Starting phenix.real_space_refine
on Wed Mar  4 07:05:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pim_13442/03_2026/7pim_13442.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pim_13442/03_2026/7pim_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pim_13442/03_2026/7pim_13442.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pim_13442/03_2026/7pim_13442.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pim_13442/03_2026/7pim_13442.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pim_13442/03_2026/7pim_13442.map"
  }
  resolution = 4.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.71, per 1000 atoms: 0.23
  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: 1.01
  Conformation dependent library (CDL) restraints added in 441.8 milliseconds
  

  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: 0.30
  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: 1.88

  Time building geometry restraints manager: 1.40 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
  selection = chain 'D'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'C'
  selection = chain 'E'
  selection = chain 'H'
}

Set up NCS constraints
  Number of NCS constrained groups: 2
  pdb_interpretation.ncs_group {
  reference = chain 'B'
  selection = chain 'A'
  selection = chain 'D'
  selection = chain 'F'
}
pdb_interpretation.ncs_group {
  reference = chain 'G'
  selection = chain 'C'
  selection = chain 'E'
  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:             0.100
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     11.660
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.830
-------------------------------------------------------------------------------
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 : 45.46
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  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
 ARG   0.001   0.000   ARG A 453 
 TYR   0.004   0.001   TYR A 313 
 PHE   0.003   0.000   PHE A 285 
 TRP   0.004   0.000   TRP F 371 
 HIS   0.001   0.000   HIS F 316 

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

*********************** 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
  109 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 108
  time to evaluate  : 0.101 
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: B  197 GLN cc_start: 0.9472 (tp40) cc_final: 0.9260 (tp-100)
REVERT: B  198 VAL cc_start: 0.9426 (m) cc_final: 0.9199 (p)
REVERT: B  233 LYS cc_start: 0.9508 (ttpp) cc_final: 0.9226 (ttpp)
REVERT: B  251 HIS cc_start: 0.9069 (t-90) cc_final: 0.8855 (t70)
REVERT: B  264 TYR cc_start: 0.7754 (m-10) cc_final: 0.7297 (m-10)
REVERT: B  266 GLU cc_start: 0.9245 (pm20) cc_final: 0.8981 (pm20)
REVERT: B  268 ASN cc_start: 0.8900 (t0) cc_final: 0.8596 (p0)
REVERT: B  308 PHE cc_start: 0.8456 (t80) cc_final: 0.7860 (t80)
REVERT: B  339 LEU cc_start: 0.9189 (mm) cc_final: 0.8922 (mm)
REVERT: B  344 PHE cc_start: 0.9382 (t80) cc_final: 0.8734 (t80)
REVERT: B  362 GLU cc_start: 0.9397 (mp0) cc_final: 0.9159 (mp0)
REVERT: B  441 LYS cc_start: 0.9204 (ttmm) cc_final: 0.8763 (mtpt)
REVERT: B  491 HIS cc_start: 0.9172 (m170) cc_final: 0.8507 (t-170)
  outliers start: 1
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0724
  time to fit residues: 9.1149
Evaluate side-chains
  82 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.105 
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  : 0.008 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 6
  average time/residue: 0.3930
  time to fit residues: 2.3785
Evaluate side-chains
  1 residues out of total 11 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 1
  time to evaluate  : 0.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 107 optimal weight:    0.0980
   chunk 10 optimal weight:    0.0770
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    0.0870
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    0.0060
   overall best weight:    0.2332
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** F 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 = 0.3715 r_free = 0.3715 target = 0.094955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.072323 restraints weight = 10362.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.074835 restraints weight = 7192.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.076653 restraints weight = 5471.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.078015 restraints weight = 4451.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.079000 restraints weight = 3795.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.180831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.160430 restraints weight = 609.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.164180 restraints weight = 287.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.166918 restraints weight = 165.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.169218 restraints weight = 112.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.170571 restraints weight = 84.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.4850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.3411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  11592  Z= 0.133
  Angle     :  0.525   6.210  15712  Z= 0.277
  Chirality :  0.039   0.183   1684
  Planarity :  0.004   0.032   2068
  Dihedral  :  4.036  43.216   1568
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 52.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.22), residues: 1396
  helix:  1.01 (0.18), residues: 812
  sheet: -0.49 (0.46), residues: 136
  loop :  0.72 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  49 
 TYR   0.021   0.001   TYR D 422 
 PHE   0.023   0.001   PHE A 255 
 TRP   0.002   0.000   TRP B 232 
 HIS   0.003   0.001   HIS F 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (11592)
  covalent geometry    : angle       0.52530 (15712)
  hydrogen bonds       : bond        0.04795 (  636)
  hydrogen bonds       : angle       6.39361 ( 1872)

