Starting phenix.real_space_refine
on Thu Jun  5 10:18:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xbx_38232/06_2025/8xbx_38232.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xbx_38232/06_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xbx_38232/06_2025/8xbx_38232.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xbx_38232/06_2025/8xbx_38232.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xbx_38232/06_2025/8xbx_38232.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xbx_38232/06_2025/8xbx_38232.cif"
  }
  resolution = 4.36
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 4.29, per 1000 atoms: 0.73
  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: 1.54
  Conformation dependent library (CDL) restraints added in 749.1 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: 2.39
  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: 1.71

  Time building geometry restraints manager: 1.80 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:             1.690
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.700
  Find NCS groups from input model:        0.150
  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:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.560
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (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
 HIS   0.004   0.001   HIS M 294 
 PHE   0.009   0.002   PHE L 248 
 TYR   0.010   0.002   TYR K 178 
 ARG   0.015   0.002   ARG M 299 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12930 (  280)
  hydrogen bonds       : angle       6.17028 (  773)
  covalent geometry    : bond        0.00496 ( 6032)
  covalent geometry    : angle       0.89824 ( 8298)

*********************** 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  : 0.604 
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: 0.1992
  time to fit residues: 9.1393
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  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 51 optimal weight:   20.0000
   chunk 28 optimal weight:    5.9990
   chunk 17 optimal weight:    8.9990
   chunk 34 optimal weight:    0.0370
   chunk 27 optimal weight:   10.0000
   chunk 53 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   chunk 32 optimal weight:    0.1980
   chunk 39 optimal weight:    6.9990
   chunk 61 optimal weight:    7.9990
   overall best weight:    2.8464

-------------------------------------------------------------------------------
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 = 0.4271 r_free = 0.4271 target = 0.087601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.065695 restraints weight = 67110.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.068318 restraints weight = 22805.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.069139 restraints weight = 9879.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6174
moved from start:          0.2639

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= 0.165
  Angle     :  0.562   5.854   8298  Z= 0.310
  Chirality :  0.041   0.167    950
  Planarity :  0.004   0.030    944
  Dihedral  : 22.089  69.187   1144
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.32), residues: 651
  helix:  0.67 (0.31), residues: 282
  sheet:  0.84 (0.36), residues: 162
  loop : -0.72 (0.42), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS L 244 
 PHE   0.011   0.001   PHE M 126 
 TYR   0.014   0.002   TYR K 178 
 ARG   0.005   0.001   ARG M 170 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04819 (  280)
  hydrogen bonds       : angle       4.47237 (  773)
  covalent geometry    : bond        0.00349 ( 6032)
  covalent geometry    : angle       0.56194 ( 8298)

*********************** 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  : 0.657 
Fit side-chains
REVERT: K  210 MET cc_start: 0.5900 (ptm) cc_final: 0.5535 (ptm)
REVERT: L  326 MET cc_start: 0.4581 (tpp) cc_final: 0.4285 (mmm)
REVERT: M  210 MET cc_start: 0.1866 (ppp) cc_final: 0.1629 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.1976
  time to fit residues: 6.8800
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  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 24 optimal weight:   20.0000
   chunk 46 optimal weight:   20.0000
   chunk 26 optimal weight:   30.0000
   chunk 44 optimal weight:    9.9990
   chunk 31 optimal weight:   20.0000
   chunk 38 optimal weight:   20.0000
   chunk 27 optimal weight:    6.9990
   chunk 17 optimal weight:    5.9990
   chunk 64 optimal weight:   20.0000
   chunk 40 optimal weight:    7.9990
   chunk 43 optimal weight:    5.9990
   overall best weight:    7.3990

