Starting phenix.real_space_refine
on Wed Jul 30 20:48:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ip3_35630/07_2025/8ip3_35630.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ip3_35630/07_2025/8ip3_35630.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ip3_35630/07_2025/8ip3_35630.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ip3_35630/07_2025/8ip3_35630.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ip3_35630/07_2025/8ip3_35630.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ip3_35630/07_2025/8ip3_35630.cif"
  }
  resolution = 2.6
  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=   0.001 sd=   0.027
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: 6
    Type Number    sf(0)   Gaussians
     Mg     12      5.21       5
     S      65      5.16       5
     Cl      1      4.86       5
     C    8275      2.51       5
     N    2155      2.21       5
     O    2360      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12868
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2571
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 319, 2571
          Classifications: {'peptide': 319}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 8, 'TRANS': 310}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' CL': 1, ' MG': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' MG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "E"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 6.29, per 1000 atoms: 0.49
  Number of scatterers: 12868
  At special positions: 0
  Unit cell: (108.81, 106.95, 141.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      1     17.00
     S      65     16.00
     Mg     12     11.99
     O    2360      8.00
     N    2155      7.00
     C    8275      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: 3.52
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3040

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 5 sheets defined
      72.4% alpha, 9.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 104 through 112
    Processing helix  chain 'A' and resid 114 through 119
      removed outlier: 3.564A  pdb=" N   ARG A 119 " --> pdb=" O   ARG A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 173
      Proline residue:  A 168  - end of helix
    Processing helix  chain 'A' and resid 183 through 219
      removed outlier: 3.625A  pdb=" N   ARG A 187 " --> pdb=" O   PRO A 183 " (cutoff:3.500A)
      Proline residue:  A 209  - end of helix
    Processing helix  chain 'A' and resid 227 through 261
      removed outlier: 4.050A  pdb=" N   GLU A 261 " --> pdb=" O   GLU A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 269
      removed outlier: 3.516A  pdb=" N   LEU A 265 " --> pdb=" O   GLU A 261 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   CYS A 269 " --> pdb=" O   LEU A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 275
      removed outlier: 3.932A  pdb=" N   ASP A 275 " --> pdb=" O   SER A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 283
      removed outlier: 4.099A  pdb=" N   LYS A 281 " --> pdb=" O   GLN A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 359
    Processing helix  chain 'A' and resid 371 through 401
      removed outlier: 4.425A  pdb=" N   TRP A 375 " --> pdb=" O   HIS A 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 112
    Processing helix  chain 'B' and resid 114 through 119
      removed outlier: 3.565A  pdb=" N   ARG B 119 " --> pdb=" O   ARG B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 173
      Proline residue:  B 168  - end of helix
    Processing helix  chain 'B' and resid 183 through 219
      removed outlier: 3.625A  pdb=" N   ARG B 187 " --> pdb=" O   PRO B 183 " (cutoff:3.500A)
      Proline residue:  B 209  - end of helix
    Processing helix  chain 'B' and resid 227 through 261
      removed outlier: 4.051A  pdb=" N   GLU B 261 " --> pdb=" O   GLU B 257 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 261 through 269
      removed outlier: 3.517A  pdb=" N   LEU B 265 " --> pdb=" O   GLU B 261 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   CYS B 269 " --> pdb=" O   LEU B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 275
      removed outlier: 3.932A  pdb=" N   ASP B 275 " --> pdb=" O   SER B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 283
      removed outlier: 4.099A  pdb=" N   LYS B 281 " --> pdb=" O   GLN B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 359
    Processing helix  chain 'B' and resid 371 through 401
      removed outlier: 4.424A  pdb=" N   TRP B 375 " --> pdb=" O   HIS B 371 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 104 through 112
    Processing helix  chain 'C' and resid 114 through 119
      removed outlier: 3.564A  pdb=" N   ARG C 119 " --> pdb=" O   ARG C 116 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 173
      Proline residue:  C 168  - end of helix
    Processing helix  chain 'C' and resid 183 through 219
      removed outlier: 3.625A  pdb=" N   ARG C 187 " --> pdb=" O   PRO C 183 " (cutoff:3.500A)
      Proline residue:  C 209  - end of helix
    Processing helix  chain 'C' and resid 227 through 261
      removed outlier: 4.051A  pdb=" N   GLU C 261 " --> pdb=" O   GLU C 257 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 261 through 269
      removed outlier: 3.516A  pdb=" N   LEU C 265 " --> pdb=" O   GLU C 261 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   CYS C 269 " --> pdb=" O   LEU C 265 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 269 through 275
      removed outlier: 3.931A  pdb=" N   ASP C 275 " --> pdb=" O   SER C 271 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 275 through 283
      removed outlier: 4.099A  pdb=" N   LYS C 281 " --> pdb=" O   GLN C 277 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 287 through 359
    Processing helix  chain 'C' and resid 371 through 401
      removed outlier: 4.425A  pdb=" N   TRP C 375 " --> pdb=" O   HIS C 371 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 112
    Processing helix  chain 'D' and resid 114 through 119
      removed outlier: 3.565A  pdb=" N   ARG D 119 " --> pdb=" O   ARG D 116 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 159 through 173
      Proline residue:  D 168  - end of helix
    Processing helix  chain 'D' and resid 183 through 219
      removed outlier: 3.625A  pdb=" N   ARG D 187 " --> pdb=" O   PRO D 183 " (cutoff:3.500A)
      Proline residue:  D 209  - end of helix
    Processing helix  chain 'D' and resid 227 through 261
      removed outlier: 4.050A  pdb=" N   GLU D 261 " --> pdb=" O   GLU D 257 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 261 through 269
      removed outlier: 3.517A  pdb=" N   LEU D 265 " --> pdb=" O   GLU D 261 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   CYS D 269 " --> pdb=" O   LEU D 265 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 269 through 275
      removed outlier: 3.932A  pdb=" N   ASP D 275 " --> pdb=" O   SER D 271 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 275 through 283
      removed outlier: 4.099A  pdb=" N   LYS D 281 " --> pdb=" O   GLN D 277 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 287 through 359
    Processing helix  chain 'D' and resid 371 through 401
      removed outlier: 4.425A  pdb=" N   TRP D 375 " --> pdb=" O   HIS D 371 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 104 through 112
    Processing helix  chain 'E' and resid 114 through 119
      removed outlier: 3.565A  pdb=" N   ARG E 119 " --> pdb=" O   ARG E 116 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 159 through 173
      Proline residue:  E 168  - end of helix
    Processing helix  chain 'E' and resid 183 through 219
      removed outlier: 3.625A  pdb=" N   ARG E 187 " --> pdb=" O   PRO E 183 " (cutoff:3.500A)
      Proline residue:  E 209  - end of helix
    Processing helix  chain 'E' and resid 227 through 261
      removed outlier: 4.051A  pdb=" N   GLU E 261 " --> pdb=" O   GLU E 257 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 261 through 269
      removed outlier: 3.517A  pdb=" N   LEU E 265 " --> pdb=" O   GLU E 261 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   CYS E 269 " --> pdb=" O   LEU E 265 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 269 through 275
      removed outlier: 3.932A  pdb=" N   ASP E 275 " --> pdb=" O   SER E 271 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 275 through 283
      removed outlier: 4.099A  pdb=" N   LYS E 281 " --> pdb=" O   GLN E 277 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 287 through 359
    Processing helix  chain 'E' and resid 371 through 401
      removed outlier: 4.424A  pdb=" N   TRP E 375 " --> pdb=" O   HIS E 371 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 103
      removed outlier: 4.191A  pdb=" N   LYS A 141 " --> pdb=" O   LEU A 152 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 103
      removed outlier: 4.192A  pdb=" N   LYS B 141 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 97 through 103
      removed outlier: 4.192A  pdb=" N   LYS C 141 " --> pdb=" O   LEU C 152 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 97 through 103
      removed outlier: 4.192A  pdb=" N   LYS D 141 " --> pdb=" O   LEU D 152 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 97 through 103
      removed outlier: 4.192A  pdb=" N   LYS E 141 " --> pdb=" O   LEU E 152 " (cutoff:3.500A)