*********************** 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
  87 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.105 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  233 LYS cc_start: 0.9596 (ttpp) cc_final: 0.9244 (ttpp)
REVERT: F  251 HIS cc_start: 0.9108 (t-90) cc_final: 0.8812 (t70)
REVERT: F  264 TYR cc_start: 0.7427 (m-10) cc_final: 0.7225 (m-10)
REVERT: F  266 GLU cc_start: 0.9069 (pm20) cc_final: 0.8768 (pm20)
REVERT: F  268 ASN cc_start: 0.8519 (t0) cc_final: 0.8280 (p0)
REVERT: F  286 GLN cc_start: 0.8705 (pm20) cc_final: 0.7679 (pm20)
REVERT: F  308 PHE cc_start: 0.8557 (t80) cc_final: 0.7813 (t80)
REVERT: F  321 MET cc_start: 0.7925 (tpt) cc_final: 0.7678 (tpt)
REVERT: F  339 LEU cc_start: 0.9276 (mm) cc_final: 0.8989 (mm)
REVERT: F  344 PHE cc_start: 0.9452 (t80) cc_final: 0.8758 (t80)
REVERT: F  346 GLN cc_start: 0.8378 (tm-30) cc_final: 0.8025 (tm-30)
REVERT: F  350 ASP cc_start: 0.7929 (m-30) cc_final: 0.7295 (m-30)
REVERT: F  362 GLU cc_start: 0.9352 (mp0) cc_final: 0.9125 (mp0)
REVERT: F  369 LEU cc_start: 0.9674 (tp) cc_final: 0.9468 (mt)
REVERT: F  396 TYR cc_start: 0.9175 (t80) cc_final: 0.8941 (t80)
REVERT: F  466 ILE cc_start: 0.8687 (mm) cc_final: 0.8392 (mm)
REVERT: F  473 GLN cc_start: 0.9318 (mp10) cc_final: 0.9071 (mp10)
REVERT: F  491 HIS cc_start: 0.9219 (m170) cc_final: 0.8468 (t-170)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.0711
  time to fit residues: 7.1631
Evaluate side-chains
  72 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.115 
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  : 0.009 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 3
  average time/residue: 0.4123
  time to fit residues: 1.2541
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  : 0.005 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 92 optimal weight:    7.9990
   chunk 90 optimal weight:    0.0170
   chunk 22 optimal weight:    0.0060
   chunk 110 optimal weight:    9.9990
   chunk 29 optimal weight:    0.7980
   chunk 6 optimal weight:    8.9990
   chunk 44 optimal weight:    7.9990
   chunk 3 optimal weight:   30.0000
   chunk 69 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0370
   overall best weight:    0.7714
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 201 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 = 0.3682 r_free = 0.3682 target = 0.094399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.071767 restraints weight = 10576.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.074121 restraints weight = 7357.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.075923 restraints weight = 5624.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.077246 restraints weight = 4584.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.078194 restraints weight = 3921.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4623 r_free = 0.4623 target = 0.205258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.182888 restraints weight = 596.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.189459 restraints weight = 239.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4557 r_free = 0.4557 target = 0.195796 restraints weight = 122.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4593 r_free = 0.4593 target = 0.199426 restraints weight = 63.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4615 r_free = 0.4615 target = 0.201519 restraints weight = 34.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.4986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.4050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  11592  Z= 0.130
  Angle     :  0.511   5.604  15712  Z= 0.266
  Chirality :  0.037   0.126   1684
  Planarity :  0.005   0.072   2068
  Dihedral  :  4.044  37.248   1568
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 53.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.22), residues: 1396
  helix:  0.67 (0.18), residues: 796
  sheet: -0.54 (0.46), residues: 136
  loop :  0.48 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D 476 
 TYR   0.014   0.001   TYR D 422 
 PHE   0.016   0.001   PHE D 255 
 TRP   0.003   0.001   TRP A 371 
 HIS   0.003   0.001   HIS B 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (11592)
  covalent geometry    : angle       0.51149 (15712)
  hydrogen bonds       : bond        0.04043 (  636)
  hydrogen bonds       : angle       6.19534 ( 1872)

