K 142 " --> pdb=" O   HIS K 138 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 145 through 146
      No H-bonds generated for 'chain 'K' and resid 145 through 146'
    Processing helix  chain 'K' and resid 147 through 151
    Processing helix  chain 'K' and resid 167 through 178
    Processing helix  chain 'K' and resid 181 through 188
    Processing helix  chain 'K' and resid 196 through 214
      removed outlier: 3.933A  pdb=" N   LEU K 204 " --> pdb=" O   GLN K 200 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   TYR K 205 " --> pdb=" O   THR K 201 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLN K 206 " --> pdb=" O   GLN K 202 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ALA K 209 " --> pdb=" O   TYR K 205 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   VAL K 212 " --> pdb=" O   SER K 208 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   GLU K 213 " --> pdb=" O   ALA K 209 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   SER K 214 " --> pdb=" O   MET K 210 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 225 through 231
      removed outlier: 3.532A  pdb=" N   ARG K 229 " --> pdb=" O   THR K 225 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 237 through 260
    Processing helix  chain 'K' and resid 291 through 296
      removed outlier: 3.879A  pdb=" N   ALA K 295 " --> pdb=" O   ILE K 291 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 106 through 113
    Processing helix  chain 'L' and resid 132 through 144
      removed outlier: 3.675A  pdb=" N   VAL L 142 " --> pdb=" O   HIS L 138 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 145 through 146
      No H-bonds generated for 'chain 'L' and resid 145 through 146'
    Processing helix  chain 'L' and resid 147 through 151
    Processing helix  chain 'L' and resid 167 through 178
    Processing helix  chain 'L' and resid 181 through 188
    Processing helix  chain 'L' and resid 196 through 214
      removed outlier: 3.933A  pdb=" N   LEU L 204 " --> pdb=" O   GLN L 200 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   TYR L 205 " --> pdb=" O   THR L 201 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLN L 206 " --> pdb=" O   GLN L 202 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ALA L 209 " --> pdb=" O   TYR L 205 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   VAL L 212 " --> pdb=" O   SER L 208 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   GLU L 213 " --> pdb=" O   ALA L 209 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   SER L 214 " --> pdb=" O   MET L 210 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 225 through 231
      removed outlier: 3.532A  pdb=" N   ARG L 229 " --> pdb=" O   THR L 225 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 237 through 260
    Processing helix  chain 'L' and resid 291 through 296
      removed outlier: 3.879A  pdb=" N   ALA L 295 " --> pdb=" O   ILE L 291 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 106 through 113
    Processing helix  chain 'M' and resid 132 through 144
      removed outlier: 3.675A  pdb=" N   VAL M 142 " --> pdb=" O   HIS M 138 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 145 through 146
      No H-bonds generated for 'chain 'M' and resid 145 through 146'
    Processing helix  chain 'M' and resid 147 through 151
    Processing helix  chain 'M' and resid 167 through 178
    Processing helix  chain 'M' and resid 181 through 188
    Processing helix  chain 'M' and resid 196 through 214
      removed outlier: 3.933A  pdb=" N   LEU M 204 " --> pdb=" O   GLN M 200 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   TYR M 205 " --> pdb=" O   THR M 201 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLN M 206 " --> pdb=" O   GLN M 202 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ALA M 209 " --> pdb=" O   TYR M 205 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   VAL M 212 " --> pdb=" O   SER M 208 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   GLU M 213 " --> pdb=" O   ALA M 209 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   SER M 214 " --> pdb=" O   MET M 210 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 225 through 231
      removed outlier: 3.533A  pdb=" N   ARG M 229 " --> pdb=" O   THR M 225 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 237 through 260
    Processing helix  chain 'M' and resid 291 through 296
      removed outlier: 3.879A  pdb=" N   ALA M 295 " --> pdb=" O   ILE M 291 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'K' and resid 189 through 193
      removed outlier: 5.370A  pdb=" N   LYS K 156 " --> pdb=" O   TYR K 216 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LEU K 218 " --> pdb=" O   LYS K 156 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   ALA K 217 " --> pdb=" O   ALA K 262 " (cutoff:3.500A)
      removed outlier: 7.679A  pdb=" N   VAL K 264 " --> pdb=" O   ALA K 217 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   LEU K 219 " --> pdb=" O   VAL K 264 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   THR K 266 " --> pdb=" O   LEU K 219 " (cutoff:3.500A)