-------------------------------------------------------------------------------
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
** 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 = 0.3868 r_free = 0.3868 target = 0.061217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.048341 restraints weight = 76736.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 11)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.048341 restraints weight = 83442.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.048341 restraints weight = 83442.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6197
moved from start:          0.5636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.092   6032  Z= 0.381
  Angle     :  0.822   9.751   8298  Z= 0.452
  Chirality :  0.051   0.207    950
  Planarity :  0.005   0.052    944
  Dihedral  : 23.854  80.411   1144
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 29.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.51 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.29), residues: 651
  helix: -0.30 (0.28), residues: 282
  sheet:  0.85 (0.41), residues: 126
  loop : -1.23 (0.35), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.002   HIS K 244 
 PHE   0.016   0.002   PHE M 126 
 TYR   0.017   0.002   TYR K 178 
 ARG   0.006   0.001   ARG M 170 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15454 (  280)
  hydrogen bonds       : angle       5.22338 (  773)
  covalent geometry    : bond        0.00804 ( 6032)
  covalent geometry    : angle       0.82150 ( 8298)

*********************** 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
  25 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 24
  time to evaluate  : 0.613 
Fit side-chains
   revert: symmetry clash
REVERT: K  251 MET cc_start: 0.4554 (mtm) cc_final: 0.4339 (mmp)
REVERT: L  149 ASP cc_start: 0.8463 (t70) cc_final: 0.8260 (p0)
REVERT: L  210 MET cc_start: 0.1643 (ppp) cc_final: 0.1225 (ppp)
REVERT: L  326 MET cc_start: 0.4015 (tpp) cc_final: 0.3757 (tpp)
REVERT: M  211 MET cc_start: 0.3867 (ttt) cc_final: 0.3262 (ttt)
  outliers start: 1
  outliers final: 0
  residues processed: 25
  average time/residue: 0.1721
  time to fit residues: 6.4858
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  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 22 optimal weight:   20.0000
   chunk 27 optimal weight:   30.0000
   chunk 5 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   chunk 46 optimal weight:   40.0000
   chunk 2 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 49 optimal weight:    7.9990
   chunk 48 optimal weight:    6.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3862 r_free = 0.3862 target = 0.062413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.055348 restraints weight = 73453.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.054063 restraints weight = 166099.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.053262 restraints weight = 174440.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5522
moved from start:          0.6132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   6032  Z= 0.217
  Angle     :  0.610   7.512   8298  Z= 0.334
  Chirality :  0.042   0.146    950
  Planarity :  0.003   0.029    944
  Dihedral  : 23.528  82.965   1144
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 18.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.31), residues: 651
  helix: -0.09 (0.29), residues: 282
  sheet:  1.03 (0.39), residues: 150
  loop : -0.78 (0.38), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS K 244 
 PHE   0.012   0.002   PHE K 166 
 TYR   0.023   0.001   TYR K 159 
 ARG   0.009   0.000   ARG K 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08162 (  280)
  hydrogen bonds       : angle       4.50538 (  773)
  covalent geometry    : bond        0.00467 ( 6032)
  covalent geometry    : angle       0.61028 ( 8298)

*********************** 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
  25 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
REVERT: K  251 MET cc_start: 0.4478 (mtm) cc_final: 0.3472 (mmt)
REVERT: L  125 MET cc_start: 0.8279 (mpp) cc_final: 0.8036 (mpp)
REVERT: L  210 MET cc_start: -0.0197 (ppp) cc_final: -0.0807 (ppp)
REVERT: L  326 MET cc_start: 0.3469 (tpp) cc_final: 0.2942 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.1644
  time to fit residues: 6.2447
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  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 36 optimal weight:    7.9990
   chunk 4 optimal weight:    5.9990
   chunk 2 optimal weight:   20.0000
   chunk 9 optimal weight:    8.9990
   chunk 10 optimal weight:    6.9990
   chunk 28 optimal weight:    8.9990
   chunk 21 optimal weight:    0.9980
   chunk 22 optimal weight:   20.0000
   chunk 34 optimal weight:    0.4980
   chunk 14 optimal weight:    8.9990
   overall best weight:    3.4986

