Starting phenix.real_space_refine
on Tue Jun 10 14:09:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pim_13442/06_2025/7pim_13442.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pim_13442/06_2025/7pim_13442.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pim_13442/06_2025/7pim_13442.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pim_13442/06_2025/7pim_13442.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pim_13442/06_2025/7pim_13442.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pim_13442/06_2025/7pim_13442.cif"
  }
  resolution = 4.6
  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=   0.000 sd=   0.003
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
     Fe      4      7.16       5
     S      36      5.16       5
     C    7192      2.51       5
     N    1932      2.21       5
     O    2156      1.98       5
     H     524      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.07s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 11844
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "B"
      Number of atoms: 2688
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2688
          Classifications: {'peptide': 335}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 316}
    Chain: "G"
      Number of atoms: 261
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 261
          Classifications: {'peptide': 18}
          Link IDs: {'TRANS': 17}
    Chain: "A"
      Number of atoms: 2688
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2688
          Classifications: {'peptide': 335}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 316}
    Chain: "C"
      Number of atoms: 261
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 261
          Classifications: {'peptide': 18}
          Link IDs: {'TRANS': 17}
    Chain: "D"
      Number of atoms: 2688
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2688
          Classifications: {'peptide': 335}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 316}
    Chain: "E"
      Number of atoms: 261
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 261
          Classifications: {'peptide': 18}
          Link IDs: {'TRANS': 17}
    Chain: "F"
      Number of atoms: 2688
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2688
          Classifications: {'peptide': 335}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 316}
    Chain: "H"
      Number of atoms: 261
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 261
          Classifications: {'peptide': 18}
          Link IDs: {'TRANS': 17}
    Chain: "B"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 12
          Unusual residues: {' FE': 1, 'LDP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 12
          Unusual residues: {' FE': 1, 'LDP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 12
          Unusual residues: {' FE': 1, 'LDP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "F"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 12
          Unusual residues: {' FE': 1, 'LDP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 7.32, per 1000 atoms: 0.62
  Number of scatterers: 11844
  At special positions: 0
  Unit cell: (103.984, 91.12, 121.136, 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)
     Fe      4     26.01
     S      36     16.00
     O    2156      8.00
     N    1932      7.00
     C    7192      6.00
     H     524      1.00
    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: 3.30
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2688

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 12 sheets defined
      62.3% alpha, 7.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.21
  Creating SS restraints...
    Processing helix  chain 'B' and resid 169 through 181
      removed outlier: 3.558A  pdb=" N   THR B 181 " --> pdb=" O   HIS B 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 213
      removed outlier: 3.583A  pdb=" N   ARG B 200 " --> pdb=" O   ASP B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 243
    Processing helix  chain 'B' and resid 248 through 262
      removed outlier: 3.593A  pdb=" N   GLU B 253 " --> pdb=" O   GLY B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 284
    Processing helix  chain 'B' and resid 295 through 305
      removed outlier: 3.680A  pdb=" N   PHE B 299 " --> pdb=" O   SER B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 335
    Processing helix  chain 'B' and resid 335 through 340
    Processing helix  chain 'B' and resid 341 through 356
    Processing helix  chain 'B' and resid 359 through 374
      removed outlier: 3.523A  pdb=" N   TYR B 370 " --> pdb=" O   LEU B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 389 through 395
    Processing helix  chain 'B' and resid 395 through 404
      removed outlier: 3.911A  pdb=" N   LEU B 403 " --> pdb=" O   LEU B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 413 through 420
    Processing helix  chain 'B' and resid 436 through 451
      removed outlier: 3.525A  pdb=" N   ALA B 440 " --> pdb=" O   SER B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 471 through 496
      removed outlier: 3.540A  pdb=" N   GLY B 481 " --> pdb=" O   ARG B 477 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 41 through 57
      removed outlier: 3.939A  pdb=" N   ALA G  55 " --> pdb=" O   ALA G  51 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ALA G  56 " --> pdb=" O   ALA G  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 181
      removed outlier: 3.558A  pdb=" N   THR A 181 " --> pdb=" O   HIS A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 213
      removed outlier: 3.583A  pdb=" N   ARG A 200 " --> pdb=" O   ASP A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 243
    Processing helix  chain 'A' and resid 248 through 262
      removed outlier: 3.592A  pdb=" N   GLU A 253 " --> pdb=" O   GLY A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 284
    Processing helix  chain 'A' and resid 295 through 305
      removed outlier: 3.681A  pdb=" N   PHE A 299 " --> pdb=" O   SER A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 335
    Processing helix  chain 'A' and resid 335 through 340
    Processing helix  chain 'A' and resid 341 through 356
    Processing helix  chain 'A' and resid 359 through 374
      removed outlier: 3.523A  pdb=" N   TYR A 370 " --> pdb=" O   LEU A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 395
    Processing helix  chain 'A' and resid 395 through 404
      removed outlier: 3.912A  pdb=" N   LEU A 403 " --> pdb=" O   LEU A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 420
    Processing helix  chain 'A' and resid 436 through 451
      removed outlier: 3.525A  pdb=" N   ALA A 440 " --> pdb=" O   SER A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 496
      removed outlier: 3.541A  pdb=" N   GLY A 481 " --> pdb=" O   ARG A 477 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 41 through 57
      removed outlier: 3.938A  pdb=" N   ALA C  55 " --> pdb=" O   ALA C  51 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ALA C  56 " --> pdb=" O   ALA C  52 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 169 through 181
      removed outlier: 3.558A  pdb=" N   THR D 181 " --> pdb=" O   HIS D 177 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 196 through 213
      removed outlier: 3.584A  pdb=" N   ARG D 200 " --> pdb=" O   ASP D 196 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 225 through 243
    Processing helix  chain 'D' and resid 248 through 262
      removed outlier: 3.592A  pdb=" N   GLU D 253 " --> pdb=" O   GLY D 249 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 272 through 284
    Processing helix  chain 'D' and resid 295 through 305
      removed outlier: 3.680A  pdb=" N   PHE D 299 " --> pdb=" O   SER D 295 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 327 through 335
    Processing helix  chain 'D' and resid 335 through 340
    Processing helix  chain 'D' and resid 341 through 356
    Processing helix  chain 'D' and resid 359 through 374
      removed outlier: 3.523A  pdb=" N   TYR D 370 " --> pdb=" O   LEU D 366 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 389 through 395
    Processing helix  chain 'D' and resid 395 through 404
      removed outlier: 3.912A  pdb=" N   LEU D 403 " --> pdb=" O   LEU D 399 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 413 through 420
    Processing helix  chain 'D' and resid 436 through 451
      removed outlier: 3.526A  pdb=" N   ALA D 440 " --> pdb=" O   SER D 436 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 471 through 496
      removed outlier: 3.541A  pdb=" N   GLY D 481 " --> pdb=" O   ARG D 477 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 41 through 57
      removed outlier: 3.938A  pdb=" N   ALA E  55 " --> pdb=" O   ALA E  51 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ALA E  56 " --> pdb=" O   ALA E  52 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 169 through 181
      removed outlier: 3.558A  pdb=" N   THR F 181 " --> pdb=" O   HIS F 177 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 196 through 213
      removed outlier: 3.583A  pdb=" N   ARG F 200 " --> pdb=" O   ASP F 196 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 225 through 243
    Processing helix  chain 'F' and resid 248 through 262
      removed outlier: 3.593A  pdb=" N   GLU F 253 " --> pdb=" O   GLY F 249 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 272 through 284
    Processing helix  chain 'F' and resid 295 through 305
      removed outlier: 3.681A  pdb=" N   PHE F 299 " --> pdb=" O   SER F 295 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 327 through 335
    Processing helix  chain 'F' and resid 335 through 340
    Processing helix  chain 'F' and resid 341 through 356
    Processing helix  chain 'F' and resid 359 through 374
      removed outlier: 3.524A  pdb=" N   TYR F 370 " --> pdb=" O   LEU F 366 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 389 through 395
    Processing helix  chain 'F' and resid 395 through 404
      removed outlier: 3.912A  pdb=" N   LEU F 403 " --> pdb=" O   LEU F 399 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 413 through 420
    Processing helix  chain 'F' and resid 436 through 451
      removed outlier: 3.525A  pdb=" N   ALA F 440 " --> pdb=" O   SER F 436 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 471 through 496
      removed outlier: 3.541A  pdb=" N   GLY F 481 " --> pdb=" O   ARG F 477 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 41 through 57
      removed outlier: 3.938A  pdb=" N   ALA H  55 " --> pdb=" O   ALA H  51 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ALA H  56 " --> pdb=" O   ALA H  52 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 286 through 289
      removed outlier: 6.500A  pdb=" N   GLN B 286 " --> pdb=" O   PHE B 308 " (cutoff:3.500A)
      removed outlier: 7.276A  pdb=" N   CYS B 310 " --> pdb=" O   GLN B 286 " (cutoff:3.500A)
      removed outlier: 5.612A  pdb=" N   ARG B 288 " --> pdb=" O   CYS B 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 384 through 387
      removed outlier: 6.231A  pdb=" N   LEU B 378 " --> pdb=" O   SER B 434 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 456 through 460
    Processing sheet with id=AA4, first strand: chain 'A' and resid 286 through 289
      removed outlier: 6.500A  pdb=" N   GLN A 286 " --> pdb=" O   PHE A 308 " (cutoff:3.500A)
      removed outlier: 7.276A  pdb=" N   CYS A 310 " --> pdb=" O   GLN A 286 " (cutoff:3.500A)
      removed outlier: 5.612A  pdb=" N   ARG A 288 " --> pdb=" O   CYS A 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 384 through 387
      removed outlier: 6.232A  pdb=" N   LEU A 378 " --> pdb=" O   SER A 434 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 456 through 460
    Processing sheet with id=AA7, first strand: chain 'D' and resid 286 through 289
      removed outlier: 6.500A  pdb=" N   GLN D 286 " --> pdb=" O   PHE D 308 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   CYS D 310 " --> pdb=" O   GLN D 286 " (cutoff:3.500A)
      removed outlier: 5.612A  pdb=" N   ARG D 288 " --> pdb=" O   CYS D 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'D' and resid 384 through 387
      removed outlier: 6.232A  pdb=" N   LEU D 378 " --> pdb=" O   SER D 434 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 456 through 460
    Processing sheet with id=AB1, first strand: chain 'F' and resid 286 through 289
      removed outlier: 6.500A  pdb=" N   GLN F 286 " --> pdb=" O   PHE F 308 " (cutoff:3.500A)
      removed outlier: 7.276A  pdb=" N   CYS F 310 " --> pdb=" O   GLN F 286 " (cutoff:3.500A)
      removed outlier: 5.612A  pdb=" N   ARG F 288 " --> pdb=" O   CYS F 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'F' and resid 384 through 387
      removed outlier: 6.231A  pdb=" N   LEU F 378 " --> pdb=" O   SER F 434 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 456 through 460