      removed outlier: 7.303A  pdb=" N   VAL K 221 " --> pdb=" O   THR K 266 " (cutoff:3.500A)
      removed outlier: 8.633A  pdb=" N   GLN K 268 " --> pdb=" O   VAL K 221 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   ILE K 265 " --> pdb=" O   THR K 123 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   MET K 125 " --> pdb=" O   ILE K 265 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ASN K 267 " --> pdb=" O   MET K 125 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   GLY K 127 " --> pdb=" O   ASN K 267 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   ILE K 122 " --> pdb=" O   THR K 298 " (cutoff:3.500A)
      removed outlier: 8.606A  pdb=" N   LEU K 300 " --> pdb=" O   ILE K 122 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   GLU K 124 " --> pdb=" O   LEU K 300 " (cutoff:3.500A)
      removed outlier: 7.745A  pdb=" N   LEU K 302 " --> pdb=" O   GLU K 124 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   PHE K 126 " --> pdb=" O   LEU K 302 " (cutoff:3.500A)
      removed outlier: 9.077A  pdb=" N   LYS K 304 " --> pdb=" O   PHE K 126 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   ARG K 299 " --> pdb=" O   TYR K 315 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 189 through 193
      removed outlier: 5.370A  pdb=" N   LYS L 156 " --> pdb=" O   TYR L 216 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LEU L 218 " --> pdb=" O   LYS L 156 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   ALA L 217 " --> pdb=" O   ALA L 262 " (cutoff:3.500A)
      removed outlier: 7.678A  pdb=" N   VAL L 264 " --> pdb=" O   ALA L 217 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   LEU L 219 " --> pdb=" O   VAL L 264 " (cutoff:3.500A)
      removed outlier: 7.852A  pdb=" N   THR L 266 " --> pdb=" O   LEU L 219 " (cutoff:3.500A)
      removed outlier: 7.302A  pdb=" N   VAL L 221 " --> pdb=" O   THR L 266 " (cutoff:3.500A)
      removed outlier: 8.633A  pdb=" N   GLN L 268 " --> pdb=" O   VAL L 221 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ILE L 265 " --> pdb=" O   THR L 123 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   MET L 125 " --> pdb=" O   ILE L 265 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ASN L 267 " --> pdb=" O   MET L 125 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   GLY L 127 " --> pdb=" O   ASN L 267 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   ILE L 122 " --> pdb=" O   THR L 298 " (cutoff:3.500A)
      removed outlier: 8.606A  pdb=" N   LEU L 300 " --> pdb=" O   ILE L 122 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   GLU L 124 " --> pdb=" O   LEU L 300 " (cutoff:3.500A)
      removed outlier: 7.746A  pdb=" N   LEU L 302 " --> pdb=" O   GLU L 124 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   PHE L 126 " --> pdb=" O   LEU L 302 " (cutoff:3.500A)
      removed outlier: 9.077A  pdb=" N   LYS L 304 " --> pdb=" O   PHE L 126 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   ARG L 299 " --> pdb=" O   TYR L 315 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'M' and resid 189 through 193
      removed outlier: 5.370A  pdb=" N   LYS M 156 " --> pdb=" O   TYR M 216 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   LEU M 218 " --> pdb=" O   LYS M 156 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   ALA M 217 " --> pdb=" O   ALA M 262 " (cutoff:3.500A)
      removed outlier: 7.679A  pdb=" N   VAL M 264 " --> pdb=" O   ALA M 217 " (cutoff:3.500A)
      removed outlier: 6.056A  pdb=" N   LEU M 219 " --> pdb=" O   VAL M 264 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   THR M 266 " --> pdb=" O   LEU M 219 " (cutoff:3.500A)
      removed outlier: 7.303A  pdb=" N   VAL M 221 " --> pdb=" O   THR M 266 " (cutoff:3.500A)
      removed outlier: 8.633A  pdb=" N   GLN M 268 " --> pdb=" O   VAL M 221 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   ILE M 265 " --> pdb=" O   THR M 123 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   MET M 125 " --> pdb=" O   ILE M 265 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ASN M 267 " --> pdb=" O   MET M 125 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   GLY M 127 " --> pdb=" O   ASN M 267 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   ILE M 122 " --> pdb=" O   THR M 298 " (cutoff:3.500A)
      removed outlier: 8.606A  pdb=" N   LEU M 300 " --> pdb=" O   ILE M 122 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   GLU M 124 " --> pdb=" O   LEU M 300 " (cutoff:3.500A)
      removed outlier: 7.746A  pdb=" N   LEU M 302 " --> pdb=" O   GLU M 124 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   PHE M 126 " --> pdb=" O   LEU M 302 " (cutoff:3.500A)
      removed outlier: 9.076A  pdb=" N   LYS M 304 " --> pdb=" O   PHE M 126 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   ARG M 299 " --> pdb=" O   TYR M 315 " (cutoff:3.500A)

    231 hydrogen bonds defined for protein.