    1015 hydrogen bonds defined for protein.
    2970 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 5.52

  Time building geometry restraints manager: 4.12 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4210
        1.34 -     1.46: 2437
        1.46 -     1.58: 6318
        1.58 -     1.69: 0
        1.69 -     1.81: 120
  Bond restraints: 13085
  Sorted by residual:
  bond pdb=" C   SER B 348 "
       pdb=" O   SER B 348 "
    ideal  model  delta    sigma   weight residual
    1.237  1.245 -0.008 1.17e-02 7.31e+03 5.01e-01
  bond pdb=" C   SER E 348 "
       pdb=" O   SER E 348 "
    ideal  model  delta    sigma   weight residual
    1.237  1.245 -0.008 1.17e-02 7.31e+03 4.74e-01
  bond pdb=" CA  LEU D 354 "
       pdb=" C   LEU D 354 "
    ideal  model  delta    sigma   weight residual
    1.523  1.515  0.008 1.30e-02 5.92e+03 4.19e-01
  bond pdb=" CA  LEU C 354 "
       pdb=" C   LEU C 354 "
    ideal  model  delta    sigma   weight residual
    1.523  1.515  0.008 1.30e-02 5.92e+03 4.11e-01
  bond pdb=" C   SER D 348 "
       pdb=" O   SER D 348 "
    ideal  model  delta    sigma   weight residual
    1.237  1.244 -0.007 1.17e-02 7.31e+03 4.03e-01
  ... (remaining 13080 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.04: 17215
        1.04 -     2.09: 375
        2.09 -     3.13: 55
        3.13 -     4.17: 20
        4.17 -     5.21: 20
  Bond angle restraints: 17685
  Sorted by residual:
  angle pdb=" C   LEU E 351 "
        pdb=" N   PHE E 352 "
        pdb=" CA  PHE E 352 "
      ideal   model   delta    sigma   weight residual
     121.14  117.47    3.67 1.75e+00 3.27e-01 4.41e+00
  angle pdb=" C   LEU C 351 "
        pdb=" N   PHE C 352 "
        pdb=" CA  PHE C 352 "
      ideal   model   delta    sigma   weight residual
     121.14  117.47    3.67 1.75e+00 3.27e-01 4.39e+00
  angle pdb=" C   LEU B 351 "
        pdb=" N   PHE B 352 "
        pdb=" CA  PHE B 352 "
      ideal   model   delta    sigma   weight residual
     121.14  117.47    3.67 1.75e+00 3.27e-01 4.39e+00
  angle pdb=" C   LEU A 351 "
        pdb=" N   PHE A 352 "
        pdb=" CA  PHE A 352 "
      ideal   model   delta    sigma   weight residual
     121.14  117.47    3.67 1.75e+00 3.27e-01 4.39e+00
  angle pdb=" C   LEU D 351 "
        pdb=" N   PHE D 352 "
        pdb=" CA  PHE D 352 "
      ideal   model   delta    sigma   weight residual
     121.14  117.48    3.66 1.75e+00 3.27e-01 4.37e+00
  ... (remaining 17680 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.51: 7428
       17.51 -    35.03: 462
       35.03 -    52.54: 35
       52.54 -    70.05: 5
       70.05 -    87.57: 5
  Dihedral angle restraints: 7935
    sinusoidal: 3270
      harmonic: 4665
  Sorted by residual:
  dihedral pdb=" CB  GLU E 147 "
           pdb=" CG  GLU E 147 "
           pdb=" CD  GLU E 147 "
           pdb=" OE1 GLU E 147 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.57  -87.57     1      3.00e+01 1.11e-03 1.02e+01
  dihedral pdb=" CB  GLU D 147 "
           pdb=" CG  GLU D 147 "
           pdb=" CD  GLU D 147 "
           pdb=" OE1 GLU D 147 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.54  -87.54     1      3.00e+01 1.11e-03 1.02e+01
  dihedral pdb=" CB  GLU B 147 "
           pdb=" CG  GLU B 147 "
           pdb=" CD  GLU B 147 "
           pdb=" OE1 GLU B 147 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.54  -87.54     1      3.00e+01 1.11e-03 1.02e+01
  ... (remaining 7932 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1379
       0.029 -    0.058: 420
       0.058 -    0.086: 156
       0.086 -    0.115: 75
       0.115 -    0.144: 20
  Chirality restraints: 2050
  Sorted by residual:
  chirality pdb=" CA  LEU A 167 "
            pdb=" N   LEU A 167 "
            pdb=" C   LEU A 167 "
            pdb=" CB  LEU A 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.16e-01
  chirality pdb=" CA  LEU C 167 "
            pdb=" N   LEU C 167 "
            pdb=" C   LEU C 167 "
            pdb=" CB  LEU C 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.16e-01
  chirality pdb=" CA  LEU B 167 "
            pdb=" N   LEU B 167 "
            pdb=" C   LEU B 167 "
            pdb=" CB  LEU B 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.09e-01
  ... (remaining 2047 not shown)

