Starting phenix.real_space_refine
on Sun Aug 24 02:56:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wzh_37952/08_2025/8wzh_37952.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wzh_37952/08_2025/8wzh_37952.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wzh_37952/08_2025/8wzh_37952.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wzh_37952/08_2025/8wzh_37952.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wzh_37952/08_2025/8wzh_37952.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wzh_37952/08_2025/8wzh_37952.cif"
  }
  resolution = 3.7
  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=   0.007
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
     P      12      5.49       5
     S      52      5.16       5
     C   10392      2.51       5
     N    2884      2.21       5
     O    3024      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 136 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16368
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "B"
      Number of atoms: 4001
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 4001
          Classifications: {'peptide': 497}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460}
    Chain: "A"
      Number of atoms: 4001
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 4001
          Classifications: {'peptide': 497}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460}
    Chain: "C"
      Number of atoms: 4001
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 4001
          Classifications: {'peptide': 497}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460}
    Chain: "D"
      Number of atoms: 4001
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 4001
          Classifications: {'peptide': 497}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460}
    Chain: "B"
      Number of atoms: 91
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 91
          Unusual residues: {'HEM': 1, 'NDP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 91
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 91
          Unusual residues: {'HEM': 1, 'NDP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 91
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 91
          Unusual residues: {'HEM': 1, 'NDP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 91
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 91
          Unusual residues: {'HEM': 1, 'NDP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.46, per 1000 atoms: 0.27
  Number of scatterers: 16368
  At special positions: 0
  Unit cell: (110.21, 114.49, 86.67, 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      52     16.00
     P      12     15.00
     O    3024      8.00
     N    2884      7.00
     C   10392      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.44
  Conformation dependent library (CDL) restraints added in 719.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3712

  Finding SS restraints...
    Secondary structure from input PDB file:
      80 helices and 8 sheets defined
      40.2% alpha, 15.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'B' and resid 6 through 9
    Processing helix  chain 'B' and resid 10 through 19
    Processing helix  chain 'B' and resid 54 through 65
      removed outlier: 3.685A  pdb=" N   THR B  58 " --> pdb=" O   ASP B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 101
      removed outlier: 3.564A  pdb=" N   GLU B 101 " --> pdb=" O   LYS B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 159
      No H-bonds generated for 'chain 'B' and resid 157 through 159'
    Processing helix  chain 'B' and resid 160 through 169
    Processing helix  chain 'B' and resid 178 through 189
      removed outlier: 3.691A  pdb=" N   VAL B 182 " --> pdb=" O   ASP B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 200
    Processing helix  chain 'B' and resid 201 through 205
      removed outlier: 4.020A  pdb=" N   ILE B 205 " --> pdb=" O   ASP B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 246 through 257
      removed outlier: 3.605A  pdb=" N   GLN B 255 " --> pdb=" O   ALA B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 272
    Processing helix  chain 'B' and resid 285 through 291
    Processing helix  chain 'B' and resid 324 through 329
    Processing helix  chain 'B' and resid 348 through 366
      removed outlier: 3.629A  pdb=" N   PHE B 356 " --> pdb=" O   GLN B 352 " (cutoff:3.500A)
      Proline residue:  B 359  - end of helix
    Processing helix  chain 'B' and resid 369 through 373
    Processing helix  chain 'B' and resid 415 through 419
      removed outlier: 3.930A  pdb=" N   LEU B 419 " --> pdb=" O   PRO B 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 440 through 451
      removed outlier: 3.855A  pdb=" N   LEU B 451 " --> pdb=" O   TYR B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 468
    Processing helix  chain 'B' and resid 471 through 486
    Processing helix  chain 'B' and resid 486 through 501
    Processing helix  chain 'A' and resid 6 through 9
    Processing helix  chain 'A' and resid 10 through 19
    Processing helix  chain 'A' and resid 54 through 65
      removed outlier: 3.683A  pdb=" N   THR A  58 " --> pdb=" O   ASP A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 101
      removed outlier: 3.565A  pdb=" N   GLU A 101 " --> pdb=" O   LYS A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 159
      No H-bonds generated for 'chain 'A' and resid 157 through 159'
    Processing helix  chain 'A' and resid 160 through 169
    Processing helix  chain 'A' and resid 178 through 189
      removed outlier: 3.692A  pdb=" N   VAL A 182 " --> pdb=" O   ASP A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 200
    Processing helix  chain 'A' and resid 201 through 205
      removed outlier: 4.020A  pdb=" N   ILE A 205 " --> pdb=" O   ASP A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 257
      removed outlier: 3.604A  pdb=" N   GLN A 255 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 272
    Processing helix  chain 'A' and resid 285 through 291
    Processing helix  chain 'A' and resid 324 through 330
    Processing helix  chain 'A' and resid 348 through 366
      removed outlier: 3.629A  pdb=" N   PHE A 356 " --> pdb=" O   GLN A 352 " (cutoff:3.500A)
      Proline residue:  A 359  - end of helix
    Processing helix  chain 'A' and resid 369 through 373
    Processing helix  chain 'A' and resid 415 through 419
      removed outlier: 3.930A  pdb=" N   LEU A 419 " --> pdb=" O   PRO A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 451
      removed outlier: 3.856A  pdb=" N   LEU A 451 " --> pdb=" O   TYR A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 468
    Processing helix  chain 'A' and resid 471 through 486
    Processing helix  chain 'A' and resid 486 through 501
    Processing helix  chain 'C' and resid 6 through 9
    Processing helix  chain 'C' and resid 10 through 19
    Processing helix  chain 'C' and resid 54 through 65
      removed outlier: 3.685A  pdb=" N   THR C  58 " --> pdb=" O   ASP C  54 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 97 through 101
      removed outlier: 3.564A  pdb=" N   GLU C 101 " --> pdb=" O   LYS C  98 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 157 through 159
      No H-bonds generated for 'chain 'C' and resid 157 through 159'
    Processing helix  chain 'C' and resid 160 through 169
    Processing helix  chain 'C' and resid 178 through 189
      removed outlier: 3.692A  pdb=" N   VAL C 182 " --> pdb=" O   ASP C 178 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 192 through 200
    Processing helix  chain 'C' and resid 201 through 205
      removed outlier: 4.020A  pdb=" N   ILE C 205 " --> pdb=" O   ASP C 202 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 246 through 257
      removed outlier: 3.605A  pdb=" N   GLN C 255 " --> pdb=" O   ALA C 251 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 259 through 272
    Processing helix  chain 'C' and resid 285 through 291
    Processing helix  chain 'C' and resid 324 through 330
    Processing helix  chain 'C' and resid 348 through 366
      removed outlier: 3.628A  pdb=" N   PHE C 356 " --> pdb=" O   GLN C 352 " (cutoff:3.500A)
      Proline residue:  C 359  - end of helix
    Processing helix  chain 'C' and resid 369 through 373
    Processing helix  chain 'C' and resid 415 through 419
      removed outlier: 3.930A  pdb=" N   LEU C 419 " --> pdb=" O   PRO C 416 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 440 through 451
      removed outlier: 3.856A  pdb=" N   LEU C 451 " --> pdb=" O   TYR C 447 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 452 through 468
    Processing helix  chain 'C' and resid 471 through 486
    Processing helix  chain 'C' and resid 486 through 501
    Processing helix  chain 'D' and resid 6 through 9
    Processing helix  chain 'D' and resid 10 through 19
    Processing helix  chain 'D' and resid 54 through 65
      removed outlier: 3.683A  pdb=" N   THR D  58 " --> pdb=" O   ASP D  54 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 97 through 101
      removed outlier: 3.564A  pdb=" N   GLU D 101 " --> pdb=" O   LYS D  98 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 157 through 159
      No H-bonds generated for 'chain 'D' and resid 157 through 159'
    Processing helix  chain 'D' and resid 160 through 169
    Processing helix  chain 'D' and resid 178 through 189
      removed outlier: 3.692A  pdb=" N   VAL D 182 " --> pdb=" O   ASP D 178 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 192 through 200
    Processing helix  chain 'D' and resid 201 through 205
      removed outlier: 4.020A  pdb=" N   ILE D 205 " --> pdb=" O   ASP D 202 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 246 through 257
      removed outlier: 3.605A  pdb=" N   GLN D 255 " --> pdb=" O   ALA D 251 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 259 through 272
    Processing helix  chain 'D' and resid 285 through 291
    Processing helix  chain 'D' and resid 324 through 330
    Processing helix  chain 'D' and resid 348 through 366
      removed outlier: 3.628A  pdb=" N   PHE D 356 " --> pdb=" O   GLN D 352 " (cutoff:3.500A)
      Proline residue:  D 359  - end of helix
    Processing helix  chain 'D' and resid 369 through 373
    Processing helix  chain 'D' and resid 415 through 419
      removed outlier: 3.930A  pdb=" N   LEU D 419 " --> pdb=" O   PRO D 416 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 440 through 451
      removed outlier: 3.856A  pdb=" N   LEU D 451 " --> pdb=" O   TYR D 447 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 452 through 468
    Processing helix  chain 'D' and resid 471 through 486
    Processing helix  chain 'D' and resid 486 through 501
    Processing sheet with id=AA1, first strand: chain 'B' and resid 42 through 44
      removed outlier: 3.738A  pdb=" N   ARG D 430 " --> pdb=" O   THR B  43 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 343 through 344
      removed outlier: 3.678A  pdb=" N   GLY B 314 " --> pdb=" O   PHE B 279 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   ILE B 281 " --> pdb=" O   PRO B 312 " (cutoff:3.500A)
      removed outlier: 5.589A  pdb=" N   LEU B 316 " --> pdb=" O   GLU B  86 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   GLU B  86 " --> pdb=" O   LEU B 316 " (cutoff:3.500A)
      removed outlier: 5.740A  pdb=" N   LEU B 318 " --> pdb=" O   TYR B  84 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   TYR B  84 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 429 through 431
      removed outlier: 3.532A  pdb=" N   ARG B 430 " --> pdb=" O   THR D  43 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 42 through 44
      removed outlier: 3.507A  pdb=" N   ARG C 430 " --> pdb=" O   THR A  43 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 344
      removed outlier: 3.678A  pdb=" N   GLY A 314 " --> pdb=" O   PHE A 279 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   ILE A 281 " --> pdb=" O   PRO A 312 " (cutoff:3.500A)
      removed outlier: 5.588A  pdb=" N   LEU A 316 " --> pdb=" O   GLU A  86 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   GLU A  86 " --> pdb=" O   LEU A 316 " (cutoff:3.500A)
      removed outlier: 5.740A  pdb=" N   LEU A 318 " --> pdb=" O   TYR A  84 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   TYR A  84 " --> pdb=" O   LEU A 318 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 429 through 431
      removed outlier: 3.627A  pdb=" N   ARG A 430 " --> pdb=" O   THR C  43 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 343 through 344
      removed outlier: 3.678A  pdb=" N   GLY C 314 " --> pdb=" O   PHE C 279 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   ILE C 281 " --> pdb=" O   PRO C 312 " (cutoff:3.500A)
      removed outlier: 5.589A  pdb=" N   LEU C 316 " --> pdb=" O   GLU C  86 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   GLU C  86 " --> pdb=" O   LEU C 316 " (cutoff:3.500A)
      removed outlier: 5.739A  pdb=" N   LEU C 318 " --> pdb=" O   TYR C  84 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   TYR C  84 " --> pdb=" O   LEU C 318 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 343 through 344
      removed outlier: 3.679A  pdb=" N   GLY D 314 " --> pdb=" O   PHE D 279 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   ILE D 281 " --> pdb=" O   PRO D 312 " (cutoff:3.500A)
      removed outlier: 5.589A  pdb=" N   LEU D 316 " --> pdb=" O   GLU D  86 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   GLU D  86 " --> pdb=" O   LEU D 316 " (cutoff:3.500A)
      removed outlier: 5.740A  pdb=" N   LEU D 318 " --> pdb=" O   TYR D  84 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   TYR D  84 " --> pdb=" O   LEU D 318 " (cutoff:3.500A)