    675 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      49 hydrogen bonds
      98 hydrogen bond angles
      0 basepair planarities
      19 basepair parallelities
      36 stacking parallelities
  Total time for adding SS restraints: 0.95

  Time building geometry restraints manager: 0.46 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1849
        1.34 -     1.46: 1254
        1.46 -     1.57: 2801
        1.57 -     1.69: 74
        1.69 -     1.81: 54
  Bond restraints: 6032
  Sorted by residual:
  bond pdb=" C1'  DC J  16 "
       pdb=" N1   DC J  16 "
    ideal  model  delta    sigma   weight residual
    1.468  1.557 -0.089 1.40e-02 5.10e+03 4.08e+01
  bond pdb=" C1'  DC J   1 "
       pdb=" N1   DC J   1 "
    ideal  model  delta    sigma   weight residual
    1.468  1.557 -0.089 1.40e-02 5.10e+03 4.00e+01
  bond pdb=" C1'  DC I 154 "
       pdb=" N1   DC I 154 "
    ideal  model  delta    sigma   weight residual
    1.468  1.556 -0.088 1.40e-02 5.10e+03 3.95e+01
  bond pdb=" C1'  DC I 155 "
       pdb=" N1   DC I 155 "
    ideal  model  delta    sigma   weight residual
    1.468  1.556 -0.088 1.40e-02 5.10e+03 3.94e+01
  bond pdb=" C1'  DC I 152 "
       pdb=" N1   DC I 152 "
    ideal  model  delta    sigma   weight residual
    1.468  1.556 -0.088 1.40e-02 5.10e+03 3.94e+01
  ... (remaining 6027 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 7886
        1.60 -     3.20: 267
        3.20 -     4.80: 100
        4.80 -     6.40: 3
        6.40 -     8.00: 42
  Bond angle restraints: 8298
  Sorted by residual:
  angle pdb=" C3'  DG I 149 "
        pdb=" C2'  DG I 149 "
        pdb=" C1'  DG I 149 "
      ideal   model   delta    sigma   weight residual
     102.50   98.02    4.48 1.20e+00 6.94e-01 1.39e+01
  angle pdb=" O3'  DC J  10 "
        pdb=" P    DG J  11 "
        pdb=" O5'  DG J  11 "
      ideal   model   delta    sigma   weight residual
     104.00   96.98    7.02 1.90e+00 2.77e-01 1.37e+01
  angle pdb=" C3'  DC J  16 "
        pdb=" C2'  DC J  16 "
        pdb=" C1'  DC J  16 "
      ideal   model   delta    sigma   weight residual
     102.50   98.09    4.41 1.20e+00 6.94e-01 1.35e+01
  angle pdb=" O3'  DG J   2 "
        pdb=" P    DT J   3 "
        pdb=" O5'  DT J   3 "
      ideal   model   delta    sigma   weight residual
     104.00   97.02    6.98 1.90e+00 2.77e-01 1.35e+01
  angle pdb=" O3'  DA I 153 "
        pdb=" P    DC I 154 "
        pdb=" O5'  DC I 154 "
      ideal   model   delta    sigma   weight residual
     104.00   97.02    6.98 1.90e+00 2.77e-01 1.35e+01
  ... (remaining 8293 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.90: 2999
       15.90 -    31.80: 311
       31.80 -    47.69: 122
       47.69 -    63.59: 79
       63.59 -    79.49: 6
  Dihedral angle restraints: 3517
    sinusoidal: 1633
      harmonic: 1884
  Sorted by residual:
  dihedral pdb=" CA  VAL L 334 "
           pdb=" C   VAL L 334 "
           pdb=" N   GLY L 335 "
           pdb=" CA  GLY L 335 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.12  -27.88     0      5.00e+00 4.00e-02 3.11e+01
  dihedral pdb=" CA  VAL M 334 "
           pdb=" C   VAL M 334 "
           pdb=" N   GLY M 335 "
           pdb=" CA  GLY M 335 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.14  -27.86     0      5.00e+00 4.00e-02 3.10e+01
  dihedral pdb=" CA  VAL K 334 "
           pdb=" C   VAL K 334 "
           pdb=" N   GLY K 335 "
           pdb=" CA  GLY K 335 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.16  -27.84     0      5.00e+00 4.00e-02 3.10e+01
  ... (remaining 3514 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 582
       0.030 -    0.060: 221
       0.060 -    0.090: 67
       0.090 -    0.120: 54
       0.120 -    0.150: 26
  Chirality restraints: 950
  Sorted by residual:
  chirality pdb=" CA  ILE M 311 "
            pdb=" N   ILE M 311 "
            pdb=" C   ILE M 311 "
            pdb=" CB  ILE M 311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.61e-01
  chirality pdb=" CA  ILE K 311 "
            pdb=" N   ILE K 311 "
            pdb=" C   ILE K 311 "
            pdb=" CB  ILE K 311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.54e-01
  chirality pdb=" CA  ILE L 311 "
            pdb=" N   ILE L 311 "
            pdb=" C   ILE L 311 "
            pdb=" CB  ILE L 311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.48e-01
  ... (remaining 947 not shown)

  Planarity restraints: 944
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE K 126 "    0.008 2.00e-02 2.50e+03   1.71e-02 2.94e+00
        pdb=" C   PHE K 126 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   PHE K 126 "    0.011 2.00e-02 2.50e+03
        pdb=" N   GLY K 127 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE L 126 "   -0.008 2.00e-02 2.50e+03   1.71e-02 2.92e+00
        pdb=" C   PHE L 126 "    0.030 2.00e-02 2.50e+03
        pdb=" O   PHE L 126 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   GLY L 127 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE M 126 "    0.008 2.00e-02 2.50e+03   1.71e-02 2.92e+00
