Starting phenix.real_space_refine
on Fri Oct 10 13:20:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xbx_38232/10_2025/8xbx_38232.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xbx_38232/10_2025/8xbx_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xbx_38232/10_2025/8xbx_38232.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xbx_38232/10_2025/8xbx_38232.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xbx_38232/10_2025/8xbx_38232.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xbx_38232/10_2025/8xbx_38232.map"
  }
  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-2.0-5842/lib/python3.9/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: 1.64, per 1000 atoms: 0.28
  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: 0.56
  Conformation dependent library (CDL) restraints added in 339.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.77
  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: 0.78

  Time building geometry restraints manager: 0.70 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
    1.490  1.557 -0.067 3.00e-02 1.11e+03 5.05e+00
  bond pdb=" C1'  DC J   1 "
       pdb=" N1   DC J   1 "
    ideal  model  delta    sigma   weight residual
    1.490  1.557 -0.067 3.00e-02 1.11e+03 4.91e+00
  bond pdb=" C1'  DC I 154 "
       pdb=" N1   DC I 154 "
    ideal  model  delta    sigma   weight residual
    1.490  1.556 -0.066 3.00e-02 1.11e+03 4.83e+00
  bond pdb=" C1'  DC I 155 "
       pdb=" N1   DC I 155 "
    ideal  model  delta    sigma   weight residual
    1.490  1.556 -0.066 3.00e-02 1.11e+03 4.83e+00
  bond pdb=" C1'  DC I 152 "
       pdb=" N1   DC I 152 "
    ideal  model  delta    sigma   weight residual
    1.490  1.556 -0.066 3.00e-02 1.11e+03 4.82e+00
  ... (remaining 6027 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 7855
        1.60 -     3.20: 298
        3.20 -     4.80: 100
        4.80 -     6.40: 3
        6.40 -     8.00: 42
  Bond angle restraints: 8298
  Sorted by residual:
  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 1.50e+00 4.44e-01 2.19e+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 1.50e+00 4.44e-01 2.17e+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 1.50e+00 4.44e-01 2.17e+01
  angle pdb=" O3'  DG J   4 "
        pdb=" P    DG J   5 "
        pdb=" O5'  DG J   5 "
      ideal   model   delta    sigma   weight residual
     104.00   97.04    6.96 1.50e+00 4.44e-01 2.16e+01
  angle pdb=" O3'  DC I 151 "
        pdb=" P    DC I 152 "
        pdb=" O5'  DC I 152 "
      ideal   model   delta    sigma   weight residual
     104.00   97.04    6.96 1.50e+00 4.44e-01 2.15e+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: 546
       0.030 -    0.060: 252
       0.060 -    0.090: 91
       0.090 -    0.120: 43
       0.120 -    0.150: 18
  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:             1.410
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.800
  Find NCS groups from input model:        0.050
  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:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5805
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      :  0.005   0.067   6032  Z= 0.215
  Angle     :  0.898   8.000   8298  Z= 0.538
  Chirality :  0.044   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 aren 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
  covalent geometry    : bond        0.00496 ( 6032)
  covalent geometry    : angle       0.89824 ( 8298)
  hydrogen bonds       : bond        0.12930 (  280)
  hydrogen bonds       : angle       6.17028 (  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  : 0.214 
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: 0.0835
  time to fit residues: 3.8152
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  : 0.259 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
K 114 GLN
K 206 GLN
L 267 ASN
M 101 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.082362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.060669 restraints weight = 71213.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.062969 restraints weight = 22868.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.064017 restraints weight = 9711.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.064179 restraints weight = 6314.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.064179 restraints weight = 5947.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6332
moved from start:          0.4286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.100   6032  Z= 0.345
  Angle     :  0.775  10.360   8298  Z= 0.420
  Chirality :  0.050   0.194    950
  Planarity :  0.005   0.052    944
  Dihedral  : 23.895  76.396   1144
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 23.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  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 aren not related in a simple way.