*********************** 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: 0
    poor density    : 83
  time to evaluate  : 0.099 
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: B  197 GLN cc_start: 0.9694 (tp-100) cc_final: 0.9462 (tp-100)
REVERT: B  233 LYS cc_start: 0.9616 (ttpp) cc_final: 0.9251 (ttpp)
REVERT: B  251 HIS cc_start: 0.9151 (t-90) cc_final: 0.8909 (t70)
REVERT: B  258 LEU cc_start: 0.9351 (mt) cc_final: 0.9104 (mm)
REVERT: B  266 GLU cc_start: 0.9144 (pm20) cc_final: 0.8759 (pm20)
REVERT: B  268 ASN cc_start: 0.8642 (t0) cc_final: 0.8254 (p0)
REVERT: B  280 LYS cc_start: 0.9026 (mmmm) cc_final: 0.8683 (mmmm)
REVERT: B  308 PHE cc_start: 0.8502 (t80) cc_final: 0.7802 (t80)
REVERT: B  339 LEU cc_start: 0.9260 (mm) cc_final: 0.8953 (mm)
REVERT: B  344 PHE cc_start: 0.9393 (t80) cc_final: 0.8701 (t80)
REVERT: B  350 ASP cc_start: 0.8056 (m-30) cc_final: 0.7765 (m-30)
REVERT: B  362 GLU cc_start: 0.9322 (mp0) cc_final: 0.9093 (mp0)
REVERT: B  466 ILE cc_start: 0.8722 (mm) cc_final: 0.8385 (mm)
REVERT: B  473 GLN cc_start: 0.9336 (mp10) cc_final: 0.9075 (mp10)
REVERT: B  479 LEU cc_start: 0.9445 (mt) cc_final: 0.9128 (mt)
REVERT: B  491 HIS cc_start: 0.9224 (m170) cc_final: 0.8285 (t-170)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.0687
  time to fit residues: 6.6231
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  : 0.078 
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  : 0.008 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 2
  average time/residue: 0.7298
  time to fit residues: 1.4745
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  : 0.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 124 optimal weight:    0.0270
   chunk 126 optimal weight:    2.9990
   chunk 108 optimal weight:    7.9990
   chunk 103 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0770
   chunk 79 optimal weight:    9.9990
   chunk 45 optimal weight:    7.9990
   chunk 42 optimal weight:    0.0170
   chunk 82 optimal weight:    6.9990
   chunk 31 optimal weight:    6.9990
   chunk 129 optimal weight:    9.9990
   overall best weight:    0.7436
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 201 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 = 0.3669 r_free = 0.3669 target = 0.093695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.070928 restraints weight = 10697.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.073207 restraints weight = 7464.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.074958 restraints weight = 5752.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.076251 restraints weight = 4716.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.077247 restraints weight = 4051.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4656 r_free = 0.4656 target = 0.207065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.181611 restraints weight = 569.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.188810 restraints weight = 254.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.194839 restraints weight = 133.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4592 r_free = 0.4592 target = 0.199034 restraints weight = 70.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4631 r_free = 0.4631 target = 0.202068 restraints weight = 39.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.4912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.4332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  11592  Z= 0.144
  Angle     :  0.542   8.814  15712  Z= 0.275
  Chirality :  0.038   0.181   1684
  Planarity :  0.004   0.053   2068
  Dihedral  :  4.008  36.430   1568
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 57.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.22), residues: 1396
  helix:  0.49 (0.18), residues: 796
  sheet: -0.58 (0.47), residues: 136
  loop :  0.40 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  46 
 TYR   0.027   0.001   TYR F 264 
 PHE   0.019   0.001   PHE D 194 
 TRP   0.003   0.001   TRP F 371 
 HIS   0.002   0.001   HIS F 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (11592)
  covalent geometry    : angle       0.54240 (15712)
  hydrogen bonds       : bond        0.04054 (  636)
  hydrogen bonds       : angle       6.36857 ( 1872)

*********************** 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
  82 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.125 
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: 0.9700 (tp-100) cc_final: 0.9465 (tp-100)
REVERT: B  233 LYS cc_start: 0.9611 (ttpp) cc_final: 0.9244 (ttpp)
REVERT: B  266 GLU cc_start: 0.9151 (pm20) cc_final: 0.8771 (pm20)
REVERT: B  268 ASN cc_start: 0.8646 (t0) cc_final: 0.8253 (p0)
REVERT: B  308 PHE cc_start: 0.8594 (t80) cc_final: 0.7900 (t80)
REVERT: B  339 LEU cc_start: 0.9259 (mm) cc_final: 0.8958 (mm)
REVERT: B  344 PHE cc_start: 0.9376 (t80) cc_final: 0.8685 (t80)
REVERT: B  350 ASP cc_start: 0.8098 (m-30) cc_final: 0.7798 (m-30)
REVERT: B  362 GLU cc_start: 0.9319 (mp0) cc_final: 0.8962 (mp0)
REVERT: B  466 ILE cc_start: 0.8681 (mm) cc_final: 0.8373 (mm)
REVERT: B  473 GLN cc_start: 0.9342 (mp10) cc_final: 0.9093 (mp10)
REVERT: B  491 HIS cc_start: 0.9219 (m170) cc_final: 0.8351 (t-170)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.0754
  time to fit residues: 7.2237
Evaluate side-chains
  69 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.076 
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  : 0.013 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 2
  average time/residue: 0.4846
  time to fit residues: 0.9824
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  : 0.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 85 optimal weight:    0.0980
   chunk 23 optimal weight:    6.9990
   chunk 27 optimal weight:    8.9990
   chunk 67 optimal weight:   50.0000
   chunk 125 optimal weight:    6.9990
   chunk 119 optimal weight:    0.7980
   chunk 78 optimal weight:    0.0870
   chunk 107 optimal weight:    0.2980
   chunk 93 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.4358
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 201 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 = 0.093781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.071441 restraints weight = 10709.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.073784 restraints weight = 7439.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.075507 restraints weight = 5695.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.076820 restraints weight = 4657.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.077846 restraints weight = 3983.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4633 r_free = 0.4633 target = 0.202787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.173512 restraints weight = 583.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.180866 restraints weight = 289.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.187031 restraints weight = 155.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4656 r_free = 0.4656 target = 0.192760 restraints weight = 88.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4676 r_free = 0.4676 target = 0.195684 restraints weight = 54.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.5042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.4451