        pdb=" C   PHE M 126 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   PHE M 126 "    0.011 2.00e-02 2.50e+03
        pdb=" N   GLY M 127 "    0.010 2.00e-02 2.50e+03
  ... (remaining 941 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1277
        2.79 -     3.32: 5585
        3.32 -     3.84: 10197
        3.84 -     4.37: 12539
        4.37 -     4.90: 19772
  Nonbonded interactions: 49370
  Sorted by model distance:
  nonbonded pdb=" N   THR L 103 "
            pdb=" O   GLY L 151 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" N   THR K 103 "
            pdb=" O   GLY K 151 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" N   THR M 103 "
            pdb=" O   GLY M 151 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" O   ARG K 130 "
            pdb=" NH2 ARG K 310 "
     model   vdw
     2.354 3.120
  nonbonded pdb=" O   ARG M 130 "
            pdb=" NH2 ARG M 310 "
     model   vdw
     2.354 3.120
  ... (remaining 49365 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.120
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5601
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      :  0.006   0.089   6032  Z= 0.479
  Angle     :  0.917   8.000   8298  Z= 0.629
  Chirality :  0.045   0.150    950
  Planarity :  0.006   0.059    944
  Dihedral  : 18.157  79.490   2317
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 13.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.16 (0.30), residues: 651
  helix:  0.12 (0.30), residues: 264
  sheet:  0.76 (0.36), residues: 159
  loop : -0.86 (0.37), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.002   ARG M 299 
 TYR   0.010   0.002   TYR K 178 
 PHE   0.009   0.002   PHE L 248 
 HIS   0.004   0.001   HIS M 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00618 /  0.48 ( 6032)
  covalent geometry    : angle       0.91697 /  0.63 ( 8298)
  hydrogen bonds       : bond        0.12930 / 13.61 (  280)
  hydrogen bonds       : angle       6.17028 /  8.29 (  773)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.201 
Fit side-chains
REVERT: L  210 MET cc_start: 0.2434 (tmm) cc_final: 0.1427 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.0763
  time to fit residues: 3.5231
Evaluate side-chains
  22 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 49 optimal weight:   30.0000
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:   50.0000
   chunk 33 optimal weight:   20.0000
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:   30.0000
   chunk 51 optimal weight:   30.0000
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:   30.0000
   chunk 27 optimal weight:    3.9990
   overall best weight:    6.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 101 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 = 0.4273 r_free = 0.4273 target = 0.086846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.065466 restraints weight = 67101.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.068091 restraints weight = 19222.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.068917 restraints weight = 8390.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.068995 restraints weight = 5820.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.068995 restraints weight = 5587.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5911
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.091   6032  Z= 0.263
  Angle     :  0.879  12.280   8298  Z= 0.453
  Chirality :  0.056   0.424    950
  Planarity :  0.005   0.041    944
  Dihedral  : 22.191  59.630   1144
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 15.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.31), residues: 651
  helix:  0.27 (0.30), residues: 282
  sheet:  0.39 (0.36), residues: 159
  loop : -1.01 (0.38), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.002   ARG M 310 
 TYR   0.036   0.003   TYR K 216 
 PHE   0.017   0.002   PHE M 126 
 HIS   0.006   0.002   HIS K 244 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00477 /  0.26 ( 6032)
  covalent geometry    : angle       0.87895 /  0.45 ( 8298)
  hydrogen bonds       : bond        0.14977 / 17.11 (  280)
  hydrogen bonds       : angle       5.26312 /  6.90 (  773)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.150 
Fit side-chains
REVERT: K  158 MET cc_start: 0.8770 (mmp) cc_final: 0.8523 (mpp)
REVERT: K  210 MET cc_start: 0.5913 (ptm) cc_final: 0.5644 (ptm)
REVERT: L  210 MET cc_start: 0.1928 (tmm) cc_final: 0.1718 (ppp)
REVERT: L  326 MET cc_start: 0.4599 (tpp) cc_final: 0.4348 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.0639
  time to fit residues: 2.2526
Evaluate side-chains
  21 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 14 optimal weight:   40.0000
   chunk 40 optimal weight:    5.9990
   chunk 12 optimal weight:    8.9990
   chunk 21 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 59 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 57 optimal weight:   10.0000
   chunk 23 optimal weight:    8.9990
   overall best weight:    4.1988