  whole: -0.32 (0.30), residues: 651
  helix: -0.06 (0.29), residues: 282
  sheet:  0.72 (0.36), residues: 153
  loop : -0.93 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG M 310 
 TYR   0.023   0.003   TYR K 216 
 PHE   0.019   0.002   PHE M 126 
 HIS   0.007   0.002   HIS K 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00752 ( 6032)
  covalent geometry    : angle       0.77517 ( 8298)
  hydrogen bonds       : bond        0.11160 (  280)
  hydrogen bonds       : angle       5.23621 (  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
  24 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.214 
Fit side-chains
REVERT: K  210 MET cc_start: 0.5547 (ptm) cc_final: 0.5216 (ptm)
REVERT: L  149 ASP cc_start: 0.8623 (t70) cc_final: 0.8400 (p0)
REVERT: L  210 MET cc_start: 0.1983 (tmm) cc_final: 0.1755 (ppp)
REVERT: L  326 MET cc_start: 0.4540 (tpp) cc_final: 0.4311 (mmm)
REVERT: M  211 MET cc_start: 0.7367 (ttt) cc_final: 0.7133 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0640
  time to fit residues: 2.3859
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  : 0.213 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 14 optimal weight:   30.0000
   chunk 40 optimal weight:   10.0000
   chunk 12 optimal weight:    6.9990
   chunk 21 optimal weight:    7.9990
   chunk 45 optimal weight:   30.0000
   chunk 32 optimal weight:    0.9990
   chunk 59 optimal weight:   30.0000
   chunk 33 optimal weight:   20.0000
   chunk 57 optimal weight:    0.9980
   chunk 23 optimal weight:    6.9990
   overall best weight:    4.5988

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

Flipped N/Q/H residues before XYZ refinement:
L 267 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.062305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.055755 restraints weight = 74346.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.054893 restraints weight = 113780.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.054085 restraints weight = 119649.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.053945 restraints weight = 98350.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.053840 restraints weight = 94625.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5556
moved from start:          0.5232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   6032  Z= 0.232
  Angle     :  0.615   7.394   8298  Z= 0.339
  Chirality :  0.042   0.143    950
  Planarity :  0.004   0.032    944
  Dihedral  : 23.943  85.099   1144
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 20.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  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 aren not related in a simple way.
  whole: -0.06 (0.30), residues: 651
  helix:  0.07 (0.29), residues: 282
  sheet:  1.06 (0.37), residues: 150
  loop : -0.83 (0.39), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG M 170 
 TYR   0.012   0.002   TYR M 232 
 PHE   0.011   0.001   PHE M 248 
 HIS   0.007   0.001   HIS K 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 ( 6032)
  covalent geometry    : angle       0.61530 ( 8298)
  hydrogen bonds       : bond        0.08162 (  280)
  hydrogen bonds       : angle       4.48521 (  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  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: L  125 MET cc_start: 0.8240 (mpp) cc_final: 0.7996 (mpp)
REVERT: L  210 MET cc_start: -0.0176 (tmm) cc_final: -0.0443 (ppp)
REVERT: L  326 MET cc_start: 0.3696 (tpp) cc_final: 0.3215 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0726
  time to fit residues: 2.5824
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 29 optimal weight:   30.0000
   chunk 18 optimal weight:   10.0000
   chunk 48 optimal weight:   50.0000
   chunk 22 optimal weight:   10.0000
   chunk 41 optimal weight:    0.0010
   chunk 28 optimal weight:    7.9990
   chunk 65 optimal weight:   30.0000
   chunk 7 optimal weight:   50.0000
   chunk 46 optimal weight:   40.0000
   chunk 51 optimal weight:   20.0000
   chunk 52 optimal weight:    7.9990
   overall best weight:    7.1998

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

Flipped N/Q/H residues before XYZ refinement:
L 206 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.058898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.055496 restraints weight = 78325.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.054077 restraints weight = 150876.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.053219 restraints weight = 166456.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.052667 restraints weight = 183753.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.052385 restraints weight = 166864.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5419
moved from start:          0.7821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.105   6032  Z= 0.362
  Angle     :  0.832  12.756   8298  Z= 0.444
  Chirality :  0.050   0.216    950
  Planarity :  0.005   0.043    944
  Dihedral  : 24.137 117.641   1144
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 37.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  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 aren not related in a simple way.