  Planarity restraints: 2235
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 163 "    0.011 2.00e-02 2.50e+03   2.17e-02 4.71e+00
        pdb=" C   LEU B 163 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   LEU B 163 "    0.014 2.00e-02 2.50e+03
        pdb=" N   PHE B 164 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU E 163 "   -0.011 2.00e-02 2.50e+03   2.16e-02 4.66e+00
        pdb=" C   LEU E 163 "    0.037 2.00e-02 2.50e+03
        pdb=" O   LEU E 163 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   PHE E 164 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 163 "    0.011 2.00e-02 2.50e+03   2.14e-02 4.58e+00
        pdb=" C   LEU A 163 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   LEU A 163 "    0.014 2.00e-02 2.50e+03
        pdb=" N   PHE A 164 "    0.012 2.00e-02 2.50e+03
  ... (remaining 2232 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2582
        2.78 -     3.31: 13000
        3.31 -     3.84: 21592
        3.84 -     4.37: 25684
        4.37 -     4.90: 45039
  Nonbonded interactions: 107897
  Sorted by model distance:
  nonbonded pdb=" OG  SER D  99 "
            pdb=" OH  TYR D 154 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OG  SER E  99 "
            pdb=" OH  TYR E 154 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OG  SER C  99 "
            pdb=" OH  TYR C 154 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OG  SER B  99 "
            pdb=" OH  TYR B 154 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OG  SER A  99 "
            pdb=" OH  TYR A 154 "
     model   vdw
     2.256 3.040
  ... (remaining 107892 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 'A' and (resid 83 through 401 or resid 502))
  selection = (chain 'B' and (resid 83 through 401 or resid 502))
  selection = (chain 'C' and (resid 83 through 401 or resid 502))
  selection = (chain 'D' and (resid 83 through 401 or resid 502))
  selection = (chain 'E' and (resid 83 through 401 or resid 502))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     31.870
  Find NCS groups from input model:        0.770
  Set up NCS constraints:                  0.040
  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:16.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
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      :  0.002   0.018  13085  Z= 0.116
  Angle     :  0.425   5.214  17685  Z= 0.224
  Chirality :  0.037   0.144   2050
  Planarity :  0.003   0.029   2235
  Dihedral  : 10.758  87.566   4895
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  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:  3.79 (0.21), residues: 1585
  helix:  3.32 (0.15), residues: 1040
  sheet:  2.16 (0.38), residues: 145
  loop :  0.33 (0.34), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 162 
 HIS   0.001   0.000   HIS C 223 
 PHE   0.016   0.001   PHE D 352 
 TYR   0.012   0.001   TYR E 299 
 ARG   0.001   0.000   ARG B 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08434 ( 1015)
  hydrogen bonds       : angle       4.40704 ( 2970)
  covalent geometry    : bond        0.00236 (13085)
  covalent geometry    : angle       0.42491 (17685)

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

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

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 1.626 
Fit side-chains
REVERT: A  383 MET cc_start: 0.6980 (mmp) cc_final: 0.6550 (mtp)
REVERT: C  383 MET cc_start: 0.6789 (mmp) cc_final: 0.6236 (mtm)
REVERT: D  383 MET cc_start: 0.6884 (mmp) cc_final: 0.6458 (mtp)
REVERT: E  383 MET cc_start: 0.7061 (mmp) cc_final: 0.6482 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 208
  average time/residue: 1.2883
  time to fit residues: 291.3066
Evaluate side-chains
  152 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 1.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 130 optimal weight:    1.9990
   chunk 117 optimal weight:    3.9990
   chunk 65 optimal weight:    0.0870
   chunk 40 optimal weight:   10.0000
   chunk 79 optimal weight:    4.9990
   chunk 62 optimal weight:    6.9990
   chunk 121 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 90 optimal weight:    7.9990
   chunk 140 optimal weight:    2.9990
   overall best weight:    2.2166