    636 hydrogen bonds defined for protein.
    1872 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: 3.75

  Time building geometry restraints manager: 3.87 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 524
        1.03 -     1.23: 0
        1.23 -     1.42: 5068
        1.42 -     1.62: 6480
        1.62 -     1.81: 44
  Bond restraints: 12116
  Sorted by residual:
  bond pdb=" C3  LDP D 501 "
       pdb=" O1  LDP D 501 "
    ideal  model  delta    sigma   weight residual
    1.353  1.401 -0.048 2.00e-02 2.50e+03 5.84e+00
  bond pdb=" C3  LDP B 501 "
       pdb=" O1  LDP B 501 "
    ideal  model  delta    sigma   weight residual
    1.353  1.401 -0.048 2.00e-02 2.50e+03 5.75e+00
  bond pdb=" C3  LDP A 501 "
       pdb=" O1  LDP A 501 "
    ideal  model  delta    sigma   weight residual
    1.353  1.400 -0.047 2.00e-02 2.50e+03 5.63e+00
  bond pdb=" C3  LDP F 501 "
       pdb=" O1  LDP F 501 "
    ideal  model  delta    sigma   weight residual
    1.353  1.400 -0.047 2.00e-02 2.50e+03 5.58e+00
  bond pdb=" C4  LDP A 501 "
       pdb=" O2  LDP A 501 "
    ideal  model  delta    sigma   weight residual
    1.355  1.402 -0.047 2.00e-02 2.50e+03 5.43e+00
  ... (remaining 12111 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.95: 16856
        5.95 -    11.89: 0
       11.89 -    17.84: 0
       17.84 -    23.79: 16
       23.79 -    29.73: 32
  Bond angle restraints: 16904
  Sorted by residual:
  angle pdb=" CA  ALA C  52 "
        pdb=" CB  ALA C  52 "
        pdb=" HB3 ALA C  52 "
      ideal   model   delta    sigma   weight residual
     109.00   79.27   29.73 3.00e+00 1.11e-01 9.82e+01
  angle pdb=" CA  ALA H  52 "
        pdb=" CB  ALA H  52 "
        pdb=" HB3 ALA H  52 "
      ideal   model   delta    sigma   weight residual
     109.00   79.31   29.69 3.00e+00 1.11e-01 9.79e+01
  angle pdb=" CA  ALA G  52 "
        pdb=" CB  ALA G  52 "
        pdb=" HB3 ALA G  52 "
      ideal   model   delta    sigma   weight residual
     109.00   79.33   29.67 3.00e+00 1.11e-01 9.78e+01
  angle pdb=" CA  ALA E  52 "
        pdb=" CB  ALA E  52 "
        pdb=" HB3 ALA E  52 "
      ideal   model   delta    sigma   weight residual
     109.00   79.37   29.63 3.00e+00 1.11e-01 9.75e+01
  angle pdb=" CA  ALA G  52 "
        pdb=" CB  ALA G  52 "
        pdb=" HB1 ALA G  52 "
      ideal   model   delta    sigma   weight residual
     109.00   79.60   29.40 3.00e+00 1.11e-01 9.60e+01
  ... (remaining 16899 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.80: 6728
       13.80 -    27.61: 272
       27.61 -    41.41: 52
       41.41 -    55.22: 16
       55.22 -    69.02: 8
  Dihedral angle restraints: 7076
    sinusoidal: 2924
      harmonic: 4152
  Sorted by residual:
  dihedral pdb=" CA  ILE G  42 "
           pdb=" CB  ILE G  42 "
           pdb=" CG1 ILE G  42 "
           pdb=" CD1 ILE G  42 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  113.79  -53.79     3      1.50e+01 4.44e-03 9.23e+00
  dihedral pdb=" CA  ILE C  42 "
           pdb=" CB  ILE C  42 "
           pdb=" CG1 ILE C  42 "
           pdb=" CD1 ILE C  42 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  113.75  -53.75     3      1.50e+01 4.44e-03 9.23e+00
  dihedral pdb=" CA  ILE H  42 "
           pdb=" CB  ILE H  42 "
           pdb=" CG1 ILE H  42 "
           pdb=" CD1 ILE H  42 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  113.75  -53.75     3      1.50e+01 4.44e-03 9.23e+00
  ... (remaining 7073 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.022: 1096
       0.022 -    0.045: 341
       0.045 -    0.067: 143
       0.067 -    0.089: 52
       0.089 -    0.112: 52
  Chirality restraints: 1684
  Sorted by residual:
  chirality pdb=" CA  ILE B 409 "
            pdb=" N   ILE B 409 "
            pdb=" C   ILE B 409 "
            pdb=" CB  ILE B 409 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.12e-01
  chirality pdb=" CA  ILE D 409 "
            pdb=" N   ILE D 409 "
            pdb=" C   ILE D 409 "
            pdb=" CB  ILE D 409 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.11 2.00e-01 2.50e+01 3.11e-01
  chirality pdb=" CA  ILE A 466 "
            pdb=" N   ILE A 466 "
            pdb=" C   ILE A 466 "
            pdb=" CB  ILE A 466 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.11 2.00e-01 2.50e+01 3.05e-01
  ... (remaining 1681 not shown)