  whole: -1.08 (0.30), residues: 651
  helix: -0.75 (0.28), residues: 285
  sheet:  0.70 (0.43), residues: 123
  loop : -1.28 (0.36), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG M 170 
 TYR   0.019   0.002   TYR K 232 
 PHE   0.034   0.002   PHE M 259 
 HIS   0.010   0.002   HIS K 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00790 ( 6032)
  covalent geometry    : angle       0.83196 ( 8298)
  hydrogen bonds       : bond        0.13259 (  280)
  hydrogen bonds       : angle       5.43232 (  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
  26 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  251 MET cc_start: 0.4011 (mtp) cc_final: 0.3277 (mmp)
REVERT: L  210 MET cc_start: -0.0477 (tmm) cc_final: -0.1691 (ppp)
REVERT: L  326 MET cc_start: 0.2996 (tpp) cc_final: 0.2574 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.0786
  time to fit residues: 2.9747
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  : 0.212 
-------------------------------------------------------------------------------
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:    0.2980
   chunk 28 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 45 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 36 optimal weight:    7.9990
   chunk 53 optimal weight:    6.9990
   chunk 38 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   chunk 16 optimal weight:    6.9990
   chunk 5 optimal weight:   30.0000
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
L 206 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.061769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.050604 restraints weight = 71036.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.050022 restraints weight = 106635.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.050021 restraints weight = 120817.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.049897 restraints weight = 123587.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.049897 restraints weight = 120044.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5956
moved from start:          0.7412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6032  Z= 0.143
  Angle     :  0.597   8.780   8298  Z= 0.320
  Chirality :  0.041   0.201    950
  Planarity :  0.003   0.050    944
  Dihedral  : 23.992  88.292   1144
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 15.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  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 aren not related in a simple way.
  whole: -0.26 (0.31), residues: 651
  helix: -0.17 (0.29), residues: 285
  sheet:  0.87 (0.41), residues: 150
  loop : -0.72 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG M 170 
 TYR   0.021   0.002   TYR K 159 
 PHE   0.020   0.002   PHE L 248 
 HIS   0.004   0.001   HIS M 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6032)
  covalent geometry    : angle       0.59703 ( 8298)
  hydrogen bonds       : bond        0.04715 (  280)
  hydrogen bonds       : angle       4.51424 (  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  : 0.218 
Fit side-chains
   revert: symmetry clash
REVERT: K  251 MET cc_start: 0.3342 (mtp) cc_final: 0.2987 (mmp)
REVERT: L  210 MET cc_start: 0.0816 (tmm) cc_final: 0.0209 (ppp)
REVERT: L  326 MET cc_start: 0.3918 (tpp) cc_final: 0.3668 (tpp)
REVERT: M  211 MET cc_start: 0.0372 (ttt) cc_final: -0.0413 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0572
  time to fit residues: 2.2334
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  : 0.197 
-------------------------------------------------------------------------------
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:   50.0000
   chunk 29 optimal weight:   20.0000
   chunk 6 optimal weight:   40.0000
   chunk 22 optimal weight:    8.9990
   chunk 35 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9980
   chunk 18 optimal weight:   20.0000
   chunk 4 optimal weight:   10.0000
   chunk 42 optimal weight:    4.9990
   chunk 21 optimal weight:   10.0000
   chunk 53 optimal weight:    8.9990
   overall best weight:    6.1988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.057677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.054891 restraints weight = 83046.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.054889 restraints weight = 125846.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.054826 restraints weight = 123784.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.054749 restraints weight = 100832.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.054749 restraints weight = 154756.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5260
moved from start:          0.8898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.093   6032  Z= 0.309
  Angle     :  0.754  10.914   8298  Z= 0.406
  Chirality :  0.047   0.205    950
  Planarity :  0.005   0.055    944
  Dihedral  : 24.080 101.401   1144
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 34.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  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 aren not related in a simple way.