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

Flipped N/Q/H residues before XYZ refinement:
A 121 GLN
B 121 GLN
E 362 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.109177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.080861 restraints weight = 20131.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.2998 rms_B_bonded: 2.56
r_work: 0.2825 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.1222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  13085  Z= 0.235
  Angle     :  0.536   8.016  17685  Z= 0.278
  Chirality :  0.042   0.216   2050
  Planarity :  0.004   0.032   2235
  Dihedral  :  4.003  14.119   1720
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  6.71 %
    Favored  : 92.30 %
  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:  3.50 (0.21), residues: 1585
  helix:  3.16 (0.15), residues: 1020
  sheet:  2.05 (0.39), residues: 145
  loop :  0.19 (0.35), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 196 
 HIS   0.003   0.001   HIS C 122 
 PHE   0.023   0.002   PHE A 395 
 TYR   0.025   0.002   TYR C 299 
 ARG   0.004   0.000   ARG B 165 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05250 ( 1015)
  hydrogen bonds       : angle       4.12468 ( 2970)
  covalent geometry    : bond        0.00547 (13085)
  covalent geometry    : angle       0.53572 (17685)

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

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

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 156
  time to evaluate  : 2.306 
Fit side-chains
REVERT: A   94 GLN cc_start: 0.8257 (mp10) cc_final: 0.7860 (mp10)
REVERT: A  383 MET cc_start: 0.7064 (mmp) cc_final: 0.6416 (mtp)
REVERT: C  350 SER cc_start: 0.8166 (t) cc_final: 0.7923 (m)
REVERT: C  383 MET cc_start: 0.6994 (mmp) cc_final: 0.6312 (mtm)
REVERT: D  350 SER cc_start: 0.8500 (OUTLIER) cc_final: 0.8261 (p)
REVERT: D  383 MET cc_start: 0.6965 (mmp) cc_final: 0.6303 (mtp)
REVERT: E   94 GLN cc_start: 0.8244 (mp10) cc_final: 0.7729 (mp10)
REVERT: E  350 SER cc_start: 0.8293 (t) cc_final: 0.7892 (p)
REVERT: E  355 MET cc_start: 0.8100 (ttm) cc_final: 0.7827 (ttm)
REVERT: E  362 ASN cc_start: 0.7909 (m110) cc_final: 0.7653 (m-40)
REVERT: E  383 MET cc_start: 0.7122 (mmp) cc_final: 0.6301 (mtp)
  outliers start: 14
  outliers final: 5
  residues processed: 160
  average time/residue: 1.3470
  time to fit residues: 235.8027
Evaluate side-chains
  145 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 139
  time to evaluate  : 1.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  350 SER
Chi-restraints excluded: chain D residue  355 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 152 optimal weight:    9.9990
   chunk 135 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 129 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 105 optimal weight:    0.7980
   chunk 56 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 104 optimal weight:    0.7980
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
B 121 GLN
B 362 ASN
E 121 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.109637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.080841 restraints weight = 19855.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 2.54
r_work: 0.2903 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.1359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  13085  Z= 0.186
  Angle     :  0.490   8.872  17685  Z= 0.258
  Chirality :  0.041   0.214   2050
  Planarity :  0.004   0.036   2235
  Dihedral  :  3.965  14.314   1720
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  :  7.14 %
    Favored  : 91.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.46 (0.21), residues: 1585
  helix:  2.88 (0.15), residues: 1050
  sheet:  2.07 (0.40), residues: 145
  loop :  0.70 (0.36), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 375 
 HIS   0.002   0.001   HIS C 122 
 PHE   0.019   0.002   PHE A 352 
 TYR   0.020   0.002   TYR C 299 
 ARG   0.003   0.000   ARG B 165 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04999 ( 1015)
  hydrogen bonds       : angle       4.02168 ( 2970)
  covalent geometry    : bond        0.00426 (13085)
  covalent geometry    : angle       0.49041 (17685)

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

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

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 161
  time to evaluate  : 1.456 
Fit side-chains
REVERT: A   94 GLN cc_start: 0.8195 (mp10) cc_final: 0.7788 (mp10)
REVERT: A  359 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.7710 (t80)
REVERT: A  383 MET cc_start: 0.6776 (mmp) cc_final: 0.6159 (mtp)
REVERT: B  355 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7760 (ttp)
REVERT: B  359 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7763 (t80)
REVERT: B  362 ASN cc_start: 0.7819 (m110) cc_final: 0.7559 (m-40)
REVERT: B  383 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6318 (mpp)
REVERT: C  383 MET cc_start: 0.6938 (mmp) cc_final: 0.6227 (mtm)
REVERT: D  359 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7653 (t80)
REVERT: D  383 MET cc_start: 0.6865 (mmp) cc_final: 0.6234 (mtp)
REVERT: D  391 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6554 (ttp-170)
REVERT: E   94 GLN cc_start: 0.8206 (mp10) cc_final: 0.7773 (mp10)
REVERT: E  350 SER cc_start: 0.8134 (t) cc_final: 0.7767 (p)
REVERT: E  355 MET cc_start: 0.8027 (ttm) cc_final: 0.7774 (ttm)
REVERT: E  383 MET cc_start: 0.6941 (mmp) cc_final: 0.6142 (mtp)
  outliers start: 26
  outliers final: 7
  residues processed: 169
  average time/residue: 1.2966
  time to fit residues: 239.7914
Evaluate side-chains
  165 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 152
  time to evaluate  : 2.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain B residue  257 GLU
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain B residue  359 PHE
Chi-restraints excluded: chain B residue  383 MET
Chi-restraints excluded: chain D residue  314 ARG
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  355 MET
Chi-restraints excluded: chain D residue  359 PHE
Chi-restraints excluded: chain D residue  391 ARG
Chi-restraints excluded: chain E residue  338 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 122 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9990
   chunk 151 optimal weight:    4.9990
   chunk 84 optimal weight:    4.9990
   chunk 71 optimal weight:    8.9990
   chunk 109 optimal weight:    2.9990
   chunk 134 optimal weight:    0.8980
   chunk 63 optimal weight:    0.0570
   chunk 70 optimal weight:    0.9980
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.7300