  Planarity restraints: 2136
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE F 166 "   -0.015 5.00e-02 4.00e+02   2.31e-02 8.56e-01
        pdb=" N   PRO F 167 "    0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO F 167 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO F 167 "   -0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 166 "    0.015 5.00e-02 4.00e+02   2.30e-02 8.46e-01
        pdb=" N   PRO B 167 "   -0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO B 167 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO B 167 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 166 "    0.015 5.00e-02 4.00e+02   2.29e-02 8.42e-01
        pdb=" N   PRO A 167 "   -0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO A 167 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 167 "    0.013 5.00e-02 4.00e+02
  ... (remaining 2133 not shown)

  Histogram of nonbonded interaction distances:
        1.67 -     2.25: 196
        2.25 -     2.84: 6144
        2.84 -     3.43: 17764
        3.43 -     4.01: 24627
        4.01 -     4.60: 35671
  Nonbonded interactions: 84402
  Sorted by model distance:
  nonbonded pdb="HG13 ILE E  42 "
            pdb="HD12 ILE E  42 "
     model   vdw
     1.666 1.952
  nonbonded pdb="HG13 ILE H  42 "
            pdb="HD12 ILE H  42 "
     model   vdw
     1.667 1.952
  nonbonded pdb="HG13 ILE C  42 "
            pdb="HD12 ILE C  42 "
     model   vdw
     1.667 1.952
  nonbonded pdb="HG13 ILE G  42 "
            pdb="HD12 ILE G  42 "
     model   vdw
     1.668 1.952
  nonbonded pdb="HG12 ILE E  42 "
            pdb="HD11 ILE E  42 "
     model   vdw
     1.676 1.952
  ... (remaining 84397 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
  selection = chain 'G'
  selection = chain 'H'
}

Set up NCS constraints
  Number of NCS constrained groups: 2
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
}
pdb_interpretation.ncs_group {
  reference = chain 'C'
  selection = chain 'E'
  selection = chain 'G'
  selection = chain 'H'
}
Set refine NCS operators
  NCS operators will be refined.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.95
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:             0.330
  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:             0.310
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.080
  Set scattering table:                    0.130
  Process input model:                     30.250
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.050
  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:3.030
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
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   0.048  11592  Z= 0.101
  Angle     :  0.406   3.557  15712  Z= 0.230
  Chirality :  0.032   0.112   1684
  Planarity :  0.002   0.023   2068
  Dihedral  :  8.305  69.020   4252
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 45.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  6.02 %
    Favored  : 93.31 %
  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:  2.23 (0.24), residues: 1396
  helix:  2.56 (0.20), residues: 760
  sheet: -0.61 (0.47), residues: 136
  loop :  0.49 (0.28), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP F 371 
 HIS   0.001   0.000   HIS F 316 
 PHE   0.003   0.000   PHE A 285 
 TYR   0.004   0.001   TYR A 313 
 ARG   0.001   0.000   ARG A 453 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22780 (  636)
  hydrogen bonds       : angle       7.95411 ( 1872)
  covalent geometry    : bond        0.00189 (11592)
  covalent geometry    : angle       0.40593 (15712)

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

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

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 109
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 GLN cc_start: 0.9491 (tp40) cc_final: 0.9273 (tp-100)
REVERT: A  198 VAL cc_start: 0.9435 (m) cc_final: 0.9202 (p)
REVERT: A  201 GLN cc_start: 0.9499 (mm110) cc_final: 0.9295 (pt0)
REVERT: A  233 LYS cc_start: 0.9503 (ttpp) cc_final: 0.9215 (ttpp)
REVERT: A  251 HIS cc_start: 0.9097 (t-90) cc_final: 0.8889 (t70)
REVERT: A  264 TYR cc_start: 0.7727 (m-10) cc_final: 0.7280 (m-10)
REVERT: A  266 GLU cc_start: 0.9248 (pm20) cc_final: 0.8977 (pm20)
REVERT: A  268 ASN cc_start: 0.8882 (t0) cc_final: 0.8575 (p0)
REVERT: A  308 PHE cc_start: 0.8445 (t80) cc_final: 0.7858 (t80)
REVERT: A  339 LEU cc_start: 0.9166 (mm) cc_final: 0.8897 (mm)
REVERT: A  344 PHE cc_start: 0.9385 (t80) cc_final: 0.8766 (t80)
REVERT: A  356 LEU cc_start: 0.9635 (tt) cc_final: 0.9379 (tt)
REVERT: A  362 GLU cc_start: 0.9405 (mp0) cc_final: 0.9168 (mp0)
REVERT: A  441 LYS cc_start: 0.9228 (ttmm) cc_final: 0.8781 (mtpt)
REVERT: A  491 HIS cc_start: 0.9169 (m170) cc_final: 0.8508 (t-170)
  outliers start: 1
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1829
  time to fit residues: 23.3033
Evaluate side-chains
  80 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.314 
Evaluate side-chains
  7 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 6
  time to evaluate  : 0.019 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 6
  average time/residue: 0.7643
  time to fit residues: 4.6335
Evaluate side-chains
  3 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 3
  time to evaluate  : 0.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 114 optimal weight:    0.0370
   chunk 103 optimal weight:    0.7980
   chunk 57 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 106 optimal weight:    9.9990
   chunk 41 optimal weight:    7.9990
   chunk 64 optimal weight:    0.0040
   chunk 79 optimal weight:    7.9990
   chunk 123 optimal weight:    2.9990
   overall best weight:    0.7272
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
F 286 GLN
** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.093588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.071418 restraints weight = 10021.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.073771 restraints weight = 7002.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.075518 restraints weight = 5330.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.182851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.161551 restraints weight = 650.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.165269 restraints weight = 301.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.168098 restraints weight = 172.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.4847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.3394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  11592  Z= 0.130
  Angle     :  0.527   6.204  15712  Z= 0.274
  Chirality :  0.038   0.172   1684
  Planarity :  0.004   0.020   2068
  Dihedral  :  4.044  42.071   1568
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 51.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  1.00 %
    Favored  : 98.66 %
  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:  1.04 (0.22), residues: 1396
  helix:  1.04 (0.18), residues: 808
  sheet: -0.55 (0.46), residues: 136
  loop :  0.75 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP D 232 
 HIS   0.003   0.001   HIS F 491 
 PHE   0.024   0.001   PHE A 255 
 TYR   0.019   0.001   TYR B 422 
 ARG   0.006   0.001   ARG H  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04624 (  636)
  hydrogen bonds       : angle       6.36767 ( 1872)
  covalent geometry    : bond        0.00268 (11592)
  covalent geometry    : angle       0.52719 (15712)

