Starting phenix.real_space_refine
on Sat Jun 14 18:11:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wzj_37954/06_2025/8wzj_37954.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wzj_37954/06_2025/8wzj_37954.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wzj_37954/06_2025/8wzj_37954.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wzj_37954/06_2025/8wzj_37954.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wzj_37954/06_2025/8wzj_37954.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wzj_37954/06_2025/8wzj_37954.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.012
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 44 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 16368
  Number of models: 1
  Model: ""
    Number of chains: 2
    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: "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}
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 8.82, per 1000 atoms: 0.54
  Number of scatterers: 16368
  At special positions: 0
  Unit cell: (108.07, 114.49, 84.53, 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: 4.10
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  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:
      76 helices and 8 sheets defined
      39.0% alpha, 15.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.94
  Creating SS restraints...
    Processing helix  chain 'B' and resid 10 through 19
    Processing helix  chain 'B' and resid 54 through 65
    Processing helix  chain 'B' and resid 97 through 101
    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
    Processing helix  chain 'B' and resid 192 through 201
    Processing helix  chain 'B' and resid 202 through 205
      removed outlier: 3.657A  pdb=" N   ILE B 205 " --> pdb=" O   ASP B 202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 202 through 205'
    Processing helix  chain 'B' and resid 246 through 257
      removed outlier: 3.893A  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: 3.915A  pdb=" N   PHE B 356 " --> pdb=" O   GLN B 352 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   TYR B 358 " --> pdb=" O   ARG B 354 " (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: 3.650A  pdb=" N   LEU B 419 " --> pdb=" O   PRO B 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 440 through 450
    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 10 through 19
    Processing helix  chain 'A' and resid 54 through 65
    Processing helix  chain 'A' and resid 97 through 101
    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
    Processing helix  chain 'A' and resid 192 through 201
    Processing helix  chain 'A' and resid 202 through 205
      removed outlier: 3.657A  pdb=" N   ILE A 205 " --> pdb=" O   ASP A 202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 202 through 205'
    Processing helix  chain 'A' and resid 246 through 257
      removed outlier: 3.894A  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 329
    Processing helix  chain 'A' and resid 348 through 366
      removed outlier: 3.914A  pdb=" N   PHE A 356 " --> pdb=" O   GLN A 352 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   TYR A 358 " --> pdb=" O   ARG A 354 " (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: 3.649A  pdb=" N   LEU A 419 " --> pdb=" O   PRO A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 450
    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 10 through 19
    Processing helix  chain 'C' and resid 54 through 65
    Processing helix  chain 'C' and resid 97 through 101
    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
    Processing helix  chain 'C' and resid 192 through 201
    Processing helix  chain 'C' and resid 202 through 205
      removed outlier: 3.658A  pdb=" N   ILE C 205 " --> pdb=" O   ASP C 202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 202 through 205'
    Processing helix  chain 'C' and resid 246 through 257
      removed outlier: 3.894A  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 329
    Processing helix  chain 'C' and resid 348 through 366
      removed outlier: 3.914A  pdb=" N   PHE C 356 " --> pdb=" O   GLN C 352 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   TYR C 358 " --> pdb=" O   ARG C 354 " (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: 3.650A  pdb=" N   LEU C 419 " --> pdb=" O   PRO C 416 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 440 through 450
    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 10 through 19
    Processing helix  chain 'D' and resid 54 through 65
    Processing helix  chain 'D' and resid 97 through 101
    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
    Processing helix  chain 'D' and resid 192 through 201
    Processing helix  chain 'D' and resid 202 through 205
      removed outlier: 3.658A  pdb=" N   ILE D 205 " --> pdb=" O   ASP D 202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 202 through 205'
    Processing helix  chain 'D' and resid 246 through 257