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= 0.151
  Angle     :  0.557   8.287  15712  Z= 0.281
  Chirality :  0.038   0.197   1684
  Planarity :  0.006   0.098   2068
  Dihedral  :  4.081  35.937   1568
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 59.84
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.22), residues: 1396
  helix:  0.29 (0.18), residues: 796
  sheet: -0.54 (0.46), residues: 136
  loop :  0.39 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 445 
 TYR   0.034   0.001   TYR B 264 
 PHE   0.024   0.002   PHE A 376 
 TRP   0.003   0.001   TRP A 371 
 HIS   0.011   0.001   HIS A 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (11592)
  covalent geometry    : angle       0.55723 (15712)
  hydrogen bonds       : bond        0.03923 (  636)
  hydrogen bonds       : angle       6.41904 ( 1872)

*********************** 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
  79 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.063 
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: B  197 GLN cc_start: 0.9691 (tp-100) cc_final: 0.9453 (tp-100)
REVERT: B  233 LYS cc_start: 0.9612 (ttpp) cc_final: 0.9224 (ttpp)
REVERT: B  251 HIS cc_start: 0.9115 (t70) cc_final: 0.8847 (t70)
REVERT: B  264 TYR cc_start: 0.6945 (m-80) cc_final: 0.5552 (m-80)
REVERT: B  266 GLU cc_start: 0.9086 (pm20) cc_final: 0.8694 (pm20)
REVERT: B  279 LEU cc_start: 0.9513 (mm) cc_final: 0.9313 (mm)
REVERT: B  305 PHE cc_start: 0.8862 (m-80) cc_final: 0.8632 (m-80)
REVERT: B  308 PHE cc_start: 0.8583 (t80) cc_final: 0.7892 (t80)
REVERT: B  339 LEU cc_start: 0.9224 (mm) cc_final: 0.8935 (mm)
REVERT: B  344 PHE cc_start: 0.9343 (t80) cc_final: 0.8639 (t80)
REVERT: B  350 ASP cc_start: 0.8090 (m-30) cc_final: 0.7763 (m-30)
REVERT: B  362 GLU cc_start: 0.9286 (mp0) cc_final: 0.8919 (mp0)
REVERT: B  466 ILE cc_start: 0.8651 (mm) cc_final: 0.8349 (mm)
REVERT: B  473 GLN cc_start: 0.9341 (mp10) cc_final: 0.9081 (mp10)
REVERT: B  491 HIS cc_start: 0.9175 (m170) cc_final: 0.8324 (t-170)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.0573
  time to fit residues: 5.3244
Evaluate side-chains
  68 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.100 
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  : 0.005 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 2
  average time/residue: 0.6769
  time to fit residues: 1.3661
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  : 0.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 72 optimal weight:   10.0000
   chunk 63 optimal weight:    6.9990
   chunk 45 optimal weight:    9.9990
   chunk 76 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9980
   chunk 24 optimal weight:    0.2980
   chunk 48 optimal weight:    8.9990
   chunk 59 optimal weight:    1.9990
   chunk 114 optimal weight:    0.0570
   chunk 106 optimal weight:    9.9990
   overall best weight:    0.8100
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 201 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 = 0.3692 r_free = 0.3692 target = 0.094424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.071514 restraints weight = 10456.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.073895 restraints weight = 7361.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.075643 restraints weight = 5667.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.076957 restraints weight = 4651.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.077887 restraints weight = 4001.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4633 r_free = 0.4633 target = 0.202787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.173228 restraints weight = 609.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.180676 restraints weight = 295.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4605 r_free = 0.4605 target = 0.186987 restraints weight = 156.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4655 r_free = 0.4655 target = 0.192473 restraints weight = 89.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4616 r_free = 0.4616 target = 0.196792 restraints weight = 56.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.5011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.4523

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= 0.151
  Angle     :  0.557   8.287  15712  Z= 0.281
  Chirality :  0.038   0.197   1684
  Planarity :  0.006   0.098   2068
  Dihedral  :  4.081  35.937   1568
  Min Nonbonded Distance : 1.038