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

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

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  197 GLN cc_start: 0.9525 (tp40) cc_final: 0.9221 (tp-100)
REVERT: F  198 VAL cc_start: 0.9507 (m) cc_final: 0.9186 (p)
REVERT: F  201 GLN cc_start: 0.9450 (mm110) cc_final: 0.9170 (pt0)
REVERT: F  223 GLU cc_start: 0.8940 (pm20) cc_final: 0.8520 (pp20)
REVERT: F  233 LYS cc_start: 0.9599 (ttpp) cc_final: 0.9246 (ttpp)
REVERT: F  251 HIS cc_start: 0.9140 (t-90) cc_final: 0.8844 (t70)
REVERT: F  266 GLU cc_start: 0.9113 (pm20) cc_final: 0.8804 (pm20)
REVERT: F  268 ASN cc_start: 0.8573 (t0) cc_final: 0.8326 (p0)
REVERT: F  286 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8035 (pm20)
REVERT: F  305 PHE cc_start: 0.8946 (m-80) cc_final: 0.8679 (m-80)
REVERT: F  308 PHE cc_start: 0.8581 (t80) cc_final: 0.7847 (t80)
REVERT: F  321 MET cc_start: 0.7960 (tpt) cc_final: 0.7724 (tpt)
REVERT: F  339 LEU cc_start: 0.9259 (mm) cc_final: 0.8978 (mm)
REVERT: F  344 PHE cc_start: 0.9456 (t80) cc_final: 0.8781 (t80)
REVERT: F  346 GLN cc_start: 0.8386 (tm-30) cc_final: 0.7899 (tm-30)
REVERT: F  350 ASP cc_start: 0.7956 (m-30) cc_final: 0.7329 (m-30)
REVERT: F  362 GLU cc_start: 0.9315 (mp0) cc_final: 0.9083 (mp0)
REVERT: F  369 LEU cc_start: 0.9678 (tp) cc_final: 0.9460 (mt)
REVERT: F  396 TYR cc_start: 0.9153 (t80) cc_final: 0.8937 (t80)
REVERT: F  441 LYS cc_start: 0.9119 (ttmm) cc_final: 0.8541 (mtpt)
REVERT: F  466 ILE cc_start: 0.8653 (mm) cc_final: 0.8416 (mm)
REVERT: F  473 GLN cc_start: 0.9348 (mp10) cc_final: 0.9087 (mp10)
REVERT: F  491 HIS cc_start: 0.9239 (m170) cc_final: 0.8554 (t-170)
  outliers start: 1
  outliers final: 0
  residues processed: 88
  average time/residue: 0.1847
  time to fit residues: 18.7287
Evaluate side-chains
  76 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.311 
Evaluate side-chains
  3 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 3
  time to evaluate  : 0.021 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 3
  average time/residue: 0.9175
  time to fit residues: 2.7953
Evaluate side-chains
  2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 2
  time to evaluate  : 0.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 127 optimal weight:    6.9990
   chunk 69 optimal weight:    5.9990
   chunk 68 optimal weight:    8.9990
   chunk 57 optimal weight:    0.0670
   chunk 99 optimal weight:    0.0570
   chunk 103 optimal weight:    0.9990
   chunk 98 optimal weight:    5.9990
   chunk 131 optimal weight:    1.9990
   chunk 56 optimal weight:    0.4980
   chunk 11 optimal weight:   10.0000
   chunk 108 optimal weight:    0.4980
   overall best weight:    0.4238
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 212 GLN
** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.093360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.071373 restraints weight = 10272.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.073632 restraints weight = 7182.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.075311 restraints weight = 5517.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4623 r_free = 0.4623 target = 0.204652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.181398 restraints weight = 556.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.187928 restraints weight = 246.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.193776 restraints weight = 128.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.4917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.3983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11592  Z= 0.127
  Angle     :  0.551   8.640  15712  Z= 0.280
  Chirality :  0.038   0.128   1684
  Planarity :  0.005   0.077   2068
  Dihedral  :  4.171  35.826   1568
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 51.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  2.01 %
    Favored  : 97.66 %
  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:  0.48 (0.22), residues: 1396
  helix:  0.55 (0.18), residues: 812
  sheet: -0.69 (0.46), residues: 136
  loop :  0.54 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP F 371 
 HIS   0.003   0.001   HIS D 251 
 PHE   0.016   0.001   PHE F 255 
 TYR   0.015   0.001   TYR F 264 
 ARG   0.011   0.001   ARG A 476 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04012 (  636)
  hydrogen bonds       : angle       5.98339 ( 1872)
  covalent geometry    : bond        0.00269 (11592)
  covalent geometry    : angle       0.55099 (15712)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  197 GLN cc_start: 0.9519 (tp40) cc_final: 0.9263 (tp-100)
REVERT: B  198 VAL cc_start: 0.9497 (m) cc_final: 0.9193 (p)
REVERT: B  201 GLN cc_start: 0.9439 (mm110) cc_final: 0.9155 (pt0)
REVERT: B  233 LYS cc_start: 0.9612 (ttpp) cc_final: 0.9234 (ttpp)
REVERT: B  251 HIS cc_start: 0.9150 (t-90) cc_final: 0.8936 (t70)
REVERT: B  264 TYR cc_start: 0.7262 (m-10) cc_final: 0.7008 (m-80)
REVERT: B  266 GLU cc_start: 0.9163 (pm20) cc_final: 0.8749 (pm20)
REVERT: B  268 ASN cc_start: 0.8692 (t0) cc_final: 0.8291 (p0)
REVERT: B  280 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8792 (mmmm)
REVERT: B  308 PHE cc_start: 0.8495 (t80) cc_final: 0.7791 (t80)
REVERT: B  339 LEU cc_start: 0.9246 (mm) cc_final: 0.8977 (mm)
REVERT: B  344 PHE cc_start: 0.9389 (t80) cc_final: 0.8691 (t80)
REVERT: B  362 GLU cc_start: 0.9320 (mp0) cc_final: 0.8961 (mp0)
REVERT: B  466 ILE cc_start: 0.8606 (mm) cc_final: 0.8325 (mm)
REVERT: B  491 HIS cc_start: 0.9232 (m170) cc_final: 0.8297 (t-170)
  outliers start: 1
  outliers final: 1
  residues processed: 83
  average time/residue: 0.1707
  time to fit residues: 16.4472