  whole: -0.91 (0.31), residues: 651
  helix: -0.59 (0.29), residues: 285
  sheet:  0.68 (0.46), residues: 129
  loop : -1.18 (0.35), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG M 170 
 TYR   0.021   0.002   TYR L 232 
 PHE   0.013   0.002   PHE L 248 
 HIS   0.006   0.001   HIS K 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00674 ( 6032)
  covalent geometry    : angle       0.75376 ( 8298)
  hydrogen bonds       : bond        0.12327 (  280)
  hydrogen bonds       : angle       5.20141 (  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
  25 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
REVERT: K  251 MET cc_start: 0.3327 (mtp) cc_final: 0.2622 (mmm)
REVERT: L  326 MET cc_start: 0.3305 (tpp) cc_final: 0.3034 (tpp)
REVERT: L  339 ASP cc_start: 0.5922 (m-30) cc_final: 0.5638 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0767
  time to fit residues: 2.7512
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  : 0.140 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 40 optimal weight:    4.9990
   chunk 65 optimal weight:    6.9990
   chunk 50 optimal weight:    9.9990
   chunk 10 optimal weight:    0.0050
   chunk 42 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 29 optimal weight:   40.0000
   chunk 19 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 62 optimal weight:   40.0000
   overall best weight:    1.5598

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.061258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.055377 restraints weight = 73608.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 118)---------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.049171 restraints weight = 116458.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.049077 restraints weight = 140527.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.049077 restraints weight = 134499.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.049077 restraints weight = 134500.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6032
moved from start:          0.8558

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= 0.129
  Angle     :  0.579   7.241   8298  Z= 0.312
  Chirality :  0.041   0.141    950
  Planarity :  0.003   0.053    944
  Dihedral  : 23.932  87.748   1144
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  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 aren not related in a simple way.
  whole: -0.40 (0.32), residues: 651
  helix: -0.17 (0.30), residues: 285
  sheet:  0.58 (0.44), residues: 141
  loop : -0.74 (0.38), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG M 130 
 TYR   0.012   0.001   TYR K 159 
 PHE   0.013   0.001   PHE L 248 
 HIS   0.004   0.001   HIS K 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 6032)
  covalent geometry    : angle       0.57897 ( 8298)
  hydrogen bonds       : bond        0.04454 (  280)
  hydrogen bonds       : angle       4.46072 (  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  : 0.208 
Fit side-chains
   revert: symmetry clash
REVERT: K  211 MET cc_start: 0.2357 (tpt) cc_final: 0.2132 (tpt)
REVERT: K  251 MET cc_start: 0.2979 (mtp) cc_final: 0.2112 (mmt)
REVERT: K  326 MET cc_start: 0.5814 (tpt) cc_final: 0.5597 (tpp)
REVERT: L  210 MET cc_start: 0.2503 (ppp) cc_final: 0.2240 (ppp)
REVERT: L  326 MET cc_start: 0.3834 (tpp) cc_final: 0.3450 (mmm)
REVERT: L  339 ASP cc_start: 0.7645 (m-30) cc_final: 0.7312 (m-30)
REVERT: M  211 MET cc_start: 0.4492 (ttt) cc_final: 0.4097 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0852
  time to fit residues: 3.1239
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  : 0.229 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 14 optimal weight:    8.9990
   chunk 23 optimal weight:    5.9990
   chunk 58 optimal weight:   10.0000
   chunk 45 optimal weight:    8.9990
   chunk 32 optimal weight:    8.9990
   chunk 48 optimal weight:    7.9990
   chunk 43 optimal weight:    1.9990
   chunk 39 optimal weight:    8.9990
   chunk 67 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   overall best weight:    3.5788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.058922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.053871 restraints weight = 77339.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.053386 restraints weight = 178137.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.052983 restraints weight = 187335.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.052653 restraints weight = 176819.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.052547 restraints weight = 172752.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5318
moved from start:          0.9161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   6032  Z= 0.193
  Angle     :  0.610   8.349   8298  Z= 0.327
  Chirality :  0.042   0.159    950
  Planarity :  0.004   0.046    944
  Dihedral  : 23.826  86.690   1144
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 21.52
  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 aren not related in a simple way.