    647 hydrogen bonds defined for protein.
    1833 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: 2.94

  Time building geometry restraints manager: 1.89 seconds

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

  Histogram of bond lengths:
        1.21 -     1.39: 6843
        1.39 -     1.57: 9921
        1.57 -     1.75: 20
        1.75 -     1.93: 92
        1.93 -     2.11: 12
  Bond restraints: 16888
  Sorted by residual:
  bond pdb=" O2B NDP D3002 "
       pdb=" P2B NDP D3002 "
    ideal  model  delta    sigma   weight residual
    1.833  1.616  0.217 3.80e-02 6.93e+02 3.26e+01
  bond pdb=" O2B NDP B3002 "
       pdb=" P2B NDP B3002 "
    ideal  model  delta    sigma   weight residual
    1.833  1.616  0.217 3.80e-02 6.93e+02 3.25e+01
  bond pdb=" O2B NDP A3002 "
       pdb=" P2B NDP A3002 "
    ideal  model  delta    sigma   weight residual
    1.833  1.617  0.216 3.80e-02 6.93e+02 3.23e+01
  bond pdb=" O2B NDP C3002 "
       pdb=" P2B NDP C3002 "
    ideal  model  delta    sigma   weight residual
    1.833  1.617  0.216 3.80e-02 6.93e+02 3.23e+01
  bond pdb=" O5D NDP A3002 "
       pdb=" PN  NDP A3002 "
    ideal  model  delta    sigma   weight residual
    1.757  1.589  0.168 3.50e-02 8.16e+02 2.30e+01
  ... (remaining 16883 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 19711
        2.03 -     4.06: 3203
        4.06 -     6.09: 94
        6.09 -     8.12: 20
        8.12 -    10.15: 12
  Bond angle restraints: 23040
  Sorted by residual:
  angle pdb=" O1X NDP A3002 "
        pdb=" P2B NDP A3002 "
        pdb=" O3X NDP A3002 "
      ideal   model   delta    sigma   weight residual
     117.46  111.91    5.55 1.17e+00 7.36e-01 2.26e+01
  angle pdb=" O1X NDP D3002 "
        pdb=" P2B NDP D3002 "
        pdb=" O3X NDP D3002 "
      ideal   model   delta    sigma   weight residual
     117.46  111.96    5.50 1.17e+00 7.36e-01 2.23e+01
  angle pdb=" O1X NDP B3002 "
        pdb=" P2B NDP B3002 "
        pdb=" O3X NDP B3002 "
      ideal   model   delta    sigma   weight residual
     117.46  111.97    5.49 1.17e+00 7.36e-01 2.22e+01
  angle pdb=" O1X NDP C3002 "
        pdb=" P2B NDP C3002 "
        pdb=" O3X NDP C3002 "
      ideal   model   delta    sigma   weight residual
     117.46  112.02    5.44 1.17e+00 7.36e-01 2.18e+01
  angle pdb=" O2B NDP B3002 "
        pdb=" P2B NDP B3002 "
        pdb=" O3X NDP B3002 "
      ideal   model   delta    sigma   weight residual
      97.70  107.85  -10.15 2.45e+00 1.67e-01 1.72e+01
  ... (remaining 23035 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 8836
       17.89 -    35.78: 776
       35.78 -    53.67: 148
       53.67 -    71.56: 76
       71.56 -    89.45: 24
  Dihedral angle restraints: 9860
    sinusoidal: 4080
      harmonic: 5780
  Sorted by residual:
  dihedral pdb=" CA  ASN D 439 "
           pdb=" C   ASN D 439 "
           pdb=" N   VAL D 440 "
           pdb=" CA  VAL D 440 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.46  -18.54     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  ASN A 439 "
           pdb=" C   ASN A 439 "
           pdb=" N   VAL A 440 "
           pdb=" CA  VAL A 440 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.46  -18.54     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  ASN B 439 "
           pdb=" C   ASN B 439 "
           pdb=" N   VAL B 440 "
           pdb=" CA  VAL B 440 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.48  -18.52     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 9857 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 960
       0.040 -    0.079: 701
       0.079 -    0.119: 480
       0.119 -    0.159: 167
       0.159 -    0.198: 20
  Chirality restraints: 2328
  Sorted by residual:
  chirality pdb=" C4D NDP D3002 "
            pdb=" C3D NDP D3002 "
            pdb=" C5D NDP D3002 "
            pdb=" O4D NDP D3002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.71   -2.52   -0.20 2.00e-01 2.50e+01 9.84e-01
  chirality pdb=" C4D NDP C3002 "
            pdb=" C3D NDP C3002 "
            pdb=" C5D NDP C3002 "
            pdb=" O4D NDP C3002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.71   -2.52   -0.20 2.00e-01 2.50e+01 9.72e-01
  chirality pdb=" C4D NDP A3002 "
            pdb=" C3D NDP A3002 "
            pdb=" C5D NDP A3002 "
            pdb=" O4D NDP A3002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.71   -2.52   -0.20 2.00e-01 2.50e+01 9.72e-01
  ... (remaining 2325 not shown)