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

Flipped N/Q/H residues before XYZ refinement:
C 362 ASN
E 121 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.111784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.083614 restraints weight = 19517.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 2.49
r_work: 0.2965 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.1291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  13085  Z= 0.118
  Angle     :  0.442   9.414  17685  Z= 0.233
  Chirality :  0.039   0.234   2050
  Planarity :  0.003   0.038   2235
  Dihedral  :  3.761  14.171   1720
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  9.26 %
    Favored  : 89.54 %
  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:  3.62 (0.21), residues: 1585
  helix:  3.03 (0.15), residues: 1050
  sheet:  2.10 (0.40), residues: 145
  loop :  0.72 (0.36), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 162 
 HIS   0.002   0.000   HIS C 122 
 PHE   0.020   0.001   PHE C 352 
 TYR   0.016   0.001   TYR C 299 
 ARG   0.003   0.000   ARG C 165 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04560 ( 1015)
  hydrogen bonds       : angle       3.85594 ( 2970)
  covalent geometry    : bond        0.00245 (13085)
  covalent geometry    : angle       0.44242 (17685)

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

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

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 164
  time to evaluate  : 1.594 
Fit side-chains
REVERT: A   94 GLN cc_start: 0.8208 (mp10) cc_final: 0.7748 (mp10)
REVERT: A  359 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.7463 (t80)
REVERT: A  383 MET cc_start: 0.6745 (mmp) cc_final: 0.6118 (mtp)
REVERT: B  362 ASN cc_start: 0.7791 (m110) cc_final: 0.7547 (m-40)
REVERT: C  383 MET cc_start: 0.6764 (mmp) cc_final: 0.6012 (mtm)
REVERT: D  359 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7706 (t80)
REVERT: D  383 MET cc_start: 0.6796 (mmp) cc_final: 0.6132 (mtp)
REVERT: D  391 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6484 (ttp-170)
REVERT: E   94 GLN cc_start: 0.8235 (mp10) cc_final: 0.7701 (mp10)
REVERT: E  350 SER cc_start: 0.8104 (t) cc_final: 0.7713 (p)
REVERT: E  355 MET cc_start: 0.7973 (ttm) cc_final: 0.7693 (ttm)
REVERT: E  383 MET cc_start: 0.6845 (mmp) cc_final: 0.6043 (mtp)
  outliers start: 17
  outliers final: 6
  residues processed: 169
  average time/residue: 1.5245
  time to fit residues: 280.7326
Evaluate side-chains
  166 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 157
  time to evaluate  : 2.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain B residue  257 GLU
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain C residue  197 ILE
Chi-restraints excluded: chain C residue  359 PHE
Chi-restraints excluded: chain D residue  314 ARG
Chi-restraints excluded: chain D residue  355 MET
Chi-restraints excluded: chain D residue  359 PHE
Chi-restraints excluded: chain D residue  391 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 72 optimal weight:    0.7980
   chunk 107 optimal weight:    0.9980
   chunk 128 optimal weight:    5.9990
   chunk 145 optimal weight:    4.9990
   chunk 116 optimal weight:    3.9990
   chunk 125 optimal weight:    0.5980
   chunk 143 optimal weight:    0.5980
   chunk 59 optimal weight:    9.9990
   chunk 95 optimal weight:    5.9990
   chunk 64 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   overall best weight:    1.3982

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

Flipped N/Q/H residues before XYZ refinement:
D 121 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.110088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.081554 restraints weight = 19779.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 2.52
r_work: 0.2915 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.1470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027  13085  Z= 0.165
  Angle     :  0.473   5.643  17685  Z= 0.249
  Chirality :  0.040   0.216   2050
  Planarity :  0.003   0.038   2235
  Dihedral  :  3.864  14.157   1720
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  9.19 %
    Favored  : 89.05 %
  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:  3.43 (0.21), residues: 1585
  helix:  2.86 (0.15), residues: 1070
  sheet:  2.09 (0.40), residues: 145
  loop :  0.55 (0.37), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 375 
 HIS   0.002   0.000   HIS C 122 
 PHE   0.020   0.002   PHE D 352 
 TYR   0.020   0.002   TYR C 299 
 ARG   0.005   0.000   ARG C 372 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04853 ( 1015)
  hydrogen bonds       : angle       3.92625 ( 2970)
  covalent geometry    : bond        0.00372 (13085)
  covalent geometry    : angle       0.47321 (17685)