Molprobity Statistics.
  All-atom Clashscore : 64.94
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.22), residues: 1396
  helix:  0.29 (0.18), residues: 796
  sheet: -0.54 (0.46), residues: 136
  loop :  0.39 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 445 
 TYR   0.034   0.001   TYR A 264 
 PHE   0.024   0.002   PHE D 376 
 TRP   0.003   0.001   TRP F 371 
 HIS   0.011   0.001   HIS A 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (11592)
  covalent geometry    : angle       0.55723 (15712)
  hydrogen bonds       : bond        0.03923 (  636)
  hydrogen bonds       : angle       6.41904 ( 1872)

*********************** 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
  81 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.101 
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: 0.9703 (tp-100) cc_final: 0.9470 (tp-100)
REVERT: B  233 LYS cc_start: 0.9604 (ttpp) cc_final: 0.9238 (ttpp)
REVERT: B  251 HIS cc_start: 0.9185 (t70) cc_final: 0.8899 (t70)
REVERT: B  266 GLU cc_start: 0.9216 (pm20) cc_final: 0.8803 (pm20)
REVERT: B  305 PHE cc_start: 0.8870 (m-80) cc_final: 0.8650 (m-80)
REVERT: B  308 PHE cc_start: 0.8632 (t80) cc_final: 0.7924 (t80)
REVERT: B  339 LEU cc_start: 0.9243 (mm) cc_final: 0.8934 (mm)
REVERT: B  344 PHE cc_start: 0.9380 (t80) cc_final: 0.8685 (t80)
REVERT: B  350 ASP cc_start: 0.8088 (m-30) cc_final: 0.7802 (m-30)
REVERT: B  362 GLU cc_start: 0.9318 (mp0) cc_final: 0.8956 (mp0)
REVERT: B  466 ILE cc_start: 0.8674 (mm) cc_final: 0.8393 (mm)
REVERT: B  473 GLN cc_start: 0.9362 (mp10) cc_final: 0.9102 (mp10)
REVERT: B  491 HIS cc_start: 0.9184 (m170) cc_final: 0.8325 (t-170)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0679
  time to fit residues: 6.4412
Evaluate side-chains
  67 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.099 
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  : 0.007 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 2
  average time/residue: 0.6819
  time to fit residues: 1.3777
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  : 0.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 126 optimal weight:    1.9990
   chunk 129 optimal weight:    3.9990
   chunk 86 optimal weight:    9.9990
   chunk 118 optimal weight:    9.9990
   chunk 95 optimal weight:    0.9990
   chunk 81 optimal weight:    0.3980
   chunk 52 optimal weight:    9.9990
   chunk 10 optimal weight:    9.9990
   chunk 5 optimal weight:    0.0040
   chunk 53 optimal weight:    1.9990
   chunk 84 optimal weight:    0.0070
   overall best weight:    0.6814
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 201 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 = 0.3692 r_free = 0.3692 target = 0.093334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.071263 restraints weight = 10480.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.073622 restraints weight = 7227.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.075400 restraints weight = 5495.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.076704 restraints weight = 4438.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.077716 restraints weight = 3766.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4633 r_free = 0.4633 target = 0.202787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.173808 restraints weight = 571.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.181051 restraints weight = 286.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4629 r_free = 0.4629 target = 0.187836 restraints weight = 153.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4663 r_free = 0.4663 target = 0.192271 restraints weight = 85.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4627 r_free = 0.4627 target = 0.195934 restraints weight = 57.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.5011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.4580

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= 0.151
  Angle     :  0.557   8.287  15712  Z= 0.281
  Chirality :  0.038   0.197   1684
  Planarity :  0.006   0.098   2068
  Dihedral  :  4.081  35.937   1568
  Min Nonbonded Distance : 0.637

Molprobity Statistics.
  All-atom Clashscore : 63.54
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.22), residues: 1396
  helix:  0.29 (0.18), residues: 796
  sheet: -0.54 (0.46), residues: 136
  loop :  0.39 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 445 
 TYR   0.034   0.001   TYR B 264 
 PHE   0.024   0.002   PHE B 376 
 TRP   0.003   0.001   TRP A 371 
 HIS   0.011   0.001   HIS B 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (11592)
  covalent geometry    : angle       0.55723 (15712)
  hydrogen bonds       : bond        0.03923 (  636)
  hydrogen bonds       : angle       6.41904 ( 1872)