  Planarity restraints: 3052
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" NB  HEM B3001 "   -0.011 2.00e-02 2.50e+03   1.34e-02 4.02e+00
        pdb=" C1B HEM B3001 "    0.004 2.00e-02 2.50e+03
        pdb=" C2B HEM B3001 "   -0.001 2.00e-02 2.50e+03
        pdb=" C3B HEM B3001 "    0.003 2.00e-02 2.50e+03
        pdb=" C4B HEM B3001 "   -0.014 2.00e-02 2.50e+03
        pdb=" CAB HEM B3001 "    0.020 2.00e-02 2.50e+03
        pdb=" CHB HEM B3001 "    0.021 2.00e-02 2.50e+03
        pdb=" CHC HEM B3001 "    0.000 2.00e-02 2.50e+03
        pdb=" CMB HEM B3001 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" NB  HEM A3001 "   -0.011 2.00e-02 2.50e+03   1.34e-02 4.02e+00
        pdb=" C1B HEM A3001 "    0.003 2.00e-02 2.50e+03
        pdb=" C2B HEM A3001 "   -0.001 2.00e-02 2.50e+03
        pdb=" C3B HEM A3001 "    0.003 2.00e-02 2.50e+03
        pdb=" C4B HEM A3001 "   -0.014 2.00e-02 2.50e+03
        pdb=" CAB HEM A3001 "    0.020 2.00e-02 2.50e+03
        pdb=" CHB HEM A3001 "    0.021 2.00e-02 2.50e+03
        pdb=" CHC HEM A3001 "   -0.000 2.00e-02 2.50e+03
        pdb=" CMB HEM A3001 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" NB  HEM C3001 "    0.012 2.00e-02 2.50e+03   1.31e-02 3.88e+00
        pdb=" C1B HEM C3001 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2B HEM C3001 "    0.001 2.00e-02 2.50e+03
        pdb=" C3B HEM C3001 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4B HEM C3001 "    0.013 2.00e-02 2.50e+03
        pdb=" CAB HEM C3001 "   -0.019 2.00e-02 2.50e+03
        pdb=" CHB HEM C3001 "   -0.021 2.00e-02 2.50e+03
        pdb=" CHC HEM C3001 "    0.000 2.00e-02 2.50e+03
        pdb=" CMB HEM C3001 "    0.021 2.00e-02 2.50e+03
  ... (remaining 3049 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 3826
        2.83 -     3.35: 16437
        3.35 -     3.86: 26663
        3.86 -     4.38: 32562
        4.38 -     4.90: 54551
  Nonbonded interactions: 134039
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 137 "
            pdb=" O   VAL A 375 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" OH  TYR C 137 "
            pdb=" O   VAL C 375 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" OH  TYR D 137 "
            pdb=" O   VAL D 375 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" OH  TYR B 137 "
            pdb=" O   VAL B 375 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" O   LEU A 451 "
            pdb=" NH2 ARG A 456 "
     model   vdw
     2.318 3.120
  ... (remaining 134034 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 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     17.070
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
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      :  0.013   0.217  16892  Z= 0.890
  Angle     :  1.375  10.147  23040  Z= 0.981
  Chirality :  0.070   0.198   2328
  Planarity :  0.004   0.018   3052
  Dihedral  : 15.634  89.449   6148
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  3.74 %
    Favored  : 95.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.69 (0.16), residues: 1980
  helix: -1.14 (0.17), residues: 676
  sheet: -1.12 (0.28), residues: 220
  loop : -2.43 (0.16), residues: 1084

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 127 
 TYR   0.022   0.003   TYR C 489 
 PHE   0.020   0.003   PHE C 356 
 TRP   0.020   0.003   TRP B 183 
 HIS   0.008   0.003   HIS C 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.01342 (16888)
  covalent geometry    : angle       1.37502 (23040)
  hydrogen bonds       : bond        0.15783 (  647)
  hydrogen bonds       : angle       7.44833 ( 1833)
  Misc. bond           : bond        0.08834 (    4)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 205
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
REVERT: B   59 ASP cc_start: 0.7180 (m-30) cc_final: 0.6839 (m-30)
REVERT: B  119 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7272 (mp0)
REVERT: B  259 ASP cc_start: 0.8290 (p0) cc_final: 0.7653 (p0)
REVERT: B  260 TYR cc_start: 0.7497 (t80) cc_final: 0.7095 (t80)
REVERT: B  321 ASN cc_start: 0.8352 (m-40) cc_final: 0.8136 (m-40)
REVERT: B  330 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7934 (mm-30)
REVERT: A  119 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7075 (mp0)
REVERT: A  259 ASP cc_start: 0.8077 (p0) cc_final: 0.7397 (p0)
REVERT: A  330 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7922 (mm-30)
REVERT: A  339 MET cc_start: 0.8073 (mtm) cc_final: 0.7856 (mtm)
REVERT: C   59 ASP cc_start: 0.7099 (m-30) cc_final: 0.6725 (m-30)
REVERT: C  119 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7326 (mp0)
REVERT: C  259 ASP cc_start: 0.8260 (p0) cc_final: 0.7599 (p0)
REVERT: C  260 TYR cc_start: 0.7509 (t80) cc_final: 0.7108 (t80)
REVERT: C  321 ASN cc_start: 0.8343 (m-40) cc_final: 0.8129 (m-40)
REVERT: C  330 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7927 (mm-30)
REVERT: C  339 MET cc_start: 0.8066 (mtm) cc_final: 0.7860 (mtm)
REVERT: D  119 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7134 (mp0)
REVERT: D  259 ASP cc_start: 0.8179 (p0) cc_final: 0.7496 (p0)
REVERT: D  330 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7869 (mm-30)
  outliers start: 16
  outliers final: 4
  residues processed: 217
  average time/residue: 0.1453
  time to fit residues: 46.9036
Evaluate side-chains
  154 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 146
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  119 GLU
Chi-restraints excluded: chain B residue  440 VAL
Chi-restraints excluded: chain A residue  119 GLU
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain C residue  119 GLU
Chi-restraints excluded: chain C residue  440 VAL
Chi-restraints excluded: chain D residue  119 GLU
Chi-restraints excluded: chain D residue  440 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 194 optimal weight:    0.8980
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    0.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
B  89 HIS
B 148 ASN
B 282 GLN
B 331 GLN
** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  89 HIS
A 282 GLN
A 331 GLN
** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  89 HIS
C 282 GLN
C 331 GLN
** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  89 HIS
D 282 GLN
D 331 GLN
** D 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.113160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.088499 restraints weight = 25437.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.091203 restraints weight = 15788.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.093014 restraints weight = 11752.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.094082 restraints weight = 9739.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.094923 restraints weight = 8686.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.1295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16892  Z= 0.110
  Angle     :  0.533   4.875  23040  Z= 0.271
  Chirality :  0.042   0.133   2328
  Planarity :  0.004   0.038   3052
  Dihedral  :  8.460  93.788   2268
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  :  7.83 %
    Favored  : 89.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.71 (0.18), residues: 1980
  helix:  0.76 (0.20), residues: 684
  sheet: -0.04 (0.28), residues: 272
  loop : -1.49 (0.17), residues: 1024