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

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

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 157
  time to evaluate  : 1.748 
Fit side-chains
REVERT: A   94 GLN cc_start: 0.8198 (mp10) cc_final: 0.7803 (mp10)
REVERT: A  359 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7558 (t80)
REVERT: A  383 MET cc_start: 0.6727 (mmp) cc_final: 0.6099 (mtp)
REVERT: B  344 MET cc_start: 0.8664 (mtm) cc_final: 0.8450 (mtp)
REVERT: B  359 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7478 (t80)
REVERT: C  336 MET cc_start: 0.9066 (ttp) cc_final: 0.8853 (ttm)
REVERT: C  383 MET cc_start: 0.6855 (mmp) cc_final: 0.6120 (mtm)
REVERT: D  359 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7613 (t80)
REVERT: D  383 MET cc_start: 0.6811 (mmp) cc_final: 0.6172 (mtp)
REVERT: D  391 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6489 (ttp-170)
REVERT: E   94 GLN cc_start: 0.8203 (mp10) cc_final: 0.7688 (mp10)
REVERT: E  355 MET cc_start: 0.8045 (ttm) cc_final: 0.7805 (ttm)
REVERT: E  383 MET cc_start: 0.6832 (mmp) cc_final: 0.6029 (mtp)
  outliers start: 25
  outliers final: 10
  residues processed: 166
  average time/residue: 2.1196
  time to fit residues: 382.3457
Evaluate side-chains
  166 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 152
  time to evaluate  : 3.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain B residue  257 GLU
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain B residue  359 PHE
Chi-restraints excluded: chain C residue  197 ILE
Chi-restraints excluded: chain C residue  359 PHE
Chi-restraints excluded: chain D residue  314 ARG
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  355 MET
Chi-restraints excluded: chain D residue  359 PHE
Chi-restraints excluded: chain D residue  391 ARG
Chi-restraints excluded: chain E residue  338 LEU
Chi-restraints excluded: chain E residue  349 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0770
   chunk 24 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 67 optimal weight:    2.9990
   chunk 79 optimal weight:    0.3980
   chunk 2 optimal weight:    0.6980
   chunk 46 optimal weight:    3.9990
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
D 121 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.112597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.084229 restraints weight = 19843.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 2.54
r_work: 0.2973 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.1396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  13085  Z= 0.107
  Angle     :  0.433   9.421  17685  Z= 0.228
  Chirality :  0.039   0.231   2050
  Planarity :  0.003   0.037   2235
  Dihedral  :  3.680  14.712   1720
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 10.11 %
    Favored  : 88.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.61 (0.21), residues: 1585
  helix:  3.01 (0.15), residues: 1070
  sheet:  2.05 (0.39), residues: 145
  loop :  0.64 (0.37), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 162 
 HIS   0.002   0.000   HIS C 122 
 PHE   0.020   0.001   PHE E 352 
 TYR   0.016   0.001   TYR C 299 
 ARG   0.005   0.000   ARG B 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04423 ( 1015)
  hydrogen bonds       : angle       3.77413 ( 2970)
  covalent geometry    : bond        0.00209 (13085)
  covalent geometry    : angle       0.43312 (17685)

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

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

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 169
  time to evaluate  : 2.356 
Fit side-chains
REVERT: A   94 GLN cc_start: 0.8186 (mp10) cc_final: 0.7720 (mp10)
REVERT: A  383 MET cc_start: 0.6881 (mmp) cc_final: 0.6236 (mtp)
REVERT: B  359 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7404 (t80)
REVERT: C  124 MET cc_start: 0.8703 (tpt) cc_final: 0.8442 (tpp)
REVERT: C  336 MET cc_start: 0.9008 (ttp) cc_final: 0.8790 (ttm)
REVERT: C  383 MET cc_start: 0.6628 (mmp) cc_final: 0.5858 (mtm)
REVERT: D  383 MET cc_start: 0.6753 (mmp) cc_final: 0.6096 (mtp)
REVERT: E   94 GLN cc_start: 0.8203 (mp10) cc_final: 0.7715 (mp10)
REVERT: E  124 MET cc_start: 0.8739 (tpt) cc_final: 0.8437 (tpp)
REVERT: E  349 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7951 (mp)
REVERT: E  355 MET cc_start: 0.7894 (ttm) cc_final: 0.7592 (ttm)
REVERT: E  383 MET cc_start: 0.6723 (mmp) cc_final: 0.5947 (mtp)
  outliers start: 18
  outliers final: 4
  residues processed: 174
  average time/residue: 1.3154
  time to fit residues: 251.6073
Evaluate side-chains
  165 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 159
  time to evaluate  : 1.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain B residue  359 PHE
Chi-restraints excluded: chain D residue  314 ARG
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  355 MET
Chi-restraints excluded: chain E residue  349 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 117 optimal weight:    4.9990
   chunk 116 optimal weight:    0.7980
   chunk 74 optimal weight:    0.2980
   chunk 134 optimal weight:    0.9980
   chunk 106 optimal weight:    0.7980
   chunk 20 optimal weight:   10.0000
   chunk 127 optimal weight:    0.0670
   chunk 40 optimal weight:    9.9990
   chunk 79 optimal weight:    0.9990
   chunk 149 optimal weight:    3.9990
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
D 121 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.112713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.084619 restraints weight = 20019.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.3042 rms_B_bonded: 2.57
r_work: 0.2867 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.1455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  13085  Z= 0.113
  Angle     :  0.440   8.369  17685  Z= 0.233
  Chirality :  0.039   0.208   2050
  Planarity :  0.003   0.037   2235
  Dihedral  :  3.655  14.451   1720
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 11.02 %
    Favored  : 87.99 %
  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:  3.59 (0.21), residues: 1585
  helix:  2.95 (0.15), residues: 1090
  sheet:  2.02 (0.39), residues: 145
  loop :  0.63 (0.38), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 162 
 HIS   0.002   0.000   HIS C 122 
 PHE   0.020   0.001   PHE D 352 
 TYR   0.014   0.001   TYR C 299 
 ARG   0.004   0.000   ARG B 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04437 ( 1015)
  hydrogen bonds       : angle       3.75374 ( 2970)
  covalent geometry    : bond        0.00230 (13085)
  covalent geometry    : angle       0.44032 (17685)