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.069487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.064476 restraints weight = 69508.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.063053 restraints weight = 133614.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.061944 restraints weight = 132536.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.061631 restraints weight = 135171.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.061515 restraints weight = 121482.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4866
moved from start:          0.2788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6032  Z= 0.151
  Angle     :  0.600   7.676   8298  Z= 0.321
  Chirality :  0.047   0.235    950
  Planarity :  0.003   0.037    944
  Dihedral  : 23.435  74.689   1144
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.02 (0.31), residues: 651
  helix:  0.52 (0.30), residues: 282
  sheet:  0.54 (0.36), residues: 162
  loop : -0.97 (0.38), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG M 170 
 TYR   0.023   0.002   TYR L 232 
 PHE   0.013   0.001   PHE M 126 
 HIS   0.004   0.001   HIS M 244 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.15 ( 6032)
  covalent geometry    : angle       0.60027 /  0.32 ( 8298)
  hydrogen bonds       : bond        0.04550 /  4.87 (  280)
  hydrogen bonds       : angle       4.62864 /  6.07 (  773)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.211 
Fit side-chains
REVERT: K  210 MET cc_start: 0.6930 (ptm) cc_final: 0.6561 (ptm)
REVERT: L  326 MET cc_start: 0.3472 (tpp) cc_final: 0.2941 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0748
  time to fit residues: 2.6996
Evaluate side-chains
  22 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 29 optimal weight:   30.0000
   chunk 18 optimal weight:    8.9990
   chunk 48 optimal weight:   40.0000
   chunk 22 optimal weight:   20.0000
   chunk 41 optimal weight:   10.0000
   chunk 28 optimal weight:    9.9990
   chunk 65 optimal weight:    6.9990
   chunk 7 optimal weight:   40.0000
   chunk 46 optimal weight:   20.0000
   chunk 51 optimal weight:   20.0000
   chunk 52 optimal weight:    0.6980
   overall best weight:    7.3390

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K 114 GLN
K 206 GLN
** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.081912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.060279 restraints weight = 71152.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.062617 restraints weight = 22983.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.063571 restraints weight = 10155.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.063828 restraints weight = 7083.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.063828 restraints weight = 6482.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6108
moved from start:          0.4171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   6032  Z= 0.269
  Angle     :  0.857  10.403   8298  Z= 0.441
  Chirality :  0.055   0.326    950
  Planarity :  0.005   0.038    944
  Dihedral  : 23.572  76.899   1144
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 24.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.30), residues: 651
  helix:  0.22 (0.30), residues: 282
  sheet:  0.60 (0.36), residues: 156
  loop : -1.19 (0.37), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG M 310 
 TYR   0.018   0.002   TYR M 315 
 PHE   0.018   0.002   PHE M 126 
 HIS   0.010   0.002   HIS K 244 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00485 /  0.27 ( 6032)
  covalent geometry    : angle       0.85688 /  0.44 ( 8298)
  hydrogen bonds       : bond        0.15891 / 17.63 (  280)
  hydrogen bonds       : angle       5.03212 /  6.55 (  773)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.259 
Fit side-chains
REVERT: L  210 MET cc_start: 0.0821 (ppp) cc_final: 0.0571 (ppp)
REVERT: L  326 MET cc_start: 0.4467 (tpp) cc_final: 0.4263 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0722
  time to fit residues: 2.6231
Evaluate side-chains
  22 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 13 optimal weight:   20.0000
   chunk 28 optimal weight:   20.0000
   chunk 12 optimal weight:    6.9990
   chunk 45 optimal weight:   20.0000
   chunk 66 optimal weight:    8.9990
   chunk 36 optimal weight:    7.9990
   chunk 53 optimal weight:    8.9990
   chunk 38 optimal weight:   20.0000
   chunk 33 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   chunk 5 optimal weight:    8.9990
   overall best weight:    6.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
M 101 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.063649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.055679 restraints weight = 75589.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.054762 restraints weight = 183724.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.051660 restraints weight = 177950.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.050745 restraints weight = 228094.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.050648 restraints weight = 222985.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5663