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 127 
 TYR   0.016   0.001   TYR A 489 
 PHE   0.018   0.002   PHE A 132 
 TRP   0.011   0.001   TRP D 183 
 HIS   0.004   0.001   HIS A 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (16888)
  covalent geometry    : angle       0.53342 (23040)
  hydrogen bonds       : bond        0.03796 (  647)
  hydrogen bonds       : angle       5.32544 ( 1833)
  Misc. bond           : bond        0.00537 (    4)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 182
  time to evaluate  : 0.689 
Fit side-chains
   revert: symmetry clash
REVERT: B   26 VAL cc_start: 0.7431 (OUTLIER) cc_final: 0.7228 (p)
REVERT: B   60 GLU cc_start: 0.7755 (tp30) cc_final: 0.7549 (tp30)
REVERT: B  259 ASP cc_start: 0.7239 (p0) cc_final: 0.6817 (p0)
REVERT: B  321 ASN cc_start: 0.8830 (m-40) cc_final: 0.8596 (m-40)
REVERT: A  259 ASP cc_start: 0.7121 (p0) cc_final: 0.6693 (p0)
REVERT: C   26 VAL cc_start: 0.7530 (OUTLIER) cc_final: 0.7325 (p)
REVERT: C  259 ASP cc_start: 0.7246 (p0) cc_final: 0.6785 (p0)
REVERT: C  321 ASN cc_start: 0.8833 (m-40) cc_final: 0.8606 (m-40)
REVERT: D  259 ASP cc_start: 0.7196 (p0) cc_final: 0.6765 (p0)
  outliers start: 41
  outliers final: 22
  residues processed: 199
  average time/residue: 0.1189
  time to fit residues: 37.8922
Evaluate side-chains
  167 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 143
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 VAL
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  152 ILE
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain B residue  440 VAL
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain C residue   26 VAL
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  152 ILE
Chi-restraints excluded: chain C residue  202 ASP
Chi-restraints excluded: chain C residue  423 ILE
Chi-restraints excluded: chain C residue  440 VAL
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain D residue  176 LEU
Chi-restraints excluded: chain D residue  202 ASP
Chi-restraints excluded: chain D residue  423 ILE
Chi-restraints excluded: chain D residue  440 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 165 optimal weight:    6.9990
   chunk 125 optimal weight:    0.7980
   chunk 7 optimal weight:    8.9990
   chunk 115 optimal weight:    7.9990
   chunk 42 optimal weight:    4.9990
   chunk 185 optimal weight:   10.0000
   chunk 64 optimal weight:    1.9990
   chunk 103 optimal weight:    5.9990
   chunk 145 optimal weight:    5.9990
   chunk 131 optimal weight:    3.9990
   chunk 177 optimal weight:    0.9980
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
B 407 ASN
A 407 ASN
C 407 ASN
D 407 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.111835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.087015 restraints weight = 26060.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.089696 restraints weight = 16316.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.091446 restraints weight = 12174.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.092598 restraints weight = 10161.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.093275 restraints weight = 9070.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.1667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072  16892  Z= 0.189
  Angle     :  0.577   4.897  23040  Z= 0.295
  Chirality :  0.045   0.145   2328
  Planarity :  0.004   0.045   3052
  Dihedral  :  7.973  90.190   2256
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  :  8.88 %
    Favored  : 88.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.43 (0.18), residues: 1980
  helix:  1.06 (0.20), residues: 684
  sheet: -0.01 (0.28), residues: 272
  loop : -1.34 (0.18), residues: 1024

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 210 
 TYR   0.018   0.002   TYR A 489 
 PHE   0.025   0.002   PHE B 100 
 TRP   0.013   0.001   TRP B 183 
 HIS   0.005   0.001   HIS C 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 (16888)
  covalent geometry    : angle       0.57673 (23040)
  hydrogen bonds       : bond        0.04239 (  647)
  hydrogen bonds       : angle       5.23614 ( 1833)
  Misc. bond           : bond        0.05684 (    4)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 146
  time to evaluate  : 0.655 
Fit side-chains
REVERT: B  236 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.8696 (p90)
REVERT: B  259 ASP cc_start: 0.7275 (p0) cc_final: 0.6905 (p0)
REVERT: B  321 ASN cc_start: 0.8844 (m-40) cc_final: 0.8584 (m-40)
REVERT: B  394 MET cc_start: 0.6377 (tmm) cc_final: 0.5937 (ttt)
REVERT: A  259 ASP cc_start: 0.7188 (p0) cc_final: 0.6739 (p0)
REVERT: A  260 TYR cc_start: 0.7540 (t80) cc_final: 0.7314 (t80)
REVERT: A  321 ASN cc_start: 0.8865 (m-40) cc_final: 0.8576 (m-40)
REVERT: C  236 TYR cc_start: 0.8954 (OUTLIER) cc_final: 0.8657 (p90)
REVERT: C  259 ASP cc_start: 0.7265 (p0) cc_final: 0.6861 (p0)
REVERT: C  321 ASN cc_start: 0.8866 (m-40) cc_final: 0.8601 (m-40)
REVERT: D  236 TYR cc_start: 0.8968 (OUTLIER) cc_final: 0.8692 (p90)
REVERT: D  259 ASP cc_start: 0.7291 (p0) cc_final: 0.6870 (p0)
REVERT: D  321 ASN cc_start: 0.8854 (m-40) cc_final: 0.8598 (m-40)
REVERT: D  392 MET cc_start: 0.8728 (tpt) cc_final: 0.8493 (tpt)
REVERT: D  494 GLN cc_start: 0.8078 (tp-100) cc_final: 0.7702 (tp-100)
  outliers start: 44
  outliers final: 31
  residues processed: 173
  average time/residue: 0.1228
  time to fit residues: 33.7282
Evaluate side-chains
  171 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 137
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  152 ILE
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  202 ASP
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  152 ILE
Chi-restraints excluded: chain C residue  198 PHE
Chi-restraints excluded: chain C residue  202 ASP
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  383 VAL
Chi-restraints excluded: chain C residue  423 ILE
Chi-restraints excluded: chain C residue  450 VAL
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain D residue  176 LEU
Chi-restraints excluded: chain D residue  198 PHE
Chi-restraints excluded: chain D residue  202 ASP
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  383 VAL
Chi-restraints excluded: chain D residue  423 ILE
Chi-restraints excluded: chain D residue  450 VAL
Chi-restraints excluded: chain D residue  497 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 94 optimal weight:    3.9990
   chunk 74 optimal weight:    8.9990
   chunk 145 optimal weight:    5.9990
   chunk 117 optimal weight:    2.9990
   chunk 156 optimal weight:    5.9990
   chunk 158 optimal weight:    0.0970
   chunk 37 optimal weight:    1.9990
   chunk 151 optimal weight:    0.9980
   chunk 89 optimal weight:    4.9990
   chunk 107 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    2.0184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.111396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.086828 restraints weight = 25878.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.089496 restraints weight = 16173.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.091287 restraints weight = 12089.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.092443 restraints weight = 10045.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.093065 restraints weight = 8933.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.1833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  16892  Z= 0.155
  Angle     :  0.542   6.322  23040  Z= 0.276
  Chirality :  0.043   0.132   2328
  Planarity :  0.004   0.047   3052
  Dihedral  :  7.741  88.924   2253
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 10.05 %
    Favored  : 87.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.22 (0.18), residues: 1980
  helix:  1.22 (0.20), residues: 684
  sheet:  0.18 (0.29), residues: 272
  loop : -1.22 (0.18), residues: 1024