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

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

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 163
  time to evaluate  : 1.635 
Fit side-chains
REVERT: A   94 GLN cc_start: 0.8220 (mp10) cc_final: 0.7756 (mp10)
REVERT: A  381 MET cc_start: 0.6517 (ttm) cc_final: 0.6248 (mtp)
REVERT: A  383 MET cc_start: 0.6887 (mmp) cc_final: 0.6204 (mtp)
REVERT: B   94 GLN cc_start: 0.8152 (mp10) cc_final: 0.7588 (mp10)
REVERT: B  359 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7478 (t80)
REVERT: C  124 MET cc_start: 0.8796 (tpt) cc_final: 0.8548 (tpp)
REVERT: C  383 MET cc_start: 0.6657 (mmp) cc_final: 0.5895 (mtm)
REVERT: D  359 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7333 (t80)
REVERT: D  383 MET cc_start: 0.6795 (mmp) cc_final: 0.6129 (mtp)
REVERT: E   94 GLN cc_start: 0.8185 (mp10) cc_final: 0.7700 (mp10)
REVERT: E  124 MET cc_start: 0.8811 (tpt) cc_final: 0.8497 (tpp)
REVERT: E  349 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8016 (mp)
REVERT: E  355 MET cc_start: 0.7887 (ttm) cc_final: 0.7678 (ttm)
REVERT: E  383 MET cc_start: 0.6718 (mmp) cc_final: 0.5987 (mtp)
  outliers start: 14
  outliers final: 8
  residues processed: 167
  average time/residue: 1.3007
  time to fit residues: 237.2978
Evaluate side-chains
  166 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 155
  time to evaluate  : 1.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain B residue  359 PHE
Chi-restraints excluded: chain C residue  197 ILE
Chi-restraints excluded: chain C residue  359 PHE
Chi-restraints excluded: chain D residue  257 GLU
Chi-restraints excluded: chain D residue  314 ARG
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  355 MET
Chi-restraints excluded: chain D residue  359 PHE
Chi-restraints excluded: chain E residue  338 LEU
Chi-restraints excluded: chain E residue  349 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 93 optimal weight:    6.9990
   chunk 83 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9990
   chunk 124 optimal weight:    6.9990
   chunk 71 optimal weight:    0.0870
   chunk 95 optimal weight:    0.5980
   chunk 81 optimal weight:    0.6980
   chunk 123 optimal weight:    7.9990
   chunk 74 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 118 optimal weight:    0.8980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
D 121 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.112589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.084494 restraints weight = 20125.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 2.58
r_work: 0.2922 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.1462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  13085  Z= 0.112
  Angle     :  0.439   9.816  17685  Z= 0.231
  Chirality :  0.038   0.193   2050
  Planarity :  0.003   0.037   2235
  Dihedral  :  3.619  14.501   1720
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 11.10 %
    Favored  : 87.99 %
  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:  3.65 (0.21), residues: 1585
  helix:  3.00 (0.15), residues: 1090
  sheet:  2.02 (0.39), residues: 145
  loop :  0.65 (0.38), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 162 
 HIS   0.002   0.000   HIS C 122 
 PHE   0.022   0.001   PHE E 352 
 TYR   0.016   0.001   TYR C 299 
 ARG   0.004   0.000   ARG B 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04404 ( 1015)
  hydrogen bonds       : angle       3.73486 ( 2970)
  covalent geometry    : bond        0.00226 (13085)
  covalent geometry    : angle       0.43891 (17685)

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

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

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 162
  time to evaluate  : 1.634 
Fit side-chains
REVERT: A   94 GLN cc_start: 0.8222 (mp10) cc_final: 0.7759 (mp10)
REVERT: A  381 MET cc_start: 0.6570 (ttm) cc_final: 0.6258 (mtp)
REVERT: A  383 MET cc_start: 0.6939 (mmp) cc_final: 0.6268 (mtp)
REVERT: B   94 GLN cc_start: 0.8161 (mp10) cc_final: 0.7601 (mp10)
REVERT: B  359 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7539 (t80)
REVERT: C  124 MET cc_start: 0.8791 (tpt) cc_final: 0.8561 (tpp)
REVERT: C  383 MET cc_start: 0.6712 (mmp) cc_final: 0.5914 (mtm)
REVERT: D  359 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7408 (t80)
REVERT: D  383 MET cc_start: 0.6859 (mmp) cc_final: 0.6209 (mtp)
REVERT: E   94 GLN cc_start: 0.8204 (mp10) cc_final: 0.7719 (mp10)
REVERT: E  124 MET cc_start: 0.8812 (tpt) cc_final: 0.8511 (tpp)
REVERT: E  349 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8032 (mp)
REVERT: E  355 MET cc_start: 0.7927 (ttm) cc_final: 0.7678 (ttm)
REVERT: E  383 MET cc_start: 0.6697 (mmp) cc_final: 0.5963 (mtp)
  outliers start: 13
  outliers final: 6
  residues processed: 166
  average time/residue: 1.2304
  time to fit residues: 223.5259
Evaluate side-chains
  164 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 155
  time to evaluate  : 1.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain B residue  359 PHE
Chi-restraints excluded: chain C residue  197 ILE
Chi-restraints excluded: chain D residue  314 ARG
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  355 MET
Chi-restraints excluded: chain D residue  359 PHE
Chi-restraints excluded: chain E residue  338 LEU
Chi-restraints excluded: chain E residue  349 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 131 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 144 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9980
   chunk 129 optimal weight:    0.0970
   chunk 125 optimal weight:    1.9990
   chunk 98 optimal weight:    0.6980
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
D 121 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.112857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.084745 restraints weight = 19964.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3080 rms_B_bonded: 2.58
r_work: 0.2913 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.1487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  13085  Z= 0.115
  Angle     :  0.450  10.132  17685  Z= 0.234
  Chirality :  0.038   0.191   2050
  Planarity :  0.003   0.036   2235
  Dihedral  :  3.621  14.432   1720
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 10.88 %
    Favored  : 88.27 %
  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:  3.65 (0.21), residues: 1585
  helix:  2.99 (0.15), residues: 1090
  sheet:  2.01 (0.38), residues: 145
  loop :  0.66 (0.38), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 162 
 HIS   0.001   0.000   HIS C 122 
 PHE   0.021   0.001   PHE E 352 
 TYR   0.013   0.001   TYR D 299 
 ARG   0.007   0.000   ARG C 372 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04416 ( 1015)
  hydrogen bonds       : angle       3.73604 ( 2970)
  covalent geometry    : bond        0.00236 (13085)
  covalent geometry    : angle       0.45011 (17685)