      removed outlier: 3.894A  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 329
    Processing helix  chain 'D' and resid 348 through 366
      removed outlier: 3.914A  pdb=" N   PHE D 356 " --> pdb=" O   GLN D 352 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   TYR D 358 " --> pdb=" O   ARG D 354 " (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: 3.650A  pdb=" N   LEU D 419 " --> pdb=" O   PRO D 416 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 440 through 450
    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
    Processing sheet with id=AA2, first strand: chain 'B' and resid 343 through 345
      removed outlier: 5.988A  pdb=" N   ILE B 281 " --> pdb=" O   PRO B 312 " (cutoff:3.500A)
      removed outlier: 5.660A  pdb=" N   LEU B 316 " --> pdb=" O   GLU B  86 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   GLU B  86 " --> pdb=" O   LEU B 316 " (cutoff:3.500A)
      removed outlier: 5.381A  pdb=" N   LEU B 318 " --> pdb=" O   TYR B  84 " (cutoff:3.500A)
      removed outlier: 7.163A  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
    Processing sheet with id=AA4, first strand: chain 'A' and resid 42 through 44
    Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 345
      removed outlier: 5.987A  pdb=" N   ILE A 281 " --> pdb=" O   PRO A 312 " (cutoff:3.500A)
      removed outlier: 5.659A  pdb=" N   LEU A 316 " --> pdb=" O   GLU A  86 " (cutoff:3.500A)
      removed outlier: 7.302A  pdb=" N   GLU A  86 " --> pdb=" O   LEU A 316 " (cutoff:3.500A)
      removed outlier: 5.382A  pdb=" N   LEU A 318 " --> pdb=" O   TYR A  84 " (cutoff:3.500A)
      removed outlier: 7.163A  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
    Processing sheet with id=AA7, first strand: chain 'C' and resid 343 through 345
      removed outlier: 5.987A  pdb=" N   ILE C 281 " --> pdb=" O   PRO C 312 " (cutoff:3.500A)
      removed outlier: 5.660A  pdb=" N   LEU C 316 " --> pdb=" O   GLU C  86 " (cutoff:3.500A)
      removed outlier: 7.302A  pdb=" N   GLU C  86 " --> pdb=" O   LEU C 316 " (cutoff:3.500A)
      removed outlier: 5.381A  pdb=" N   LEU C 318 " --> pdb=" O   TYR C  84 " (cutoff:3.500A)
      removed outlier: 7.163A  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 345
      removed outlier: 5.988A  pdb=" N   ILE D 281 " --> pdb=" O   PRO D 312 " (cutoff:3.500A)
      removed outlier: 5.660A  pdb=" N   LEU D 316 " --> pdb=" O   GLU D  86 " (cutoff:3.500A)
      removed outlier: 7.302A  pdb=" N   GLU D  86 " --> pdb=" O   LEU D 316 " (cutoff:3.500A)
      removed outlier: 5.382A  pdb=" N   LEU D 318 " --> pdb=" O   TYR D  84 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   TYR D  84 " --> pdb=" O   LEU D 318 " (cutoff:3.500A)

    656 hydrogen bonds defined for protein.
    1872 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 5.04

  Time building geometry restraints manager: 4.83 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: 6777
        1.39 -     1.57: 9987
        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  1.621  0.212 3.80e-02 6.93e+02 3.10e+01
  bond pdb=" O2B NDP B3002 "
       pdb=" P2B NDP B3002 "
    ideal  model  delta    sigma   weight residual
    1.833  1.622  0.211 3.80e-02 6.93e+02 3.09e+01
  bond pdb=" O2B NDP C3002 "
       pdb=" P2B NDP C3002 "
    ideal  model  delta    sigma   weight residual
    1.833  1.622  0.211 3.80e-02 6.93e+02 3.09e+01
  bond pdb=" O2B NDP A3002 "
       pdb=" P2B NDP A3002 "
    ideal  model  delta    sigma   weight residual
    1.833  1.622  0.211 3.80e-02 6.93e+02 3.08e+01
  bond pdb=" O5D NDP A3002 "
       pdb=" PN  NDP A3002 "
    ideal  model  delta    sigma   weight residual
    1.757  1.602  0.155 3.50e-02 8.16e+02 1.95e+01
  ... (remaining 16883 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.73: 22912
        4.73 -     9.45: 104
        9.45 -    14.18: 12
       14.18 -    18.91: 8
       18.91 -    23.63: 4
  Bond angle restraints: 23040
  Sorted by residual:
  angle pdb=" PA  NDP C3002 "
        pdb=" O3  NDP C3002 "
        pdb=" PN  NDP C3002 "
      ideal   model   delta    sigma   weight residual
     107.74  131.37  -23.63 1.95e+00 2.62e-01 1.46e+02
  angle pdb=" PA  NDP D3002 "
        pdb=" O3  NDP D3002 "
        pdb=" PN  NDP D3002 "
      ideal   model   delta    sigma   weight residual
     107.74  131.36  -23.62 1.95e+00 2.62e-01 1.46e+02
  angle pdb=" PA  NDP A3002 "
        pdb=" O3  NDP A3002 "
        pdb=" PN  NDP A3002 "
      ideal   model   delta    sigma   weight residual
     107.74  131.33  -23.59 1.95e+00 2.62e-01 1.46e+02
  angle pdb=" PA  NDP B3002 "
        pdb=" O3  NDP B3002 "
        pdb=" PN  NDP B3002 "
      ideal   model   delta    sigma   weight residual
     107.74  131.33  -23.59 1.95e+00 2.62e-01 1.46e+02
  angle pdb=" C5B NDP C3002 "
        pdb=" O5B NDP C3002 "
        pdb=" PA  NDP C3002 "
      ideal   model   delta    sigma   weight residual
     103.84  120.50  -16.66 1.91e+00 2.73e-01 7.57e+01