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 210 
 TYR   0.015   0.001   TYR D 489 
 PHE   0.029   0.002   PHE B 100 
 TRP   0.012   0.001   TRP C 183 
 HIS   0.004   0.001   HIS C 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 (16888)
  covalent geometry    : angle       0.54208 (23040)
  hydrogen bonds       : bond        0.03800 (  647)
  hydrogen bonds       : angle       5.07986 ( 1833)
  Misc. bond           : bond        0.03228 (    4)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 148
  time to evaluate  : 0.673 
Fit side-chains
REVERT: B  259 ASP cc_start: 0.7225 (p0) cc_final: 0.6800 (p0)
REVERT: B  321 ASN cc_start: 0.8852 (m-40) cc_final: 0.8586 (m-40)
REVERT: B  394 MET cc_start: 0.6573 (tmm) cc_final: 0.5830 (tmm)
REVERT: B  500 TYR cc_start: 0.7079 (OUTLIER) cc_final: 0.6661 (m-80)
REVERT: A  259 ASP cc_start: 0.7148 (p0) cc_final: 0.6767 (p0)
REVERT: A  494 GLN cc_start: 0.8047 (tp-100) cc_final: 0.7679 (tp-100)
REVERT: A  500 TYR cc_start: 0.7015 (OUTLIER) cc_final: 0.6613 (m-80)
REVERT: C  259 ASP cc_start: 0.7205 (p0) cc_final: 0.6777 (p0)
REVERT: C  321 ASN cc_start: 0.8867 (m-40) cc_final: 0.8599 (m-40)
REVERT: D  236 TYR cc_start: 0.8937 (OUTLIER) cc_final: 0.8699 (p90)
REVERT: D  259 ASP cc_start: 0.7284 (p0) cc_final: 0.6825 (p0)
REVERT: D  321 ASN cc_start: 0.8869 (m-40) cc_final: 0.8589 (m-40)
REVERT: D  500 TYR cc_start: 0.7112 (OUTLIER) cc_final: 0.6700 (m-80)
  outliers start: 50
  outliers final: 26
  residues processed: 178
  average time/residue: 0.1205
  time to fit residues: 34.3393
Evaluate side-chains
  176 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 146
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  152 ILE
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  500 TYR
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  500 TYR
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  152 ILE
Chi-restraints excluded: chain C residue  198 PHE
Chi-restraints excluded: chain C residue  202 ASP
Chi-restraints excluded: chain C residue  383 VAL
Chi-restraints excluded: chain C residue  423 ILE
Chi-restraints excluded: chain C residue  450 VAL
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain D residue  198 PHE
Chi-restraints excluded: chain D residue  202 ASP
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  383 VAL
Chi-restraints excluded: chain D residue  423 ILE
Chi-restraints excluded: chain D residue  450 VAL
Chi-restraints excluded: chain D residue  500 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 149 optimal weight:   10.0000
   chunk 32 optimal weight:    4.9990
   chunk 151 optimal weight:    7.9990
   chunk 157 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 28 optimal weight:    0.6980
   chunk 65 optimal weight:    4.9990
   chunk 107 optimal weight:    5.9990
   chunk 102 optimal weight:    9.9990
   chunk 145 optimal weight:    3.9990
   chunk 129 optimal weight:    0.3980
   overall best weight:    3.0186

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

Flipped N/Q/H residues before XYZ refinement:
D 424 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.112039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.087538 restraints weight = 25765.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.090089 restraints weight = 16150.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.091876 restraints weight = 12150.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.092992 restraints weight = 10120.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.093735 restraints weight = 9033.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.082  16892  Z= 0.217
  Angle     :  0.599   9.876  23040  Z= 0.303
  Chirality :  0.045   0.139   2328
  Planarity :  0.005   0.051   3052
  Dihedral  :  7.868  86.998   2252
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 10.57 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.24 (0.18), residues: 1980
  helix:  1.20 (0.20), residues: 684
  sheet:  0.18 (0.29), residues: 272
  loop : -1.22 (0.18), residues: 1024

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 210 
 TYR   0.015   0.002   TYR A 489 
 PHE   0.024   0.002   PHE B 100 
 TRP   0.014   0.001   TRP A 183 
 HIS   0.005   0.001   HIS C 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00548 (16888)
  covalent geometry    : angle       0.59873 (23040)
  hydrogen bonds       : bond        0.04229 (  647)
  hydrogen bonds       : angle       5.23474 ( 1833)
  Misc. bond           : bond        0.06462 (    4)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 153
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
REVERT: B  236 TYR cc_start: 0.8954 (OUTLIER) cc_final: 0.8751 (p90)
REVERT: B  259 ASP cc_start: 0.7204 (p0) cc_final: 0.6818 (p0)
REVERT: B  321 ASN cc_start: 0.8854 (m-40) cc_final: 0.8593 (m-40)
REVERT: B  500 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.6720 (m-80)
REVERT: A  259 ASP cc_start: 0.7127 (p0) cc_final: 0.6729 (p0)
REVERT: A  500 TYR cc_start: 0.7147 (OUTLIER) cc_final: 0.6708 (m-80)
REVERT: C  236 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.8731 (p90)
REVERT: C  259 ASP cc_start: 0.7201 (p0) cc_final: 0.6802 (p0)
REVERT: C  321 ASN cc_start: 0.8891 (m-40) cc_final: 0.8644 (m-40)
REVERT: C  500 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.6709 (m-80)
REVERT: D  236 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.8703 (p90)
REVERT: D  259 ASP cc_start: 0.7134 (p0) cc_final: 0.6736 (p0)
REVERT: D  321 ASN cc_start: 0.8887 (m-40) cc_final: 0.8592 (m-40)
REVERT: D  494 GLN cc_start: 0.7988 (tp-100) cc_final: 0.7655 (tp-100)
REVERT: D  500 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.6712 (m-80)
  outliers start: 54
  outliers final: 33
  residues processed: 191
  average time/residue: 0.1255
  time to fit residues: 37.6097
Evaluate side-chains
  185 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 145
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  152 ILE
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  500 TYR
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  202 ASP
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  500 TYR
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  152 ILE
Chi-restraints excluded: chain C residue  176 LEU
Chi-restraints excluded: chain C residue  198 PHE
Chi-restraints excluded: chain C residue  202 ASP
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  383 VAL
Chi-restraints excluded: chain C residue  423 ILE
Chi-restraints excluded: chain C residue  450 VAL
Chi-restraints excluded: chain C residue  500 TYR
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain D residue  176 LEU
Chi-restraints excluded: chain D residue  198 PHE
Chi-restraints excluded: chain D residue  202 ASP
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  323 VAL
Chi-restraints excluded: chain D residue  383 VAL
Chi-restraints excluded: chain D residue  423 ILE
Chi-restraints excluded: chain D residue  450 VAL
Chi-restraints excluded: chain D residue  497 LEU
Chi-restraints excluded: chain D residue  500 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 188 optimal weight:    8.9990
   chunk 42 optimal weight:    5.9990
   chunk 140 optimal weight:    2.9990
   chunk 154 optimal weight:    0.9980
   chunk 185 optimal weight:    4.9990
   chunk 166 optimal weight:    0.8980
   chunk 79 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 119 optimal weight:    5.9990
   chunk 60 optimal weight:    7.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
B 424 GLN
A  33 ASN
A 211 HIS
A 424 GLN
C 424 GLN
D 211 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.110223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.085483 restraints weight = 26068.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.088110 restraints weight = 16216.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.089836 restraints weight = 12138.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.090826 restraints weight = 10155.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.091592 restraints weight = 9112.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  16892  Z= 0.166
  Angle     :  0.567   8.155  23040  Z= 0.286
  Chirality :  0.044   0.135   2328
  Planarity :  0.004   0.050   3052
  Dihedral  :  7.714  85.749   2252
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 11.97 %
    Favored  : 85.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.12 (0.18), residues: 1980
  helix:  1.29 (0.20), residues: 684
  sheet:  0.29 (0.30), residues: 272
  loop : -1.17 (0.18), residues: 1024