*********************** 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
  81 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.112 
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: 0.9698 (tp-100) cc_final: 0.9460 (tp-100)
REVERT: B  233 LYS cc_start: 0.9610 (ttpp) cc_final: 0.9218 (ttpp)
REVERT: B  251 HIS cc_start: 0.9124 (t70) cc_final: 0.8851 (t70)
REVERT: B  266 GLU cc_start: 0.9111 (pm20) cc_final: 0.8658 (pm20)
REVERT: B  305 PHE cc_start: 0.8847 (m-80) cc_final: 0.8624 (m-80)
REVERT: B  308 PHE cc_start: 0.8560 (t80) cc_final: 0.7875 (t80)
REVERT: B  339 LEU cc_start: 0.9228 (mm) cc_final: 0.8936 (mm)
REVERT: B  344 PHE cc_start: 0.9347 (t80) cc_final: 0.8646 (t80)
REVERT: B  350 ASP cc_start: 0.8104 (m-30) cc_final: 0.7784 (m-30)
REVERT: B  362 GLU cc_start: 0.9297 (mp0) cc_final: 0.8928 (mp0)
REVERT: B  466 ILE cc_start: 0.8649 (mm) cc_final: 0.8352 (mm)
REVERT: B  473 GLN cc_start: 0.9371 (mp10) cc_final: 0.9072 (mp10)
REVERT: B  476 ARG cc_start: 0.5227 (mmt180) cc_final: 0.4508 (mtp85)
REVERT: B  491 HIS cc_start: 0.9174 (m170) cc_final: 0.8318 (t-170)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0762
  time to fit residues: 7.2016
Evaluate side-chains
  69 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.087 
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  : 0.008 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 2
  average time/residue: 0.6940
  time to fit residues: 1.4032
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  : 0.004 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 128 optimal weight:    6.9990
   chunk 55 optimal weight:    0.8980
   chunk 79 optimal weight:    9.9990
   chunk 121 optimal weight:    0.0070
   chunk 91 optimal weight:    8.9990
   chunk 44 optimal weight:    8.9990
   chunk 89 optimal weight:    0.9990
   chunk 57 optimal weight:    8.9990
   chunk 14 optimal weight:   10.0000
   chunk 30 optimal weight:    0.0270
   chunk 6 optimal weight:    0.1980
   overall best weight:    0.4258
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 201 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 = 0.3692 r_free = 0.3692 target = 0.093334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.071213 restraints weight = 10547.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.073623 restraints weight = 7268.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.075373 restraints weight = 5499.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.076728 restraints weight = 4443.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.077749 restraints weight = 3762.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4633 r_free = 0.4633 target = 0.202787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.173614 restraints weight = 576.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4584 r_free = 0.4584 target = 0.180425 restraints weight = 291.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.4638 r_free = 0.4638 target = 0.186863 restraints weight = 153.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4649 r_free = 0.4649 target = 0.192534 restraints weight = 90.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4621 r_free = 0.4621 target = 0.196258 restraints weight = 56.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.5015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.4580

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= 0.151
  Angle     :  0.557   8.287  15712  Z= 0.281
  Chirality :  0.038   0.197   1684
  Planarity :  0.006   0.098   2068
  Dihedral  :  4.081  35.937   1568
  Min Nonbonded Distance : 0.639

Molprobity Statistics.
  All-atom Clashscore : 63.54
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.22), residues: 1396
  helix:  0.29 (0.18), residues: 796
  sheet: -0.54 (0.46), residues: 136
  loop :  0.39 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 445 
 TYR   0.034   0.001   TYR A 264 
 PHE   0.024   0.002   PHE F 376 
 TRP   0.003   0.001   TRP F 371 
 HIS   0.011   0.001   HIS B 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (11592)
  covalent geometry    : angle       0.55720 (15712)
  hydrogen bonds       : bond        0.03923 (  636)
  hydrogen bonds       : angle       6.41905 ( 1872)