Evaluate side-chains
  74 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 73
  time to evaluate  : 0.273 
Evaluate side-chains
  2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 2
  time to evaluate  : 0.019 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 2
  average time/residue: 1.3059
  time to fit residues: 2.6491
Evaluate side-chains
  2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 2
  time to evaluate  : 0.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 122 optimal weight:    0.2980
   chunk 36 optimal weight:    8.9990
   chunk 85 optimal weight:    0.0030
   chunk 17 optimal weight:    0.0170
   chunk 38 optimal weight:    6.9990
   chunk 18 optimal weight:    9.9990
   chunk 37 optimal weight:    0.1980
   chunk 1 optimal weight:    0.1980
   chunk 49 optimal weight:    0.9980
   chunk 127 optimal weight:    0.7980
   overall best weight:    0.1428
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.093539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.070902 restraints weight = 10644.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.073272 restraints weight = 7499.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.075019 restraints weight = 5777.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.205255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.180437 restraints weight = 589.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.187473 restraints weight = 275.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.193236 restraints weight = 142.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.4864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.4286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  11592  Z= 0.131
  Angle     :  0.547   7.807  15712  Z= 0.272
  Chirality :  0.037   0.130   1684
  Planarity :  0.004   0.052   2068
  Dihedral  :  4.149  34.914   1568
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 54.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  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:  0.26 (0.22), residues: 1396
  helix:  0.37 (0.18), residues: 808
  sheet: -0.76 (0.45), residues: 136
  loop :  0.46 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP F 165 
 HIS   0.004   0.001   HIS F 215 
 PHE   0.019   0.001   PHE D 194 
 TYR   0.014   0.001   TYR A 264 
 ARG   0.003   0.000   ARG A 203 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04012 (  636)
  hydrogen bonds       : angle       6.09600 ( 1872)
  covalent geometry    : bond        0.00294 (11592)
  covalent geometry    : angle       0.54700 (15712)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  197 GLN cc_start: 0.9535 (tp40) cc_final: 0.9279 (tp-100)
REVERT: B  198 VAL cc_start: 0.9530 (m) cc_final: 0.9247 (p)
REVERT: B  201 GLN cc_start: 0.9469 (mm110) cc_final: 0.9193 (pt0)
REVERT: B  233 LYS cc_start: 0.9606 (ttpp) cc_final: 0.9238 (ttpp)
REVERT: B  264 TYR cc_start: 0.7312 (m-10) cc_final: 0.7036 (m-80)
REVERT: B  266 GLU cc_start: 0.9216 (pm20) cc_final: 0.8824 (pm20)
REVERT: B  268 ASN cc_start: 0.8758 (t0) cc_final: 0.8339 (p0)
REVERT: B  280 LYS cc_start: 0.9265 (mmmm) cc_final: 0.8819 (mmmm)
REVERT: B  308 PHE cc_start: 0.8558 (t80) cc_final: 0.7875 (t80)
REVERT: B  339 LEU cc_start: 0.9264 (mm) cc_final: 0.8950 (mm)
REVERT: B  344 PHE cc_start: 0.9405 (t80) cc_final: 0.8714 (t80)
REVERT: B  362 GLU cc_start: 0.9342 (mp0) cc_final: 0.9103 (mp0)
REVERT: B  466 ILE cc_start: 0.8652 (mm) cc_final: 0.8400 (mm)
REVERT: B  479 LEU cc_start: 0.9440 (mt) cc_final: 0.9142 (mt)
REVERT: B  491 HIS cc_start: 0.9232 (m170) cc_final: 0.8369 (t-170)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.1761
  time to fit residues: 17.0114
Evaluate side-chains
  74 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.311 
Evaluate side-chains
  2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 2
  time to evaluate  : 0.022 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 2
  average time/residue: 1.2764
  time to fit residues: 2.5926
Evaluate side-chains
  2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 2
  time to evaluate  : 0.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 126 optimal weight:    6.9990
   chunk 133 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0670
   chunk 112 optimal weight:    9.9990
   chunk 64 optimal weight:    0.0980
   chunk 29 optimal weight:    7.9990
   chunk 61 optimal weight:    0.0870
   chunk 22 optimal weight:    7.9990
   chunk 81 optimal weight:    0.8980
   chunk 72 optimal weight:    9.9990
   chunk 109 optimal weight:    2.9990
   overall best weight:    0.4298
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.094097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.071153 restraints weight = 10442.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.073489 restraints weight = 7337.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.075180 restraints weight = 5666.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.205255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 19)----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.180402 restraints weight = 587.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.187202 restraints weight = 275.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.192989 restraints weight = 146.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.4851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.4373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  11592  Z= 0.131
  Angle     :  0.547   7.807  15712  Z= 0.272
  Chirality :  0.037   0.130   1684
  Planarity :  0.004   0.052   2068
  Dihedral  :  4.149  34.914   1568
  Min Nonbonded Distance : 1.048