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 458 
 TYR   0.014   0.001   TYR D 489 
 PHE   0.021   0.002   PHE B 100 
 TRP   0.013   0.001   TRP D 183 
 HIS   0.004   0.001   HIS C 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 (16888)
  covalent geometry    : angle       0.56688 (23040)
  hydrogen bonds       : bond        0.03834 (  647)
  hydrogen bonds       : angle       5.12848 ( 1833)
  Misc. bond           : bond        0.03626 (    4)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 155
  time to evaluate  : 0.573 
Fit side-chains
REVERT: B  259 ASP cc_start: 0.7205 (p0) cc_final: 0.6777 (p0)
REVERT: B  321 ASN cc_start: 0.8846 (m-40) cc_final: 0.8587 (m-40)
REVERT: B  500 TYR cc_start: 0.7204 (OUTLIER) cc_final: 0.6681 (m-80)
REVERT: A  259 ASP cc_start: 0.7099 (p0) cc_final: 0.6809 (p0)
REVERT: A  394 MET cc_start: 0.8140 (mmp) cc_final: 0.7938 (mmm)
REVERT: A  500 TYR cc_start: 0.7171 (OUTLIER) cc_final: 0.6736 (m-80)
REVERT: C  259 ASP cc_start: 0.7195 (p0) cc_final: 0.6782 (p0)
REVERT: C  321 ASN cc_start: 0.8862 (m-40) cc_final: 0.8606 (m-40)
REVERT: C  500 TYR cc_start: 0.7217 (OUTLIER) cc_final: 0.6716 (m-80)
REVERT: D  236 TYR cc_start: 0.8921 (OUTLIER) cc_final: 0.8703 (p90)
REVERT: D  259 ASP cc_start: 0.7102 (p0) cc_final: 0.6689 (p0)
REVERT: D  500 TYR cc_start: 0.7139 (OUTLIER) cc_final: 0.6630 (m-80)
  outliers start: 50
  outliers final: 32
  residues processed: 184
  average time/residue: 0.1260
  time to fit residues: 36.0601
Evaluate side-chains
  183 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 146
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  152 ILE
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  500 TYR
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  202 ASP
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  483 THR
Chi-restraints excluded: chain A residue  500 TYR
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  152 ILE
Chi-restraints excluded: chain C residue  198 PHE
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  383 VAL
Chi-restraints excluded: chain C residue  423 ILE
Chi-restraints excluded: chain C residue  450 VAL
Chi-restraints excluded: chain C residue  500 TYR
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain D residue  198 PHE
Chi-restraints excluded: chain D residue  202 ASP
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  323 VAL
Chi-restraints excluded: chain D residue  383 VAL
Chi-restraints excluded: chain D residue  423 ILE
Chi-restraints excluded: chain D residue  450 VAL
Chi-restraints excluded: chain D residue  500 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 169 optimal weight:    2.9990
   chunk 94 optimal weight:    3.9990
   chunk 99 optimal weight:    6.9990
   chunk 171 optimal weight:    3.9990
   chunk 11 optimal weight:    9.9990
   chunk 55 optimal weight:    3.9990
   chunk 117 optimal weight:    1.9990
   chunk 102 optimal weight:   10.0000
   chunk 26 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   chunk 183 optimal weight:    0.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
B  33 ASN
** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 211 HIS
A  33 ASN
C  33 ASN
C 211 HIS
C 331 GLN
D  33 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.112320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.087749 restraints weight = 25859.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.090382 restraints weight = 16087.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.092135 restraints weight = 12065.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.093236 restraints weight = 10058.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.093857 restraints weight = 8999.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.2118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.079  16892  Z= 0.206
  Angle     :  0.599   7.589  23040  Z= 0.306
  Chirality :  0.045   0.139   2328
  Planarity :  0.005   0.052   3052
  Dihedral  :  7.789  84.203   2252
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 12.56 %
    Favored  : 84.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.20 (0.18), residues: 1980
  helix:  1.20 (0.20), residues: 684
  sheet:  0.30 (0.30), residues: 272
  loop : -1.21 (0.18), residues: 1024

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 210 
 TYR   0.014   0.002   TYR A 489 
 PHE   0.021   0.002   PHE A 132 
 TRP   0.013   0.001   TRP D 183 
 HIS   0.005   0.001   HIS C 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 (16888)
  covalent geometry    : angle       0.59911 (23040)
  hydrogen bonds       : bond        0.04118 (  647)
  hydrogen bonds       : angle       5.23393 ( 1833)
  Misc. bond           : bond        0.05642 (    4)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 155
  time to evaluate  : 0.656 
Fit side-chains
REVERT: B  259 ASP cc_start: 0.7184 (p0) cc_final: 0.6802 (p0)
REVERT: B  321 ASN cc_start: 0.8852 (m-40) cc_final: 0.8589 (m-40)
REVERT: B  494 GLN cc_start: 0.8187 (tp40) cc_final: 0.7918 (tp-100)
REVERT: B  500 TYR cc_start: 0.7236 (OUTLIER) cc_final: 0.6688 (m-80)
REVERT: A  259 ASP cc_start: 0.7139 (p0) cc_final: 0.6775 (p0)
REVERT: A  500 TYR cc_start: 0.7268 (OUTLIER) cc_final: 0.6788 (m-80)
REVERT: C  259 ASP cc_start: 0.7221 (p0) cc_final: 0.6823 (p0)
REVERT: C  321 ASN cc_start: 0.8857 (m-40) cc_final: 0.8604 (m-40)
REVERT: C  494 GLN cc_start: 0.8170 (tp40) cc_final: 0.7880 (tp-100)
REVERT: C  500 TYR cc_start: 0.7302 (OUTLIER) cc_final: 0.6804 (m-80)
REVERT: D  236 TYR cc_start: 0.8951 (OUTLIER) cc_final: 0.8712 (p90)
REVERT: D  259 ASP cc_start: 0.7119 (p0) cc_final: 0.6770 (p0)
REVERT: D  494 GLN cc_start: 0.7983 (tp-100) cc_final: 0.7680 (tp-100)
REVERT: D  500 TYR cc_start: 0.7246 (OUTLIER) cc_final: 0.6736 (m-80)
  outliers start: 50
  outliers final: 36
  residues processed: 185
  average time/residue: 0.1260
  time to fit residues: 36.4472
Evaluate side-chains
  188 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 147
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 MET
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  152 ILE
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  500 TYR
Chi-restraints excluded: chain A residue   12 MET
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  202 ASP
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  483 THR
Chi-restraints excluded: chain A residue  500 TYR
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  152 ILE
Chi-restraints excluded: chain C residue  198 PHE
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  383 VAL
Chi-restraints excluded: chain C residue  423 ILE
Chi-restraints excluded: chain C residue  450 VAL
Chi-restraints excluded: chain C residue  497 LEU
Chi-restraints excluded: chain C residue  500 TYR
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain D residue  198 PHE
Chi-restraints excluded: chain D residue  202 ASP
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  323 VAL
Chi-restraints excluded: chain D residue  383 VAL
Chi-restraints excluded: chain D residue  423 ILE
Chi-restraints excluded: chain D residue  450 VAL
Chi-restraints excluded: chain D residue  500 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 145 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   chunk 72 optimal weight:    8.9990
   chunk 14 optimal weight:    0.8980
   chunk 135 optimal weight:    4.9990
   chunk 58 optimal weight:    6.9990
   chunk 101 optimal weight:    5.9990
   chunk 118 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 188 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    2.7786