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

Flipped N/Q/H residues before XYZ refinement:
M 101 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.061162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.055477 restraints weight = 75313.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.054229 restraints weight = 156375.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.053287 restraints weight = 146150.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5504
moved from start:          0.6743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6032  Z= 0.188
  Angle     :  0.566   7.679   8298  Z= 0.312
  Chirality :  0.041   0.138    950
  Planarity :  0.003   0.023    944
  Dihedral  : 23.458  86.345   1144
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 18.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.31), residues: 651
  helix:  0.14 (0.30), residues: 282
  sheet:  0.96 (0.40), residues: 150
  loop : -0.73 (0.38), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS M 244 
 PHE   0.010   0.001   PHE M 248 
 TYR   0.011   0.001   TYR K 216 
 ARG   0.005   0.000   ARG M 170 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07117 (  280)
  hydrogen bonds       : angle       4.36799 (  773)
  covalent geometry    : bond        0.00399 ( 6032)
  covalent geometry    : angle       0.56593 ( 8298)

*********************** 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
  25 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.695 
Fit side-chains
REVERT: K  251 MET cc_start: 0.4447 (mtm) cc_final: 0.3402 (mmt)
REVERT: L  125 MET cc_start: 0.8298 (mpp) cc_final: 0.8018 (mpp)
REVERT: L  210 MET cc_start: 0.0006 (ppp) cc_final: -0.1050 (ppp)
REVERT: L  326 MET cc_start: 0.3322 (tpp) cc_final: 0.2901 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.2010
  time to fit residues: 8.3172
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  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 11 optimal weight:   20.0000
   chunk 20 optimal weight:   50.0000
   chunk 51 optimal weight:   30.0000
   chunk 14 optimal weight:   40.0000
   chunk 42 optimal weight:    8.9990
   chunk 13 optimal weight:    8.9990
   chunk 52 optimal weight:    6.9990
   chunk 58 optimal weight:   20.0000
   chunk 4 optimal weight:    5.9990
   chunk 9 optimal weight:   20.0000
   chunk 7 optimal weight:    5.9990
   overall best weight:    7.3990

-------------------------------------------------------------------------------
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**
** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 244 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 = 0.4106 r_free = 0.4106 target = 0.076350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.055936 restraints weight = 72679.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.058007 restraints weight = 25763.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.058995 restraints weight = 11544.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6416
moved from start:          0.8679

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= 0.352
  Angle     :  0.789  11.612   8298  Z= 0.426
  Chirality :  0.048   0.186    950
  Planarity :  0.005   0.036    944
  Dihedral  : 23.933  84.826   1144
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 37.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.31), residues: 651
  helix: -0.66 (0.29), residues: 285
  sheet:  0.58 (0.44), residues: 138
  loop : -1.05 (0.37), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS K 244 
 PHE   0.010   0.002   PHE M 327 
 TYR   0.018   0.002   TYR K 159 
 ARG   0.010   0.001   ARG M 170 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13001 (  280)
  hydrogen bonds       : angle       5.41621 (  773)
  covalent geometry    : bond        0.00773 ( 6032)
  covalent geometry    : angle       0.78873 ( 8298)

*********************** 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  : 0.715 
Fit side-chains
   revert: symmetry clash
REVERT: K  251 MET cc_start: 0.4822 (mtm) cc_final: 0.3945 (mmt)
REVERT: L  210 MET cc_start: 0.3689 (ppp) cc_final: 0.3466 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.2065
  time to fit residues: 7.4801
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  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 64 optimal weight:    8.9990
   chunk 11 optimal weight:    0.8980
   chunk 63 optimal weight:    8.9990
   chunk 59 optimal weight:    7.9990
   chunk 66 optimal weight:   20.0000
   chunk 27 optimal weight:   10.0000
   chunk 42 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 8 optimal weight:   30.0000
   chunk 6 optimal weight:   50.0000
   overall best weight:    6.3788

-------------------------------------------------------------------------------
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 = 0.3796 r_free = 0.3796 target = 0.058194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.054339 restraints weight = 78466.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 93)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.048843 restraints weight = 101718.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.048843 restraints weight = 192101.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5783
moved from start:          0.9675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.075   6032  Z= 0.283
  Angle     :  0.718   9.885   8298  Z= 0.388
  Chirality :  0.045   0.139    950
  Planarity :  0.005   0.067    944
  Dihedral  : 23.848  87.985   1144
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 27.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.31), residues: 651
  helix: -0.81 (0.28), residues: 285
  sheet:  0.15 (0.44), residues: 147
  loop : -0.92 (0.39), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS M 244 
 PHE   0.016   0.002   PHE L 248 
 TYR   0.018   0.002   TYR K 216 
 ARG   0.009   0.001   ARG M 170 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09909 (  280)
  hydrogen bonds       : angle       5.27389 (  773)
  covalent geometry    : bond        0.00618 ( 6032)
  covalent geometry    : angle       0.71758 ( 8298)