moved from start:          0.4798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6032  Z= 0.215
  Angle     :  0.719  10.861   8298  Z= 0.378
  Chirality :  0.051   0.258    950
  Planarity :  0.004   0.037    944
  Dihedral  : 24.092  79.608   1144
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 23.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.48 (0.30), residues: 651
  helix: -0.02 (0.29), residues: 282
  sheet:  0.60 (0.39), residues: 153
  loop : -1.25 (0.37), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG M 303 
 TYR   0.016   0.002   TYR L 232 
 PHE   0.015   0.002   PHE L 259 
 HIS   0.005   0.001   HIS K 244 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00405 /  0.22 ( 6032)
  covalent geometry    : angle       0.71898 /  0.38 ( 8298)
  hydrogen bonds       : bond        0.09250 / 10.24 (  280)
  hydrogen bonds       : angle       4.85402 /  6.19 (  773)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.189 
Fit side-chains
REVERT: L  125 MET cc_start: 0.8038 (mpp) cc_final: 0.7790 (mpp)
REVERT: L  210 MET cc_start: 0.0490 (ppp) cc_final: -0.0857 (ppp)
REVERT: L  326 MET cc_start: 0.3834 (tpp) cc_final: 0.3362 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0556
  time to fit residues: 2.0566
Evaluate side-chains
  22 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 48 optimal weight:   40.0000
   chunk 29 optimal weight:    9.9990
   chunk 6 optimal weight:    1.9990
   chunk 22 optimal weight:    9.9990
   chunk 35 optimal weight:    8.9990
   chunk 54 optimal weight:    0.0040
   chunk 18 optimal weight:    9.9990
   chunk 4 optimal weight:    7.9990
   chunk 42 optimal weight:   50.0000
   chunk 21 optimal weight:    8.9990
   chunk 53 optimal weight:    5.9990
   overall best weight:    5.0000

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.081488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.060329 restraints weight = 69633.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.062637 restraints weight = 23854.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.063347 restraints weight = 10538.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 71)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.064037 restraints weight = 7769.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 73)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.064411 restraints weight = 6139.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6039
moved from start:          0.5278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6032  Z= 0.177
  Angle     :  0.684   9.140   8298  Z= 0.355
  Chirality :  0.048   0.261    950
  Planarity :  0.004   0.042    944
  Dihedral  : 23.996  82.967   1144
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 20.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.31), residues: 651
  helix:  0.02 (0.29), residues: 285
  sheet:  0.55 (0.40), residues: 150
  loop : -1.06 (0.38), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG M 170 
 TYR   0.026   0.002   TYR L 216 
 PHE   0.017   0.002   PHE L 259 
 HIS   0.008   0.001   HIS K 244 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.18 ( 6032)
  covalent geometry    : angle       0.68365 /  0.36 ( 8298)
  hydrogen bonds       : bond        0.09237 /  9.99 (  280)
  hydrogen bonds       : angle       4.71497 /  6.12 (  773)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.181 
Fit side-chains
REVERT: K  251 MET cc_start: 0.4571 (mtm) cc_final: 0.4276 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0689
  time to fit residues: 2.4681
Evaluate side-chains
  22 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 40 optimal weight:   20.0000
   chunk 65 optimal weight:    5.9990
   chunk 50 optimal weight:    0.6980
   chunk 10 optimal weight:    8.9990
   chunk 42 optimal weight:   20.0000
   chunk 49 optimal weight:    6.9990
   chunk 29 optimal weight:   10.0000
   chunk 19 optimal weight:    3.9990
   chunk 15 optimal weight:   20.0000
   chunk 62 optimal weight:    9.9990
   overall best weight:    5.3388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L 206 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.080710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.059854 restraints weight = 70611.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.062106 restraints weight = 24850.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 76)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.063218 restraints weight = 10947.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.063386 restraints weight = 6825.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.063386 restraints weight = 6332.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6038
moved from start:          0.5659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6032  Z= 0.182
  Angle     :  0.683   8.992   8298  Z= 0.356
  Chirality :  0.049   0.264    950
  Planarity :  0.003   0.028    944
  Dihedral  : 24.040  83.484   1144