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

Flipped N/Q/H residues before XYZ refinement:
B  33 ASN
** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  33 ASN
D  33 ASN
D 331 GLN
** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.109183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.084545 restraints weight = 26175.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.087141 restraints weight = 16290.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.088839 restraints weight = 12189.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.089876 restraints weight = 10184.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.090701 restraints weight = 9120.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.2167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.078  16892  Z= 0.204
  Angle     :  0.601   8.636  23040  Z= 0.307
  Chirality :  0.045   0.137   2328
  Planarity :  0.005   0.052   3052
  Dihedral  :  7.754  82.743   2252
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 13.03 %
    Favored  : 83.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.19 (0.18), residues: 1980
  helix:  1.15 (0.20), residues: 692
  sheet:  0.40 (0.30), residues: 268
  loop : -1.21 (0.18), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 210 
 TYR   0.014   0.002   TYR C 489 
 PHE   0.020   0.002   PHE A 100 
 TRP   0.014   0.001   TRP A 183 
 HIS   0.004   0.001   HIS D 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 (16888)
  covalent geometry    : angle       0.60082 (23040)
  hydrogen bonds       : bond        0.04093 (  647)
  hydrogen bonds       : angle       5.25349 ( 1833)
  Misc. bond           : bond        0.05447 (    4)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 148
  time to evaluate  : 0.676 
Fit side-chains
REVERT: B  259 ASP cc_start: 0.7216 (p0) cc_final: 0.6791 (p0)
REVERT: B  321 ASN cc_start: 0.8853 (m-40) cc_final: 0.8598 (m-40)
REVERT: B  494 GLN cc_start: 0.8168 (tp40) cc_final: 0.7773 (tp-100)
REVERT: B  500 TYR cc_start: 0.7270 (OUTLIER) cc_final: 0.6757 (m-80)
REVERT: A  259 ASP cc_start: 0.7143 (p0) cc_final: 0.6801 (p0)
REVERT: A  500 TYR cc_start: 0.7368 (OUTLIER) cc_final: 0.6892 (m-80)
REVERT: C  259 ASP cc_start: 0.7228 (p0) cc_final: 0.6816 (p0)
REVERT: C  321 ASN cc_start: 0.8860 (m-40) cc_final: 0.8586 (m-40)
REVERT: C  500 TYR cc_start: 0.7298 (OUTLIER) cc_final: 0.6792 (m-80)
REVERT: D  236 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.8723 (p90)
REVERT: D  259 ASP cc_start: 0.7128 (p0) cc_final: 0.6781 (p0)
REVERT: D  500 TYR cc_start: 0.7317 (OUTLIER) cc_final: 0.6833 (m-80)
  outliers start: 56
  outliers final: 39
  residues processed: 184
  average time/residue: 0.1276
  time to fit residues: 36.4574
Evaluate side-chains
  183 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 139
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 MET
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  152 ILE
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  500 TYR
Chi-restraints excluded: chain A residue   12 MET
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  483 THR
Chi-restraints excluded: chain A residue  500 TYR
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  152 ILE
Chi-restraints excluded: chain C residue  176 LEU
Chi-restraints excluded: chain C residue  198 PHE
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  383 VAL
Chi-restraints excluded: chain C residue  423 ILE
Chi-restraints excluded: chain C residue  450 VAL
Chi-restraints excluded: chain C residue  483 THR
Chi-restraints excluded: chain C residue  500 TYR
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain D residue  198 PHE
Chi-restraints excluded: chain D residue  202 ASP
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  323 VAL
Chi-restraints excluded: chain D residue  383 VAL
Chi-restraints excluded: chain D residue  423 ILE
Chi-restraints excluded: chain D residue  450 VAL
Chi-restraints excluded: chain D residue  483 THR
Chi-restraints excluded: chain D residue  500 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 181 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   chunk 153 optimal weight:    3.9990
   chunk 57 optimal weight:    4.9990
   chunk 155 optimal weight:    3.9990
   chunk 43 optimal weight:    7.9990
   chunk 163 optimal weight:    4.9990
   chunk 97 optimal weight:    8.9990
   chunk 21 optimal weight:    8.9990
   chunk 158 optimal weight:    9.9990
   chunk 101 optimal weight:    7.9990
   overall best weight:    3.3788

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

Flipped N/Q/H residues before XYZ refinement:
** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.111436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.087130 restraints weight = 25985.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.089739 restraints weight = 16216.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.091465 restraints weight = 12132.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.092483 restraints weight = 10127.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.092930 restraints weight = 9078.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.2205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.090  16892  Z= 0.242
  Angle     :  0.636   8.410  23040  Z= 0.328
  Chirality :  0.046   0.135   2328
  Planarity :  0.005   0.053   3052
  Dihedral  :  7.845  81.510   2252
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 13.73 %
    Favored  : 83.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.32 (0.18), residues: 1980
  helix:  1.08 (0.20), residues: 692
  sheet:  0.08 (0.29), residues: 284
  loop : -1.25 (0.18), residues: 1004