*********************** 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
  23 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.699 
Fit side-chains
REVERT: K  251 MET cc_start: 0.4289 (mtm) cc_final: 0.3215 (mmt)
REVERT: L  243 MET cc_start: 0.6613 (tpt) cc_final: 0.5811 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.2248
  time to fit residues: 7.5761
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  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 14 optimal weight:    9.9990
   chunk 52 optimal weight:    6.9990
   chunk 41 optimal weight:   30.0000
   chunk 67 optimal weight:    8.9990
   chunk 35 optimal weight:    1.9990
   chunk 66 optimal weight:    6.9990
   chunk 63 optimal weight:    7.9990
   chunk 34 optimal weight:    6.9990
   chunk 5 optimal weight:    7.9990
   chunk 42 optimal weight:    8.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
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 = 0.3783 r_free = 0.3783 target = 0.056755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.054059 restraints weight = 81780.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.053853 restraints weight = 132534.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.053789 restraints weight = 131972.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5264
moved from start:          1.0524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.079   6032  Z= 0.289
  Angle     :  0.738  10.619   8298  Z= 0.397
  Chirality :  0.046   0.166    950
  Planarity :  0.005   0.061    944
  Dihedral  : 23.886  88.002   1144
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 32.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.31), residues: 651
  helix: -0.91 (0.29), residues: 285
  sheet:  0.30 (0.48), residues: 129
  loop : -1.10 (0.37), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS K 244 
 PHE   0.011   0.002   PHE M 126 
 TYR   0.019   0.002   TYR L 232 
 ARG   0.011   0.001   ARG M 170 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11294 (  280)
  hydrogen bonds       : angle       5.55400 (  773)
  covalent geometry    : bond        0.00635 ( 6032)
  covalent geometry    : angle       0.73771 ( 8298)

*********************** 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
  22 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.600 
Fit side-chains
REVERT: K  251 MET cc_start: 0.4363 (mtm) cc_final: 0.2745 (mmt)
REVERT: L  243 MET cc_start: 0.6140 (tpt) cc_final: 0.5097 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.1522
  time to fit residues: 5.2777
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  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 24 optimal weight:   30.0000
   chunk 61 optimal weight:   20.0000
   chunk 42 optimal weight:    3.9990
   chunk 35 optimal weight:    7.9990
   chunk 26 optimal weight:    6.9990
   chunk 13 optimal weight:    0.8980
   chunk 60 optimal weight:    9.9990
   chunk 57 optimal weight:    8.9990
   chunk 65 optimal weight:   20.0000
   chunk 23 optimal weight:    6.9990
   overall best weight:    4.9788

-------------------------------------------------------------------------------
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 = 0.3792 r_free = 0.3792 target = 0.057447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.053547 restraints weight = 77436.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.049117 restraints weight = 135456.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.048083 restraints weight = 217071.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5665
moved from start:          1.0922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068   6032  Z= 0.246
  Angle     :  0.674   9.014   8298  Z= 0.365
  Chirality :  0.044   0.148    950
  Planarity :  0.004   0.054    944
  Dihedral  : 23.785  88.798   1144
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 27.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.32), residues: 651
  helix: -0.83 (0.29), residues: 285
  sheet:  0.16 (0.49), residues: 129
  loop : -1.07 (0.38), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS K 244 
 PHE   0.015   0.002   PHE L 248 
 TYR   0.016   0.002   TYR L 159 
 ARG   0.008   0.000   ARG M 170 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09484 (  280)
  hydrogen bonds       : angle       5.30142 (  773)
  covalent geometry    : bond        0.00538 ( 6032)
  covalent geometry    : angle       0.67449 ( 8298)