Molprobity Statistics.
  All-atom Clashscore : 60.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  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:  0.26 (0.22), residues: 1396
  helix:  0.37 (0.18), residues: 808
  sheet: -0.76 (0.45), residues: 136
  loop :  0.46 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP F 165 
 HIS   0.004   0.001   HIS F 215 
 PHE   0.019   0.001   PHE F 194 
 TYR   0.014   0.001   TYR D 264 
 ARG   0.003   0.000   ARG F 203 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04012 (  636)
  hydrogen bonds       : angle       6.09600 ( 1872)
  covalent geometry    : bond        0.00294 (11592)
  covalent geometry    : angle       0.54700 (15712)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  197 GLN cc_start: 0.9539 (tp40) cc_final: 0.9284 (tp-100)
REVERT: B  198 VAL cc_start: 0.9530 (m) cc_final: 0.9245 (p)
REVERT: B  201 GLN cc_start: 0.9466 (mm110) cc_final: 0.9192 (pt0)
REVERT: B  233 LYS cc_start: 0.9607 (ttpp) cc_final: 0.9242 (ttpp)
REVERT: B  251 HIS cc_start: 0.9115 (t70) cc_final: 0.8908 (t70)
REVERT: B  264 TYR cc_start: 0.7313 (m-10) cc_final: 0.7039 (m-80)
REVERT: B  266 GLU cc_start: 0.9218 (pm20) cc_final: 0.8829 (pm20)
REVERT: B  268 ASN cc_start: 0.8757 (t0) cc_final: 0.8338 (p0)
REVERT: B  280 LYS cc_start: 0.9258 (mmmm) cc_final: 0.8809 (mmmm)
REVERT: B  308 PHE cc_start: 0.8541 (t80) cc_final: 0.7874 (t80)
REVERT: B  339 LEU cc_start: 0.9255 (mm) cc_final: 0.8932 (mm)
REVERT: B  344 PHE cc_start: 0.9387 (t80) cc_final: 0.8707 (t80)
REVERT: B  362 GLU cc_start: 0.9339 (mp0) cc_final: 0.8970 (mp0)
REVERT: B  396 TYR cc_start: 0.9137 (t80) cc_final: 0.8896 (t80)
REVERT: B  466 ILE cc_start: 0.8644 (mm) cc_final: 0.8370 (mm)
REVERT: B  491 HIS cc_start: 0.9237 (m170) cc_final: 0.8371 (t-170)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1691
  time to fit residues: 16.7008
Evaluate side-chains
  70 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.308 
Evaluate side-chains
  2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 2
  time to evaluate  : 0.019 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 2
  average time/residue: 1.2786
  time to fit residues: 2.5955
Evaluate side-chains
  2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 2
  time to evaluate  : 0.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 124 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0470
   chunk 89 optimal weight:    3.9990
   chunk 47 optimal weight:    0.4980
   chunk 127 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 3 optimal weight:    0.4980
   chunk 20 optimal weight:    0.8980
   chunk 72 optimal weight:   10.0000
   chunk 128 optimal weight:    6.9990
   chunk 135 optimal weight:    8.9990
   overall best weight:    0.5678
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.094068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.071077 restraints weight = 10723.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.073428 restraints weight = 7549.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.075211 restraints weight = 5808.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.205255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.179971 restraints weight = 615.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.186793 restraints weight = 291.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.193002 restraints weight = 149.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.4852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.4354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  11592  Z= 0.131
  Angle     :  0.547   7.807  15712  Z= 0.272
  Chirality :  0.037   0.130   1684
  Planarity :  0.004   0.052   2068
  Dihedral  :  4.149  34.914   1568
  Min Nonbonded Distance : 1.049

Molprobity Statistics.
  All-atom Clashscore : 60.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  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:  0.26 (0.22), residues: 1396
  helix:  0.37 (0.18), residues: 808
  sheet: -0.76 (0.45), residues: 136
  loop :  0.46 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP F 165 
 HIS   0.004   0.001   HIS B 215 
 PHE   0.019   0.001   PHE D 194 
 TYR   0.014   0.001   TYR A 264 
 ARG   0.003   0.000   ARG B 203 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04012 (  636)
  hydrogen bonds       : angle       6.09600 ( 1872)
  covalent geometry    : bond        0.00294 (11592)
  covalent geometry    : angle       0.54698 (15712)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  197 GLN cc_start: 0.9533 (tp40) cc_final: 0.9266 (tp-100)
REVERT: B  198 VAL cc_start: 0.9524 (m) cc_final: 0.9226 (p)
REVERT: B  201 GLN cc_start: 0.9455 (mm110) cc_final: 0.9175 (pt0)
REVERT: B  233 LYS cc_start: 0.9610 (ttpp) cc_final: 0.9239 (ttpp)
REVERT: B  251 HIS cc_start: 0.9102 (t70) cc_final: 0.8892 (t70)
REVERT: B  264 TYR cc_start: 0.7269 (m-10) cc_final: 0.7008 (m-80)
REVERT: B  266 GLU cc_start: 0.9202 (pm20) cc_final: 0.8801 (pm20)
REVERT: B  268 ASN cc_start: 0.8735 (t0) cc_final: 0.8322 (p0)
REVERT: B  280 LYS cc_start: 0.9255 (mmmm) cc_final: 0.8806 (mmmm)
REVERT: B  308 PHE cc_start: 0.8528 (t80) cc_final: 0.7869 (t80)
REVERT: B  339 LEU cc_start: 0.9255 (mm) cc_final: 0.8937 (mm)
REVERT: B  344 PHE cc_start: 0.9380 (t80) cc_final: 0.8690 (t80)
REVERT: B  362 GLU cc_start: 0.9326 (mp0) cc_final: 0.8956 (mp0)
REVERT: B  466 ILE cc_start: 0.8631 (mm) cc_final: 0.8362 (mm)
REVERT: B  491 HIS cc_start: 0.9239 (m170) cc_final: 0.8377 (t-170)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1770
  time to fit residues: 17.4420
Evaluate side-chains
  71 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.322 
Evaluate side-chains
  2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 2
  time to evaluate  : 0.020 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 2
  average time/residue: 1.2796
  time to fit residues: 2.5944
Evaluate side-chains
  2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 2
  time to evaluate  : 0.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 69 optimal weight:    6.9990
   chunk 16 optimal weight:    0.0070
   chunk 64 optimal weight:    0.0470
   chunk 29 optimal weight:    4.9990
   chunk 37 optimal weight:    0.3980
   chunk 81 optimal weight:    2.9990
   chunk 52 optimal weight:    9.9990
   chunk 11 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9990
   chunk 128 optimal weight:    9.9990
   overall best weight:    0.6900
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.093909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.070835 restraints weight = 10561.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.073164 restraints weight = 7449.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.074898 restraints weight = 5778.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.205255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.180801 restraints weight = 569.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.187508 restraints weight = 265.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.193409 restraints weight = 139.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.4852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.4377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  11592  Z= 0.131
  Angle     :  0.547   7.807  15712  Z= 0.272
  Chirality :  0.037   0.130   1684
  Planarity :  0.004   0.052   2068
  Dihedral  :  4.149  34.914   1568
  Min Nonbonded Distance : 1.049