  whole: -0.47 (0.32), residues: 651
  helix: -0.15 (0.30), residues: 285
  sheet:  0.74 (0.47), residues: 129
  loop : -0.96 (0.37), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG M 170 
 TYR   0.010   0.001   TYR L 232 
 PHE   0.009   0.001   PHE M 126 
 HIS   0.006   0.001   HIS K 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 6032)
  covalent geometry    : angle       0.60952 ( 8298)
  hydrogen bonds       : bond        0.07410 (  280)
  hydrogen bonds       : angle       4.55297 (  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  : 0.188 
Fit side-chains
   revert: symmetry clash
REVERT: K  211 MET cc_start: 0.2901 (tpt) cc_final: 0.2435 (tpt)
REVERT: K  251 MET cc_start: 0.3224 (mtp) cc_final: 0.2099 (mmt)
REVERT: L  326 MET cc_start: 0.3168 (tpp) cc_final: 0.2892 (tpp)
REVERT: L  339 ASP cc_start: 0.6530 (m-30) cc_final: 0.6320 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0841
  time to fit residues: 2.8578
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  : 0.126 
-------------------------------------------------------------------------------
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:   30.0000
   chunk 40 optimal weight:    5.9990
   chunk 48 optimal weight:    7.9990
   chunk 59 optimal weight:    9.9990
   chunk 18 optimal weight:   20.0000
   chunk 66 optimal weight:    1.9990
   chunk 4 optimal weight:    9.9990
   chunk 67 optimal weight:    8.9990
   chunk 41 optimal weight:   10.0000
   chunk 31 optimal weight:    4.9990
   chunk 17 optimal weight:    5.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** K 138 HIS ** 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 = 0.3786 r_free = 0.3786 target = 0.057255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.052870 restraints weight = 81615.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.052203 restraints weight = 246108.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.051416 restraints weight = 239207.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.050639 restraints weight = 261496.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.048733 restraints weight = 232661.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5559
moved from start:          1.0718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.081   6032  Z= 0.276
  Angle     :  0.735  10.319   8298  Z= 0.393
  Chirality :  0.046   0.150    950
  Planarity :  0.005   0.049    944
  Dihedral  : 24.250 115.514   1144
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 32.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  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 aren not related in a simple way.
  whole: -1.13 (0.32), residues: 651
  helix: -0.74 (0.29), residues: 288
  sheet:  0.13 (0.47), residues: 126
  loop : -1.03 (0.38), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG M 170 
 TYR   0.014   0.002   TYR K 159 
 PHE   0.013   0.002   PHE L 248 
 HIS   0.006   0.001   HIS K 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00604 ( 6032)
  covalent geometry    : angle       0.73526 ( 8298)
  hydrogen bonds       : bond        0.10638 (  280)
  hydrogen bonds       : angle       5.18456 (  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
  23 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.199 
Fit side-chains
REVERT: K  211 MET cc_start: 0.2813 (tpt) cc_final: 0.2240 (tpt)
REVERT: K  251 MET cc_start: 0.3434 (mtp) cc_final: 0.2485 (mmt)
REVERT: L  243 MET cc_start: 0.6741 (tpt) cc_final: 0.6107 (mmt)
REVERT: L  326 MET cc_start: 0.3408 (tpp) cc_final: 0.3109 (tpp)
REVERT: M  210 MET cc_start: -0.0566 (ppp) cc_final: -0.1026 (ppp)
REVERT: M  326 MET cc_start: 0.7524 (tpt) cc_final: 0.7245 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.0611
  time to fit residues: 2.1922
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  : 0.217 
-------------------------------------------------------------------------------
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:   50.0000
   chunk 63 optimal weight:    0.0170
   chunk 38 optimal weight:    9.9990
   chunk 7 optimal weight:   20.0000
   chunk 32 optimal weight:    0.0020
   chunk 50 optimal weight:    9.9990
   chunk 59 optimal weight:    3.9990
   chunk 55 optimal weight:   10.0000
   chunk 13 optimal weight:    4.9990