*********************** 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
  22 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.589 
Fit side-chains
REVERT: K  251 MET cc_start: 0.4174 (mtm) cc_final: 0.2731 (mmt)
REVERT: K  326 MET cc_start: 0.5629 (tpt) cc_final: 0.5375 (tpp)
REVERT: L  243 MET cc_start: 0.6855 (tpt) cc_final: 0.6198 (mmp)
REVERT: M  326 MET cc_start: 0.7639 (tpt) cc_final: 0.7401 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.1601
  time to fit residues: 5.5011
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  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 51 optimal weight:    8.9990
   chunk 41 optimal weight:   20.0000
   chunk 47 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9990
   chunk 49 optimal weight:   20.0000
   chunk 13 optimal weight:    3.9990
   chunk 55 optimal weight:    7.9990
   chunk 32 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 29 optimal weight:   10.0000
   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
L 290 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.056331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.052515 restraints weight = 83508.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 95)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.046523 restraints weight = 169183.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.046426 restraints weight = 263397.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5893
moved from start:          1.1751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.075   6032  Z= 0.281
  Angle     :  0.725   9.950   8298  Z= 0.391
  Chirality :  0.046   0.158    950
  Planarity :  0.004   0.052    944
  Dihedral  : 23.858  88.447   1144
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 31.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.31), residues: 651
  helix: -0.95 (0.29), residues: 285
  sheet:  0.15 (0.55), residues: 99
  loop : -1.37 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS M 244 
 PHE   0.014   0.002   PHE L 248 
 TYR   0.016   0.002   TYR L 159 
 ARG   0.010   0.001   ARG M 170 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10704 (  280)
  hydrogen bonds       : angle       5.51104 (  773)
  covalent geometry    : bond        0.00608 ( 6032)
  covalent geometry    : angle       0.72527 ( 8298)

********************** 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  : 0.632 
Fit side-chains
REVERT: K  251 MET cc_start: 0.3925 (mtm) cc_final: 0.2410 (mmt)
REVERT: K  326 MET cc_start: 0.5888 (tpt) cc_final: 0.5496 (tpp)
REVERT: L  243 MET cc_start: 0.6887 (tpt) cc_final: 0.6348 (mmt)
REVERT: M  210 MET cc_start: -0.0660 (ppp) cc_final: -0.2381 (mpp)
REVERT: M  326 MET cc_start: 0.7732 (tpt) cc_final: 0.7505 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.1571
  time to fit residues: 5.6838
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  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 30 optimal weight:    0.0070
   chunk 56 optimal weight:    7.9990
   chunk 5 optimal weight:    8.9990
   chunk 24 optimal weight:   30.0000
   chunk 40 optimal weight:    9.9990
   chunk 27 optimal weight:   10.0000
   chunk 49 optimal weight:   20.0000
   chunk 20 optimal weight:    9.9990
   chunk 28 optimal weight:   20.0000
   chunk 25 optimal weight:    5.9990
   chunk 23 optimal weight:    9.9990
   overall best weight:    6.6006

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

Flipped N/Q/H residues before XYZ refinement:
** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.055311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.051922 restraints weight = 84803.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 86)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.048242 restraints weight = 102125.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.048242 restraints weight = 189688.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5854
moved from start:          1.2823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.082   6032  Z= 0.308
  Angle     :  0.768  10.155   8298  Z= 0.412
  Chirality :  0.048   0.181    950
  Planarity :  0.005   0.053    944
  Dihedral  : 24.027  86.945   1144
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 35.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.80 (0.31), residues: 651
  helix: -1.13 (0.29), residues: 280
  sheet: -0.47 (0.52), residues: 106
  loop : -1.40 (0.37), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS M 244 
 PHE   0.018   0.002   PHE L 248 
 TYR   0.022   0.002   TYR L 159 
 ARG   0.011   0.001   ARG M 170 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11376 (  280)
  hydrogen bonds       : angle       5.79189 (  773)
  covalent geometry    : bond        0.00677 ( 6032)
  covalent geometry    : angle       0.76835 ( 8298)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2413.59 seconds
wall clock time: 43 minutes 15.62 seconds (2595.62 seconds total)