Molprobity Statistics.
  All-atom Clashscore : 60.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  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:  0.26 (0.22), residues: 1396
  helix:  0.37 (0.18), residues: 808
  sheet: -0.76 (0.45), residues: 136
  loop :  0.46 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP F 165 
 HIS   0.004   0.001   HIS D 215 
 PHE   0.019   0.001   PHE A 194 
 TYR   0.014   0.001   TYR A 264 
 ARG   0.003   0.000   ARG F 203 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04012 (  636)
  hydrogen bonds       : angle       6.09600 ( 1872)
  covalent geometry    : bond        0.00294 (11592)
  covalent geometry    : angle       0.54698 (15712)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  197 GLN cc_start: 0.9533 (tp40) cc_final: 0.9267 (tp-100)
REVERT: B  198 VAL cc_start: 0.9525 (m) cc_final: 0.9229 (p)
REVERT: B  201 GLN cc_start: 0.9457 (mm110) cc_final: 0.9179 (pt0)
REVERT: B  233 LYS cc_start: 0.9609 (ttpp) cc_final: 0.9234 (ttpp)
REVERT: B  251 HIS cc_start: 0.9099 (t70) cc_final: 0.8892 (t70)
REVERT: B  264 TYR cc_start: 0.7278 (m-10) cc_final: 0.7012 (m-80)
REVERT: B  266 GLU cc_start: 0.9203 (pm20) cc_final: 0.8795 (pm20)
REVERT: B  268 ASN cc_start: 0.8740 (t0) cc_final: 0.8328 (p0)
REVERT: B  280 LYS cc_start: 0.9256 (mmmm) cc_final: 0.8801 (mmmm)
REVERT: B  308 PHE cc_start: 0.8520 (t80) cc_final: 0.7863 (t80)
REVERT: B  339 LEU cc_start: 0.9250 (mm) cc_final: 0.8940 (mm)
REVERT: B  344 PHE cc_start: 0.9381 (t80) cc_final: 0.8689 (t80)
REVERT: B  362 GLU cc_start: 0.9321 (mp0) cc_final: 0.8952 (mp0)
REVERT: B  466 ILE cc_start: 0.8637 (mm) cc_final: 0.8368 (mm)
REVERT: B  491 HIS cc_start: 0.9243 (m170) cc_final: 0.8382 (t-170)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1736
  time to fit residues: 17.1666
Evaluate side-chains
  70 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.362 
Evaluate side-chains
  2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 2
  time to evaluate  : 0.022 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 2
  average time/residue: 1.2626
  time to fit residues: 2.5662
Evaluate side-chains
  2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 2
  time to evaluate  : 0.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 35 optimal weight:    9.9990
   chunk 7 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0070
   chunk 116 optimal weight:    8.9990
   chunk 100 optimal weight:    7.9990
   chunk 52 optimal weight:   10.0000
   chunk 69 optimal weight:    7.9990
   chunk 45 optimal weight:    9.9990
   chunk 42 optimal weight:    9.9990
   chunk 38 optimal weight:    8.9990
   chunk 70 optimal weight:    7.9990
   overall best weight:    5.8006
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.093906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.070924 restraints weight = 10502.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.073260 restraints weight = 7380.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.075015 restraints weight = 5698.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.205255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 21)----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.180366 restraints weight = 584.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.187200 restraints weight = 276.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.193088 restraints weight = 143.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.4853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.4363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  11592  Z= 0.131
  Angle     :  0.547   7.807  15712  Z= 0.272
  Chirality :  0.037   0.130   1684
  Planarity :  0.004   0.052   2068
  Dihedral  :  4.149  34.914   1568
  Min Nonbonded Distance : 1.049

Molprobity Statistics.
  All-atom Clashscore : 60.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  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:  0.26 (0.22), residues: 1396
  helix:  0.37 (0.18), residues: 808
  sheet: -0.76 (0.45), residues: 136
  loop :  0.46 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP F 165 
 HIS   0.004   0.001   HIS F 215 
 PHE   0.019   0.001   PHE D 194 
 TYR   0.014   0.001   TYR F 264 
 ARG   0.003   0.000   ARG B 203 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04012 (  636)
  hydrogen bonds       : angle       6.09600 ( 1872)
  covalent geometry    : bond        0.00294 (11592)
  covalent geometry    : angle       0.54698 (15712)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  197 GLN cc_start: 0.9532 (tp40) cc_final: 0.9265 (tp-100)
REVERT: B  198 VAL cc_start: 0.9524 (m) cc_final: 0.9226 (p)
REVERT: B  201 GLN cc_start: 0.9455 (mm110) cc_final: 0.9177 (pt0)
REVERT: B  233 LYS cc_start: 0.9609 (ttpp) cc_final: 0.9233 (ttpp)
REVERT: B  251 HIS cc_start: 0.9096 (t70) cc_final: 0.8889 (t70)
REVERT: B  264 TYR cc_start: 0.7269 (m-10) cc_final: 0.7007 (m-80)
REVERT: B  266 GLU cc_start: 0.9197 (pm20) cc_final: 0.8787 (pm20)
REVERT: B  268 ASN cc_start: 0.8736 (t0) cc_final: 0.8324 (p0)
REVERT: B  280 LYS cc_start: 0.9256 (mmmm) cc_final: 0.8803 (mmmm)
REVERT: B  308 PHE cc_start: 0.8516 (t80) cc_final: 0.7862 (t80)
REVERT: B  339 LEU cc_start: 0.9251 (mm) cc_final: 0.8941 (mm)
REVERT: B  344 PHE cc_start: 0.9378 (t80) cc_final: 0.8685 (t80)
REVERT: B  362 GLU cc_start: 0.9320 (mp0) cc_final: 0.8951 (mp0)
REVERT: B  466 ILE cc_start: 0.8634 (mm) cc_final: 0.8364 (mm)
REVERT: B  491 HIS cc_start: 0.9244 (m170) cc_final: 0.8384 (t-170)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1772
  time to fit residues: 17.5280
Evaluate side-chains
  71 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.332 
Evaluate side-chains
  2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 2
  time to evaluate  : 0.023 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 2
  average time/residue: 1.2856
  time to fit residues: 2.6118
Evaluate side-chains
  2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 2
  time to evaluate  : 0.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 21 optimal weight:    8.9990
   chunk 33 optimal weight:   50.0000
   chunk 88 optimal weight:    0.4980
   chunk 59 optimal weight:   10.0000
   chunk 31 optimal weight:    3.9990
   chunk 83 optimal weight:   20.0000
   chunk 124 optimal weight:    8.9990
   chunk 10 optimal weight:    0.5980
   chunk 98 optimal weight:    0.0770
   chunk 70 optimal weight:   20.0000
   chunk 79 optimal weight:   10.0000
   overall best weight:    2.8342
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.093909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.070921 restraints weight = 10429.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.073225 restraints weight = 7382.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.074970 restraints weight = 5736.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.205255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.179654 restraints weight = 625.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.186483 restraints weight = 298.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.192793 restraints weight = 154.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.4850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.4377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  11592  Z= 0.131
  Angle     :  0.547   7.807  15712  Z= 0.272
  Chirality :  0.037   0.130   1684
  Planarity :  0.004   0.052   2068
  Dihedral  :  4.149  34.914   1568
  Min Nonbonded Distance : 1.049