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 22.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.55 (0.31), residues: 651
  helix:  0.02 (0.29), residues: 288
  sheet:  0.75 (0.46), residues: 117
  loop : -1.31 (0.35), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG M 170 
 TYR   0.013   0.001   TYR L 232 
 PHE   0.013   0.002   PHE L 259 
 HIS   0.005   0.001   HIS K 244 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.18 ( 6032)
  covalent geometry    : angle       0.68331 /  0.36 ( 8298)
  hydrogen bonds       : bond        0.09192 /  9.94 (  280)
  hydrogen bonds       : angle       4.75357 /  6.18 (  773)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.127 
Fit side-chains
REVERT: K  251 MET cc_start: 0.4836 (mtm) cc_final: 0.4489 (mmp)
REVERT: L  211 MET cc_start: 0.2740 (mmt) cc_final: 0.1846 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0571
  time to fit residues: 2.1646
Evaluate side-chains
  22 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 53 optimal weight:    6.9990
   chunk 14 optimal weight:    8.9990
   chunk 23 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 45 optimal weight:   40.0000
   chunk 32 optimal weight:    7.9990
   chunk 48 optimal weight:   40.0000
   chunk 43 optimal weight:    5.9990
   chunk 39 optimal weight:    4.9990
   chunk 67 optimal weight:    0.3980
   chunk 26 optimal weight:    4.9990
   overall best weight:    3.6788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L 206 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.063328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.051078 restraints weight = 68953.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.051078 restraints weight = 78510.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.051078 restraints weight = 78510.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.051078 restraints weight = 78510.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.051078 restraints weight = 78510.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5833
moved from start:          0.5833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6032  Z= 0.144
  Angle     :  0.640   7.867   8298  Z= 0.336
  Chirality :  0.047   0.260    950
  Planarity :  0.003   0.025    944
  Dihedral  : 24.003  84.761   1144
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 19.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.22 (0.31), residues: 651
  helix:  0.17 (0.30), residues: 282
  sheet:  0.56 (0.41), residues: 150
  loop : -0.89 (0.38), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG M 170 
 TYR   0.019   0.001   TYR K 159 
 PHE   0.014   0.002   PHE L 259 
 HIS   0.005   0.001   HIS K 244 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.14 ( 6032)
  covalent geometry    : angle       0.63997 /  0.34 ( 8298)
  hydrogen bonds       : bond        0.07393 /  7.89 (  280)
  hydrogen bonds       : angle       4.59508 /  5.93 (  773)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.143 
Fit side-chains
REVERT: K  251 MET cc_start: 0.4720 (mtm) cc_final: 0.4252 (mmp)
REVERT: M  211 MET cc_start: 0.1678 (ttt) cc_final: 0.1133 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0432
  time to fit residues: 1.6418
Evaluate side-chains
  23 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 40 optimal weight:   30.0000
   chunk 48 optimal weight:   40.0000
   chunk 59 optimal weight:    8.9990
   chunk 18 optimal weight:    6.9990
   chunk 66 optimal weight:    0.0070
   chunk 4 optimal weight:    7.9990
   chunk 67 optimal weight:    8.9990
   chunk 41 optimal weight:    0.0470
   chunk 31 optimal weight:    6.9990
   chunk 17 optimal weight:    5.9990
   overall best weight:    4.0102

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L 206 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.062001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.057663 restraints weight = 76271.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.052284 restraints weight = 97551.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.052226 restraints weight = 166498.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.052214 restraints weight = 151998.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.052137 restraints weight = 153882.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5576
moved from start:          0.6160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6032  Z= 0.152
  Angle     :  0.650   7.773   8298  Z= 0.340
  Chirality :  0.048   0.270    950
  Planarity :  0.003   0.026    944
  Dihedral  : 23.946  85.722   1144
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 20.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.31), residues: 651
  helix:  0.09 (0.30), residues: 285
  sheet:  0.37 (0.40), residues: 159
  loop : -0.83 (0.39), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG M 170 
 TYR   0.018   0.001   TYR K 159 
 PHE   0.019   0.002   PHE L 259 
 HIS   0.005   0.001   HIS K 244 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.15 ( 6032)
  covalent geometry    : angle       0.64978 /  0.34 ( 8298)