*********************** 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
  81 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.100 
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: 0.9702 (tp-100) cc_final: 0.9468 (tp-100)
REVERT: B  233 LYS cc_start: 0.9606 (ttpp) cc_final: 0.9226 (ttpp)
REVERT: B  251 HIS cc_start: 0.9160 (t70) cc_final: 0.8882 (t70)
REVERT: B  266 GLU cc_start: 0.9152 (pm20) cc_final: 0.8715 (pm20)
REVERT: B  305 PHE cc_start: 0.8854 (m-80) cc_final: 0.8632 (m-80)
REVERT: B  308 PHE cc_start: 0.8602 (t80) cc_final: 0.7907 (t80)
REVERT: B  339 LEU cc_start: 0.9240 (mm) cc_final: 0.8936 (mm)
REVERT: B  344 PHE cc_start: 0.9378 (t80) cc_final: 0.8683 (t80)
REVERT: B  350 ASP cc_start: 0.8109 (m-30) cc_final: 0.7792 (m-30)
REVERT: B  362 GLU cc_start: 0.9324 (mp0) cc_final: 0.8958 (mp0)
REVERT: B  466 ILE cc_start: 0.8667 (mm) cc_final: 0.8387 (mm)
REVERT: B  473 GLN cc_start: 0.9374 (mp10) cc_final: 0.9085 (mp10)
REVERT: B  476 ARG cc_start: 0.5183 (mmt180) cc_final: 0.4488 (mtp85)
REVERT: B  491 HIS cc_start: 0.9178 (m170) cc_final: 0.8314 (t-170)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0748
  time to fit residues: 7.0284
Evaluate side-chains
  69 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.144 
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  : 0.013 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 2
  average time/residue: 0.4392
  time to fit residues: 0.8951
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  : 0.004 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 70 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 98 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0570
   chunk 104 optimal weight:    0.9990
   chunk 93 optimal weight:    4.9990
   chunk 121 optimal weight:    0.0070
   chunk 18 optimal weight:    8.9990
   chunk 110 optimal weight:    0.0970
   overall best weight:    0.3914
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 201 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 = 0.3692 r_free = 0.3692 target = 0.093334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.071208 restraints weight = 10573.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.073604 restraints weight = 7271.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.075389 restraints weight = 5519.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.076703 restraints weight = 4445.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.077732 restraints weight = 3768.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4633 r_free = 0.4633 target = 0.202786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.174110 restraints weight = 552.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.180798 restraints weight = 274.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4627 r_free = 0.4627 target = 0.188840 restraints weight = 138.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4661 r_free = 0.4661 target = 0.192959 restraints weight = 78.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4631 r_free = 0.4631 target = 0.196880 restraints weight = 52.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.5016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.4580

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= 0.151
  Angle     :  0.557   8.287  15712  Z= 0.281
  Chirality :  0.038   0.197   1684
  Planarity :  0.006   0.097   2068
  Dihedral  :  4.081  35.937   1568
  Min Nonbonded Distance : 0.652

Molprobity Statistics.
  All-atom Clashscore : 63.77
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.22), residues: 1396
  helix:  0.29 (0.18), residues: 796
  sheet: -0.54 (0.46), residues: 136
  loop :  0.39 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 445 
 TYR   0.034   0.001   TYR A 264 
 PHE   0.024   0.002   PHE B 376 
 TRP   0.003   0.001   TRP D 371 
 HIS   0.011   0.001   HIS D 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (11592)
  covalent geometry    : angle       0.55702 (15712)
  hydrogen bonds       : bond        0.03923 (  636)
  hydrogen bonds       : angle       6.41914 ( 1872)

*********************** 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
  81 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.099 
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: 0.9704 (tp-100) cc_final: 0.9469 (tp-100)
REVERT: B  233 LYS cc_start: 0.9606 (ttpp) cc_final: 0.9226 (ttpp)
REVERT: B  251 HIS cc_start: 0.9159 (t70) cc_final: 0.8881 (t70)
REVERT: B  266 GLU cc_start: 0.9155 (pm20) cc_final: 0.8718 (pm20)
REVERT: B  305 PHE cc_start: 0.8853 (m-80) cc_final: 0.8631 (m-80)
REVERT: B  308 PHE cc_start: 0.8603 (t80) cc_final: 0.7908 (t80)
REVERT: B  339 LEU cc_start: 0.9240 (mm) cc_final: 0.8936 (mm)
REVERT: B  344 PHE cc_start: 0.9378 (t80) cc_final: 0.8683 (t80)
REVERT: B  350 ASP cc_start: 0.8107 (m-30) cc_final: 0.7790 (m-30)
REVERT: B  362 GLU cc_start: 0.9324 (mp0) cc_final: 0.8957 (mp0)
REVERT: B  466 ILE cc_start: 0.8667 (mm) cc_final: 0.8386 (mm)
REVERT: B  473 GLN cc_start: 0.9374 (mp10) cc_final: 0.9085 (mp10)
REVERT: B  476 ARG cc_start: 0.5220 (mmt180) cc_final: 0.4544 (mtp85)
REVERT: B  491 HIS cc_start: 0.9178 (m170) cc_final: 0.8314 (t-170)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0739
  time to fit residues: 6.9690
Evaluate side-chains
  69 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.103 
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  : 0.007 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 2
  average time/residue: 0.6832
  time to fit residues: 1.3803
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  : 0.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 89 optimal weight:    0.0470
   chunk 40 optimal weight:    3.9990
   chunk 134 optimal weight:    7.9990
   chunk 94 optimal weight:    7.9990
   chunk 49 optimal weight:   10.0000
   chunk 3 optimal weight:   20.0000
   chunk 52 optimal weight:    7.9990
   chunk 21 optimal weight:    3.9990
   chunk 16 optimal weight:    7.9990
   chunk 107 optimal weight:    0.0670
   overall best weight:    1.7420
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 201 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 = 0.3675 r_free = 0.3675 target = 0.093383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.071684 restraints weight = 10244.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.074024 restraints weight = 6977.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.075807 restraints weight = 5256.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.077133 restraints weight = 4222.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.078086 restraints weight = 3560.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4628 r_free = 0.4628 target = 0.205580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4450 r_free = 0.4450 target = 0.175094 restraints weight = 551.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.181739 restraints weight = 294.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.187950 restraints weight = 165.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4651 r_free = 0.4651 target = 0.191828 restraints weight = 101.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4611 r_free = 0.4611 target = 0.197566 restraints weight = 71.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.4959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.4646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.144  11592  Z= 0.210
  Angle     :  0.672  15.578  15712  Z= 0.337
  Chirality :  0.041   0.252   1684
  Planarity :  0.006   0.117   2068
  Dihedral  :  4.269  34.883   1568
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 61.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.22), residues: 1396
  helix:  0.02 (0.18), residues: 792
  sheet: -0.56 (0.46), residues: 136
  loop :  0.33 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.032   0.001   ARG F 476 
 TYR   0.016   0.001   TYR D 264 
 PHE   0.014   0.001   PHE F 194 
 TRP   0.002   0.001   TRP D 371 
 HIS   0.005   0.001   HIS A 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 (11592)
  covalent geometry    : angle       0.67165 (15712)
  hydrogen bonds       : bond        0.04232 (  636)
  hydrogen bonds       : angle       6.58536 ( 1872)