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 210 
 TYR   0.014   0.002   TYR A 489 
 PHE   0.021   0.002   PHE A 100 
 TRP   0.013   0.002   TRP B 183 
 HIS   0.005   0.001   HIS C 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00610 (16888)
  covalent geometry    : angle       0.63646 (23040)
  hydrogen bonds       : bond        0.04333 (  647)
  hydrogen bonds       : angle       5.38656 ( 1833)
  Misc. bond           : bond        0.07112 (    4)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 148
  time to evaluate  : 0.714 
Fit side-chains
REVERT: B  259 ASP cc_start: 0.7186 (p0) cc_final: 0.6766 (p0)
REVERT: B  321 ASN cc_start: 0.8849 (m-40) cc_final: 0.8600 (m-40)
REVERT: B  500 TYR cc_start: 0.7282 (OUTLIER) cc_final: 0.6728 (m-80)
REVERT: A  236 TYR cc_start: 0.8959 (OUTLIER) cc_final: 0.8741 (p90)
REVERT: A  259 ASP cc_start: 0.7150 (p0) cc_final: 0.6791 (p0)
REVERT: A  500 TYR cc_start: 0.7336 (OUTLIER) cc_final: 0.6879 (m-80)
REVERT: C  259 ASP cc_start: 0.7241 (p0) cc_final: 0.6810 (p0)
REVERT: C  321 ASN cc_start: 0.8852 (m-40) cc_final: 0.8596 (m-40)
REVERT: C  500 TYR cc_start: 0.7343 (OUTLIER) cc_final: 0.6837 (m-80)
REVERT: D  236 TYR cc_start: 0.8936 (OUTLIER) cc_final: 0.8702 (p90)
REVERT: D  259 ASP cc_start: 0.7139 (p0) cc_final: 0.6688 (p0)
REVERT: D  500 TYR cc_start: 0.7403 (OUTLIER) cc_final: 0.6884 (m-80)
  outliers start: 51
  outliers final: 39
  residues processed: 182
  average time/residue: 0.1363
  time to fit residues: 37.4826
Evaluate side-chains
  187 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 142
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 MET
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  152 ILE
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  500 TYR
Chi-restraints excluded: chain A residue   12 MET
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  483 THR
Chi-restraints excluded: chain A residue  500 TYR
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  152 ILE
Chi-restraints excluded: chain C residue  176 LEU
Chi-restraints excluded: chain C residue  198 PHE
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  383 VAL
Chi-restraints excluded: chain C residue  423 ILE
Chi-restraints excluded: chain C residue  450 VAL
Chi-restraints excluded: chain C residue  483 THR
Chi-restraints excluded: chain C residue  500 TYR
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain D residue  176 LEU
Chi-restraints excluded: chain D residue  198 PHE
Chi-restraints excluded: chain D residue  202 ASP
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  323 VAL
Chi-restraints excluded: chain D residue  383 VAL
Chi-restraints excluded: chain D residue  423 ILE
Chi-restraints excluded: chain D residue  440 VAL
Chi-restraints excluded: chain D residue  450 VAL
Chi-restraints excluded: chain D residue  500 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 72 optimal weight:    7.9990
   chunk 172 optimal weight:    1.9990
   chunk 116 optimal weight:    2.9990
   chunk 51 optimal weight:    8.9990
   chunk 128 optimal weight:    8.9990
   chunk 149 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 141 optimal weight:    3.9990
   chunk 183 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 124 optimal weight:    4.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.110186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.085811 restraints weight = 26029.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.088467 restraints weight = 16140.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.090136 restraints weight = 12007.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.091274 restraints weight = 10044.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.091920 restraints weight = 8952.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069  16892  Z= 0.172
  Angle     :  0.596   8.216  23040  Z= 0.305
  Chirality :  0.044   0.133   2328
  Planarity :  0.005   0.051   3052
  Dihedral  :  7.648  80.168   2252
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 14.02 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.19), residues: 1980
  helix:  1.16 (0.20), residues: 692
  sheet:  0.25 (0.30), residues: 280
  loop : -1.22 (0.18), residues: 1008

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  68 
 TYR   0.013   0.001   TYR C 489 
 PHE   0.017   0.002   PHE D 132 
 TRP   0.014   0.001   TRP B 183 
 HIS   0.004   0.001   HIS C 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 (16888)
  covalent geometry    : angle       0.59578 (23040)
  hydrogen bonds       : bond        0.03860 (  647)
  hydrogen bonds       : angle       5.23499 ( 1833)
  Misc. bond           : bond        0.03623 (    4)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 146
  time to evaluate  : 0.687 
Fit side-chains
REVERT: B  236 TYR cc_start: 0.8932 (OUTLIER) cc_final: 0.8730 (p90)
REVERT: B  259 ASP cc_start: 0.7201 (p0) cc_final: 0.6768 (p0)
REVERT: B  321 ASN cc_start: 0.8841 (m-40) cc_final: 0.8577 (m-40)
REVERT: B  394 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6705 (ttt)
REVERT: B  500 TYR cc_start: 0.7260 (OUTLIER) cc_final: 0.6799 (m-80)
REVERT: A  259 ASP cc_start: 0.7106 (p0) cc_final: 0.6757 (p0)
REVERT: A  394 MET cc_start: 0.8080 (mmm) cc_final: 0.7263 (mmp)
REVERT: A  494 GLN cc_start: 0.7919 (tp-100) cc_final: 0.7649 (tp-100)
REVERT: A  500 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.6844 (m-80)
REVERT: C  236 TYR cc_start: 0.8924 (OUTLIER) cc_final: 0.8708 (p90)
REVERT: C  259 ASP cc_start: 0.7199 (p0) cc_final: 0.6794 (p0)
REVERT: C  321 ASN cc_start: 0.8845 (m-40) cc_final: 0.8584 (m-40)
REVERT: C  500 TYR cc_start: 0.7363 (OUTLIER) cc_final: 0.6856 (m-80)
REVERT: D  236 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.8695 (p90)
REVERT: D  259 ASP cc_start: 0.7077 (p0) cc_final: 0.6628 (p0)
REVERT: D  500 TYR cc_start: 0.7349 (OUTLIER) cc_final: 0.6892 (m-80)
  outliers start: 48
  outliers final: 35
  residues processed: 175
  average time/residue: 0.1282
  time to fit residues: 35.0437
Evaluate side-chains
  186 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 143
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 MET
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  152 ILE
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  394 MET
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  500 TYR
Chi-restraints excluded: chain A residue   12 MET
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  483 THR
Chi-restraints excluded: chain A residue  500 TYR
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  152 ILE
Chi-restraints excluded: chain C residue  176 LEU
Chi-restraints excluded: chain C residue  198 PHE
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  383 VAL
Chi-restraints excluded: chain C residue  423 ILE
Chi-restraints excluded: chain C residue  450 VAL
Chi-restraints excluded: chain C residue  500 TYR
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain D residue  198 PHE
Chi-restraints excluded: chain D residue  202 ASP
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  383 VAL
Chi-restraints excluded: chain D residue  423 ILE
Chi-restraints excluded: chain D residue  440 VAL
Chi-restraints excluded: chain D residue  450 VAL
Chi-restraints excluded: chain D residue  500 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 118 optimal weight:    1.9990
   chunk 193 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 114 optimal weight:    0.8980
   chunk 159 optimal weight:    9.9990
   chunk 127 optimal weight:    1.9990
   chunk 133 optimal weight:    2.9990
   chunk 172 optimal weight:    3.9990
   chunk 174 optimal weight:    3.9990
   chunk 157 optimal weight:    6.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  33 ASN
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 331 GLN
D 424 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.114285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.090211 restraints weight = 25731.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.092933 restraints weight = 15780.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.094710 restraints weight = 11647.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.095835 restraints weight = 9640.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.096416 restraints weight = 8580.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.2304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  16892  Z= 0.129
  Angle     :  0.567   7.806  23040  Z= 0.287
  Chirality :  0.042   0.136   2328
  Planarity :  0.004   0.050   3052
  Dihedral  :  7.452  78.528   2252
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 14.54 %
    Favored  : 82.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.19), residues: 1980
  helix:  1.31 (0.20), residues: 692
  sheet:  0.33 (0.30), residues: 284
  loop : -1.11 (0.19), residues: 1004

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  68 
 TYR   0.012   0.001   TYR A 489 
 PHE   0.017   0.001   PHE D 132 
 TRP   0.013   0.001   TRP A 183 
 HIS   0.004   0.001   HIS D 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (16888)
  covalent geometry    : angle       0.56710 (23040)
  hydrogen bonds       : bond        0.03455 (  647)
  hydrogen bonds       : angle       5.06696 ( 1833)
  Misc. bond           : bond        0.01027 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2304.72 seconds
wall clock time: 40 minutes 58.90 seconds (2458.90 seconds total)