  hydrogen bonds       : bond        0.08363 /  9.03 (  280)
  hydrogen bonds       : angle       4.55664 /  5.82 (  773)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.128 
Fit side-chains
REVERT: K  251 MET cc_start: 0.4544 (mtm) cc_final: 0.3955 (mmp)
REVERT: K  326 MET cc_start: 0.5504 (tpt) cc_final: 0.5162 (tpp)
REVERT: M  326 MET cc_start: 0.7955 (tpt) cc_final: 0.7706 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0538
  time to fit residues: 2.0344
Evaluate side-chains
  23 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 7 optimal weight:   20.0000
   chunk 32 optimal weight:    5.9990
   chunk 50 optimal weight:   20.0000
   chunk 59 optimal weight:    9.9990
   chunk 55 optimal weight:    8.9990
   chunk 13 optimal weight:    8.9990
   chunk 39 optimal weight:    5.9990
   chunk 1 optimal weight:   20.0000
   overall best weight:    5.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** M 206 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 = 0.3848 r_free = 0.3848 target = 0.060745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.057768 restraints weight = 76481.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.052152 restraints weight = 128462.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.050956 restraints weight = 225930.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.050562 restraints weight = 277014.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.050561 restraints weight = 240121.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5359
moved from start:          0.6734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   6032  Z= 0.183
  Angle     :  0.689   8.641   8298  Z= 0.363
  Chirality :  0.049   0.294    950
  Planarity :  0.004   0.029    944
  Dihedral  : 23.999  86.079   1144
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 23.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.31), residues: 651
  helix:  0.01 (0.30), residues: 282
  sheet:  0.30 (0.40), residues: 156
  loop : -0.87 (0.38), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG M 170 
 TYR   0.014   0.002   TYR L 232 
 PHE   0.012   0.002   PHE M 248 
 HIS   0.006   0.001   HIS K 244 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.18 ( 6032)
  covalent geometry    : angle       0.68922 /  0.36 ( 8298)
  hydrogen bonds       : bond        0.10216 / 11.15 (  280)
  hydrogen bonds       : angle       4.81525 /  6.19 (  773)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.170 
Fit side-chains
REVERT: K  251 MET cc_start: 0.4721 (mtm) cc_final: 0.4099 (mmp)
REVERT: K  326 MET cc_start: 0.5364 (tpt) cc_final: 0.5039 (tpp)
REVERT: L  125 MET cc_start: 0.8058 (mpp) cc_final: 0.7832 (mpp)
REVERT: M  326 MET cc_start: 0.7712 (tpt) cc_final: 0.7467 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0608
  time to fit residues: 2.2715
Evaluate side-chains
  23 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 28 optimal weight:   30.0000
   chunk 17 optimal weight:    0.9980
   chunk 15 optimal weight:   20.0000
   chunk 2 optimal weight:    9.9990
   chunk 61 optimal weight:   20.0000
   chunk 24 optimal weight:   10.0000
   chunk 63 optimal weight:    5.9990
   chunk 16 optimal weight:    7.9990
   chunk 31 optimal weight:    6.9990
   chunk 48 optimal weight:   20.0000
   chunk 42 optimal weight:    6.9990
   overall best weight:    5.7988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L 206 GLN
** M 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.060226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.056446 restraints weight = 76240.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 84)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.051236 restraints weight = 86449.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.051226 restraints weight = 167232.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.051226 restraints weight = 173251.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.051226 restraints weight = 173251.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5629
moved from start:          0.7554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6032  Z= 0.197
  Angle     :  0.718   9.350   8298  Z= 0.383
  Chirality :  0.050   0.282    950
  Planarity :  0.004   0.036    944
  Dihedral  : 24.149  87.730   1144
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 27.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.79 (0.31), residues: 651
  helix: -0.33 (0.29), residues: 288
  sheet:  0.07 (0.43), residues: 147
  loop : -0.96 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG M 170 
 TYR   0.016   0.002   TYR K 159 
 PHE   0.023   0.002   PHE L 259 
 HIS   0.006   0.001   HIS M 244 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.20 ( 6032)
  covalent geometry    : angle       0.71824 /  0.38 ( 8298)
  hydrogen bonds       : bond        0.10237 / 10.87 (  280)
  hydrogen bonds       : angle       5.09555 /  6.48 (  773)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1461.78 seconds
wall clock time: 25 minutes 40.79 seconds (1540.79 seconds total)