********************** 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
  82 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.115 
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  233 LYS cc_start: 0.9610 (ttpp) cc_final: 0.9212 (ttpp)
REVERT: B  251 HIS cc_start: 0.9178 (t70) cc_final: 0.8867 (t70)
REVERT: B  266 GLU cc_start: 0.9091 (pm20) cc_final: 0.8689 (pm20)
REVERT: B  308 PHE cc_start: 0.8548 (t80) cc_final: 0.7866 (t80)
REVERT: B  339 LEU cc_start: 0.9236 (mm) cc_final: 0.8912 (mm)
REVERT: B  344 PHE cc_start: 0.9325 (t80) cc_final: 0.8617 (t80)
REVERT: B  362 GLU cc_start: 0.9231 (mp0) cc_final: 0.8849 (mp0)
REVERT: B  473 GLN cc_start: 0.9385 (mp10) cc_final: 0.9101 (mp10)
REVERT: B  491 HIS cc_start: 0.9118 (m170) cc_final: 0.8240 (t-170)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.0815
  time to fit residues: 7.6841
Evaluate side-chains
  67 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.096 
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  : 0.008 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 2
  average time/residue: 0.4776
  time to fit residues: 0.9678
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  : 0.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 34 optimal weight:    8.9990
   chunk 119 optimal weight:    5.9990
   chunk 32 optimal weight:    8.9990
   chunk 116 optimal weight:    9.9990
   chunk 126 optimal weight:    3.9990
   chunk 26 optimal weight:    9.9990
   chunk 87 optimal weight:    0.0050
   chunk 90 optimal weight:    9.9990
   chunk 5 optimal weight:    0.0070
   chunk 103 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    2.2018
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 201 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 = 0.3698 r_free = 0.3698 target = 0.094295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.072367 restraints weight = 10577.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.074779 restraints weight = 7365.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.076506 restraints weight = 5597.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.077846 restraints weight = 4544.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.078868 restraints weight = 3852.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4628 r_free = 0.4628 target = 0.205580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.175492 restraints weight = 550.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4581 r_free = 0.4581 target = 0.181932 restraints weight = 284.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4617 r_free = 0.4617 target = 0.187408 restraints weight = 164.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4653 r_free = 0.4653 target = 0.192209 restraints weight = 101.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4668 r_free = 0.4668 target = 0.194441 restraints weight = 70.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.4976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.4674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.144  11592  Z= 0.210
  Angle     :  0.672  15.578  15712  Z= 0.337
  Chirality :  0.041   0.252   1684
  Planarity :  0.006   0.117   2068
  Dihedral  :  4.269  34.883   1568
  Min Nonbonded Distance : 0.883

Molprobity Statistics.
  All-atom Clashscore : 63.15
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.22), residues: 1396
  helix:  0.02 (0.18), residues: 792
  sheet: -0.56 (0.46), residues: 136
  loop :  0.33 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.032   0.001   ARG F 476 
 TYR   0.016   0.001   TYR A 264 
 PHE   0.014   0.001   PHE D 194 
 TRP   0.002   0.001   TRP F 371 
 HIS   0.005   0.001   HIS D 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 (11592)
  covalent geometry    : angle       0.67165 (15712)
  hydrogen bonds       : bond        0.04232 (  636)
  hydrogen bonds       : angle       6.58536 ( 1872)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1110.11 seconds
wall clock time: 20 minutes 45.03 seconds (1245.03 seconds total)