   chunk 39 optimal weight:    7.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    2.8032

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.059298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.055355 restraints weight = 73759.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.052310 restraints weight = 157109.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.051476 restraints weight = 196011.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.051252 restraints weight = 185041.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.051064 restraints weight = 185076.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5414
moved from start:          1.0597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6032  Z= 0.166
  Angle     :  0.607   7.964   8298  Z= 0.327
  Chirality :  0.042   0.142    950
  Planarity :  0.003   0.041    944
  Dihedral  : 24.007 104.089   1144
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 18.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.83 (0.32), residues: 651
  helix: -0.45 (0.29), residues: 285
  sheet:  0.50 (0.49), residues: 123
  loop : -1.06 (0.38), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG M 170 
 TYR   0.009   0.001   TYR K 159 
 PHE   0.015   0.002   PHE L 248 
 HIS   0.006   0.001   HIS K 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 6032)
  covalent geometry    : angle       0.60722 ( 8298)
  hydrogen bonds       : bond        0.06023 (  280)
  hydrogen bonds       : angle       4.69853 (  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
  23 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.211 
Fit side-chains
REVERT: K  211 MET cc_start: 0.2931 (tpt) cc_final: 0.2338 (tpt)
REVERT: K  251 MET cc_start: 0.3220 (mtp) cc_final: 0.2212 (mmt)
REVERT: L  243 MET cc_start: 0.6681 (tpt) cc_final: 0.6200 (mmt)
REVERT: L  326 MET cc_start: 0.3857 (tpp) cc_final: 0.3547 (tpp)
REVERT: M  210 MET cc_start: -0.1277 (ppp) cc_final: -0.1518 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.0885
  time to fit residues: 2.9079
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  : 0.196 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 17 optimal weight:    9.9990
   chunk 15 optimal weight:   20.0000
   chunk 2 optimal weight:   30.0000
   chunk 61 optimal weight:   10.0000
   chunk 24 optimal weight:   40.0000
   chunk 63 optimal weight:   20.0000
   chunk 16 optimal weight:    7.9990
   chunk 31 optimal weight:    6.9990
   chunk 48 optimal weight:    7.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    5.7988

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

Flipped N/Q/H residues before XYZ refinement:
** K 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 290 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.057083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.053751 restraints weight = 80435.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 72)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.050364 restraints weight = 101641.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.050363 restraints weight = 204040.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.050363 restraints weight = 202674.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.050363 restraints weight = 202674.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5708
moved from start:          1.1359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.088   6032  Z= 0.279
  Angle     :  0.699  10.163   8298  Z= 0.377
  Chirality :  0.046   0.156    950
  Planarity :  0.004   0.043    944
  Dihedral  : 24.220 114.226   1144
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 29.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.15 (0.32), residues: 651
  helix: -0.70 (0.29), residues: 285
  sheet:  0.11 (0.47), residues: 129
  loop : -1.13 (0.38), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG M 150 
 TYR   0.013   0.002   TYR L 232 
 PHE   0.010   0.002   PHE L 248 
 HIS   0.007   0.001   HIS K 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00614 ( 6032)
  covalent geometry    : angle       0.69947 ( 8298)
  hydrogen bonds       : bond        0.10676 (  280)
  hydrogen bonds       : angle       5.11761 (  773)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1255.71 seconds
wall clock time: 22 minutes 26.96 seconds (1346.96 seconds total)