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

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

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 155
  time to evaluate  : 1.668 
Fit side-chains
REVERT: A   94 GLN cc_start: 0.8231 (mp10) cc_final: 0.7774 (mp10)
REVERT: A  381 MET cc_start: 0.6609 (ttm) cc_final: 0.6349 (mtp)
REVERT: A  383 MET cc_start: 0.6947 (mmp) cc_final: 0.6248 (mtp)
REVERT: B   94 GLN cc_start: 0.8156 (mp10) cc_final: 0.7596 (mp10)
REVERT: C  124 MET cc_start: 0.8807 (tpt) cc_final: 0.8578 (tpp)
REVERT: C  383 MET cc_start: 0.6742 (mmp) cc_final: 0.5942 (mtm)
REVERT: D  359 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7362 (t80)
REVERT: D  383 MET cc_start: 0.6838 (mmp) cc_final: 0.6186 (mtp)
REVERT: E   94 GLN cc_start: 0.8209 (mp10) cc_final: 0.7728 (mp10)
REVERT: E  124 MET cc_start: 0.8841 (tpt) cc_final: 0.8541 (tpp)
REVERT: E  349 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8056 (mp)
REVERT: E  355 MET cc_start: 0.7958 (ttm) cc_final: 0.7723 (ttm)
REVERT: E  383 MET cc_start: 0.6731 (mmp) cc_final: 0.6001 (mtp)
  outliers start: 12
  outliers final: 6
  residues processed: 159
  average time/residue: 1.2266
  time to fit residues: 213.6897
Evaluate side-chains
  159 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 151
  time to evaluate  : 1.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain C residue  197 ILE
Chi-restraints excluded: chain D residue  314 ARG
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  355 MET
Chi-restraints excluded: chain D residue  359 PHE
Chi-restraints excluded: chain E residue  338 LEU
Chi-restraints excluded: chain E residue  349 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 48 optimal weight:    0.0870
   chunk 99 optimal weight:    0.8980
   chunk 87 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   chunk 101 optimal weight:    3.9990
   chunk 116 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
D 121 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.113060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.084991 restraints weight = 19972.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 2.56
r_work: 0.2915 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.1497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  13085  Z= 0.115
  Angle     :  0.445   9.544  17685  Z= 0.234
  Chirality :  0.038   0.182   2050
  Planarity :  0.003   0.037   2235
  Dihedral  :  3.607  14.441   1720
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 10.88 %
    Favored  : 88.27 %
  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:  3.67 (0.21), residues: 1585
  helix:  3.01 (0.15), residues: 1090
  sheet:  2.01 (0.38), residues: 145
  loop :  0.67 (0.38), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 162 
 HIS   0.002   0.000   HIS C 122 
 PHE   0.019   0.001   PHE E 352 
 TYR   0.015   0.001   TYR C 299 
 ARG   0.007   0.000   ARG C 372 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04418 ( 1015)
  hydrogen bonds       : angle       3.73049 ( 2970)
  covalent geometry    : bond        0.00238 (13085)
  covalent geometry    : angle       0.44511 (17685)

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

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

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 157
  time to evaluate  : 1.514 
Fit side-chains
REVERT: A   94 GLN cc_start: 0.8234 (mp10) cc_final: 0.7776 (mp10)
REVERT: A  381 MET cc_start: 0.6619 (ttm) cc_final: 0.6342 (mtp)
REVERT: A  383 MET cc_start: 0.6937 (mmp) cc_final: 0.6239 (mtp)
REVERT: B   94 GLN cc_start: 0.8155 (mp10) cc_final: 0.7501 (mp10)
REVERT: C  124 MET cc_start: 0.8801 (tpt) cc_final: 0.8575 (tpp)
REVERT: C  383 MET cc_start: 0.6667 (mmp) cc_final: 0.5861 (mtm)
REVERT: D  359 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7192 (t80)
REVERT: D  383 MET cc_start: 0.6861 (mmp) cc_final: 0.6196 (mtp)
REVERT: E   94 GLN cc_start: 0.8214 (mp10) cc_final: 0.7695 (mp10)
REVERT: E  124 MET cc_start: 0.8837 (tpt) cc_final: 0.8537 (tpp)
REVERT: E  349 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8051 (mp)
REVERT: E  383 MET cc_start: 0.6696 (mmp) cc_final: 0.5964 (mtp)
  outliers start: 12
  outliers final: 7
  residues processed: 162
  average time/residue: 1.1491
  time to fit residues: 204.6433
Evaluate side-chains
  160 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 151
  time to evaluate  : 1.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain C residue  197 ILE
Chi-restraints excluded: chain D residue  197 ILE
Chi-restraints excluded: chain D residue  314 ARG
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  355 MET
Chi-restraints excluded: chain D residue  359 PHE
Chi-restraints excluded: chain E residue  338 LEU
Chi-restraints excluded: chain E residue  349 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 118 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 122 optimal weight:    0.9980
   chunk 125 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 107 optimal weight:    0.8980
   chunk 89 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 362 ASN
D 121 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.112273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.084035 restraints weight = 19960.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3068 rms_B_bonded: 2.58
r_work: 0.2900 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.1508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13085  Z= 0.126
  Angle     :  0.462  10.091  17685  Z= 0.241
  Chirality :  0.039   0.179   2050
  Planarity :  0.003   0.037   2235
  Dihedral  :  3.645  14.391   1720
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 10.95 %
    Favored  : 88.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.64 (0.21), residues: 1585
  helix:  2.99 (0.15), residues: 1090
  sheet:  1.98 (0.38), residues: 145
  loop :  0.67 (0.38), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 162 
 HIS   0.002   0.000   HIS C 122 
 PHE   0.020   0.001   PHE D 352 
 TYR   0.017   0.001   TYR C 299 
 ARG   0.007   0.000   ARG C 372 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04513 ( 1015)
  hydrogen bonds       : angle       3.76390 ( 2970)
  covalent geometry    : bond        0.00270 (13085)
  covalent geometry    : angle       0.46241 (17685)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8890.30 seconds
wall clock time: 160 minutes 15.29 seconds (9615.29 seconds total)