Molprobity Statistics.
  All-atom Clashscore : 60.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  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:  0.26 (0.22), residues: 1396
  helix:  0.37 (0.18), residues: 808
  sheet: -0.76 (0.45), residues: 136
  loop :  0.46 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP F 165 
 HIS   0.004   0.001   HIS B 215 
 PHE   0.019   0.001   PHE A 194 
 TYR   0.014   0.001   TYR D 264 
 ARG   0.003   0.000   ARG A 203 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04012 (  636)
  hydrogen bonds       : angle       6.09600 ( 1872)
  covalent geometry    : bond        0.00294 (11592)
  covalent geometry    : angle       0.54698 (15712)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  197 GLN cc_start: 0.9532 (tp40) cc_final: 0.9265 (tp-100)
REVERT: B  198 VAL cc_start: 0.9524 (m) cc_final: 0.9226 (p)
REVERT: B  201 GLN cc_start: 0.9456 (mm110) cc_final: 0.9176 (pt0)
REVERT: B  233 LYS cc_start: 0.9609 (ttpp) cc_final: 0.9233 (ttpp)
REVERT: B  251 HIS cc_start: 0.9098 (t70) cc_final: 0.8891 (t70)
REVERT: B  264 TYR cc_start: 0.7275 (m-10) cc_final: 0.7011 (m-80)
REVERT: B  266 GLU cc_start: 0.9201 (pm20) cc_final: 0.8792 (pm20)
REVERT: B  268 ASN cc_start: 0.8738 (t0) cc_final: 0.8326 (p0)
REVERT: B  280 LYS cc_start: 0.9257 (mmmm) cc_final: 0.8803 (mmmm)
REVERT: B  308 PHE cc_start: 0.8518 (t80) cc_final: 0.7863 (t80)
REVERT: B  339 LEU cc_start: 0.9251 (mm) cc_final: 0.8941 (mm)
REVERT: B  344 PHE cc_start: 0.9381 (t80) cc_final: 0.8690 (t80)
REVERT: B  362 GLU cc_start: 0.9318 (mp0) cc_final: 0.8950 (mp0)
REVERT: B  466 ILE cc_start: 0.8635 (mm) cc_final: 0.8366 (mm)
REVERT: B  491 HIS cc_start: 0.9242 (m170) cc_final: 0.8382 (t-170)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1666
  time to fit residues: 16.4224
Evaluate side-chains
  70 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.284 
Evaluate side-chains
  2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 2
  time to evaluate  : 0.019 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 2
  average time/residue: 1.2835
  time to fit residues: 2.6026
Evaluate side-chains
  2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 2
  time to evaluate  : 0.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 126 optimal weight:    1.9990
   chunk 83 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 88 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0970
   chunk 122 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 134 optimal weight:    6.9990
   chunk 116 optimal weight:    8.9990
   overall best weight:    1.1782
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.093906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.070965 restraints weight = 10404.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.073310 restraints weight = 7344.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.074992 restraints weight = 5686.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.205255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.180605 restraints weight = 568.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.187517 restraints weight = 269.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.193466 restraints weight = 140.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.4866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.4363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  11592  Z= 0.131
  Angle     :  0.547   7.807  15712  Z= 0.272
  Chirality :  0.037   0.130   1684
  Planarity :  0.004   0.052   2068
  Dihedral  :  4.149  34.914   1568
  Min Nonbonded Distance : 1.049

Molprobity Statistics.
  All-atom Clashscore : 60.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  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:  0.26 (0.22), residues: 1396
  helix:  0.37 (0.18), residues: 808
  sheet: -0.76 (0.45), residues: 136
  loop :  0.46 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP F 165 
 HIS   0.004   0.001   HIS D 215 
 PHE   0.019   0.001   PHE D 194 
 TYR   0.014   0.001   TYR A 264 
 ARG   0.003   0.000   ARG A 203 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04012 (  636)
  hydrogen bonds       : angle       6.09600 ( 1872)
  covalent geometry    : bond        0.00294 (11592)
  covalent geometry    : angle       0.54698 (15712)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  197 GLN cc_start: 0.9534 (tp40) cc_final: 0.9268 (tp-100)
REVERT: B  198 VAL cc_start: 0.9525 (m) cc_final: 0.9229 (p)
REVERT: B  201 GLN cc_start: 0.9457 (mm110) cc_final: 0.9179 (pt0)
REVERT: B  233 LYS cc_start: 0.9609 (ttpp) cc_final: 0.9233 (ttpp)
REVERT: B  251 HIS cc_start: 0.9095 (t70) cc_final: 0.8889 (t70)
REVERT: B  264 TYR cc_start: 0.7272 (m-10) cc_final: 0.7010 (m-80)
REVERT: B  266 GLU cc_start: 0.9199 (pm20) cc_final: 0.8790 (pm20)
REVERT: B  268 ASN cc_start: 0.8737 (t0) cc_final: 0.8325 (p0)
REVERT: B  280 LYS cc_start: 0.9257 (mmmm) cc_final: 0.8803 (mmmm)
REVERT: B  308 PHE cc_start: 0.8516 (t80) cc_final: 0.7862 (t80)
REVERT: B  339 LEU cc_start: 0.9250 (mm) cc_final: 0.8940 (mm)
REVERT: B  344 PHE cc_start: 0.9377 (t80) cc_final: 0.8685 (t80)
REVERT: B  362 GLU cc_start: 0.9321 (mp0) cc_final: 0.8952 (mp0)
REVERT: B  466 ILE cc_start: 0.8637 (mm) cc_final: 0.8368 (mm)
REVERT: B  491 HIS cc_start: 0.9244 (m170) cc_final: 0.8384 (t-170)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1681
  time to fit residues: 16.6383
Evaluate side-chains
  71 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.285 
Evaluate side-chains
  2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 2
  time to evaluate  : 0.019 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 2
  average time/residue: 1.2948
  time to fit residues: 2.6261
Evaluate side-chains
  2 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 2
  time to evaluate  : 0.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 0 optimal weight:   50.0000
   chunk 11 optimal weight:    9.9990
   chunk 49 optimal weight:   10.0000
   chunk 57 optimal weight:    0.3980
   chunk 20 optimal weight:    0.7980
   chunk 70 optimal weight:    0.6980
   chunk 115 optimal weight:    4.9990
   chunk 128 optimal weight:   10.0000
   chunk 133 optimal weight:    0.8980
   chunk 38 optimal weight:    5.9990
   chunk 6 optimal weight:    0.0970
   overall best weight:    0.5778
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.093909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.070971 restraints weight = 10347.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.073272 restraints weight = 7338.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.074929 restraints weight = 5709.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.205255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.180623 restraints weight = 561.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.187546 restraints weight = 270.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.193216 restraints weight = 140.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.4864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.4377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  11592  Z= 0.131
  Angle     :  0.547   7.807  15712  Z= 0.272
  Chirality :  0.037   0.130   1684
  Planarity :  0.004   0.052   2068
  Dihedral  :  4.149  34.914   1568
  Min Nonbonded Distance : 1.049

Molprobity Statistics.
  All-atom Clashscore : 60.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  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:  0.26 (0.22), residues: 1396
  helix:  0.37 (0.18), residues: 808
  sheet: -0.76 (0.45), residues: 136
  loop :  0.46 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP F 165 
 HIS   0.004   0.001   HIS B 215 
 PHE   0.019   0.001   PHE A 194 
 TYR   0.014   0.001   TYR A 264 
 ARG   0.003   0.000   ARG D 203 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04012 (  636)
  hydrogen bonds       : angle       6.09600 ( 1872)
  covalent geometry    : bond        0.00294 (11592)
  covalent geometry    : angle       0.54698 (15712)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2426.42 seconds
wall clock time: 43 minutes 53.10 seconds (2633.10 seconds total)