  ... (remaining 23035 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.88: 9054
       18.88 -    37.76: 622
       37.76 -    56.64: 124
       56.64 -    75.52: 48
       75.52 -    94.40: 12
  Dihedral angle restraints: 9860
    sinusoidal: 4080
      harmonic: 5780
  Sorted by residual:
  dihedral pdb=" CA  ASP C 389 "
           pdb=" C   ASP C 389 "
           pdb=" N   GLY C 390 "
           pdb=" CA  GLY C 390 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.93   21.07     0      5.00e+00 4.00e-02 1.78e+01
  dihedral pdb=" CA  ASP D 389 "
           pdb=" C   ASP D 389 "
           pdb=" N   GLY D 390 "
           pdb=" CA  GLY D 390 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.94   21.06     0      5.00e+00 4.00e-02 1.77e+01
  dihedral pdb=" CA  ASP A 389 "
           pdb=" C   ASP A 389 "
           pdb=" N   GLY A 390 "
           pdb=" CA  GLY A 390 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.97   21.03     0      5.00e+00 4.00e-02 1.77e+01
  ... (remaining 9857 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 932
       0.045 -    0.090: 777
       0.090 -    0.136: 466
       0.136 -    0.181: 142
       0.181 -    0.226: 11
  Chirality restraints: 2328
  Sorted by residual:
  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   -2.49   -0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" C4D NDP B3002 "
            pdb=" C3D NDP B3002 "
            pdb=" C5D NDP B3002 "
            pdb=" O4D NDP B3002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.71   -2.49   -0.22 2.00e-01 2.50e+01 1.24e+00
  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   -2.49   -0.22 2.00e-01 2.50e+01 1.24e+00
  ... (remaining 2325 not shown)

  Planarity restraints: 3052
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2N NDP A3002 "   -0.054 2.00e-02 2.50e+03   3.42e-02 1.46e+01
        pdb=" C3N NDP A3002 "   -0.012 2.00e-02 2.50e+03
        pdb=" C4N NDP A3002 "   -0.007 2.00e-02 2.50e+03
        pdb=" C7N NDP A3002 "    0.030 2.00e-02 2.50e+03
        pdb=" N1N NDP A3002 "    0.043 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1C HEM B3001 "    0.044 2.00e-02 2.50e+03   2.54e-02 1.46e+01
        pdb=" C2C HEM B3001 "    0.023 2.00e-02 2.50e+03
        pdb=" C3C HEM B3001 "    0.013 2.00e-02 2.50e+03
        pdb=" C4C HEM B3001 "    0.003 2.00e-02 2.50e+03
        pdb=" CAC HEM B3001 "   -0.027 2.00e-02 2.50e+03
        pdb=" CHC HEM B3001 "   -0.049 2.00e-02 2.50e+03
        pdb=" CHD HEM B3001 "   -0.008 2.00e-02 2.50e+03
        pdb=" CMC HEM B3001 "   -0.001 2.00e-02 2.50e+03
        pdb=" NC  HEM B3001 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2N NDP D3002 "    0.054 2.00e-02 2.50e+03   3.41e-02 1.45e+01
        pdb=" C3N NDP D3002 "    0.012 2.00e-02 2.50e+03
        pdb=" C4N NDP D3002 "    0.007 2.00e-02 2.50e+03
        pdb=" C7N NDP D3002 "   -0.030 2.00e-02 2.50e+03
        pdb=" N1N NDP D3002 "   -0.043 2.00e-02 2.50e+03
  ... (remaining 3049 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.87: 5036
        2.87 -     3.38: 15764
        3.38 -     3.89: 30616
        3.89 -     4.39: 35341
        4.39 -     4.90: 58001
  Nonbonded interactions: 144758
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP D 298 "
            pdb=" OG1 THR D 300 "
     model   vdw
     2.368 3.040
  nonbonded pdb=" OD1 ASP C 298 "
            pdb=" OG1 THR C 300 "
     model   vdw
     2.368 3.040
  nonbonded pdb=" OD1 ASP B 298 "
            pdb=" OG1 THR B 300 "
     model   vdw
     2.368 3.040
  nonbonded pdb=" OD1 ASP A 298 "
            pdb=" OG1 THR A 300 "
     model   vdw
     2.369 3.040
  nonbonded pdb=" O   ARG A 388 "
            pdb=" O   ASP A 389 "
     model   vdw
     2.369 3.040
  ... (remaining 144753 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: 0.12
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.830
  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:          0.610
  Check model and map are aligned:         0.110
  Set scattering table:                    0.160
  Process input model:                     37.070
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.060
  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:12.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7035
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      :  0.014   0.212  16892  Z= 0.949
  Angle     :  1.675  23.631  23040  Z= 1.177
  Chirality :  0.076   0.226   2328
  Planarity :  0.005   0.035   3052
  Dihedral  : 14.337  94.395   6148
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 1.63
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.04 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  4.38 %
    Favored  : 94.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.17), residues: 1980
  helix: -0.22 (0.17), residues: 680
  sheet: -0.64 (0.29), residues: 276
  loop : -1.11 (0.17), residues: 1024

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.004   TRP A  15 
 HIS   0.014   0.003   HIS C 218 
 PHE   0.031   0.004   PHE D 334 
 TYR   0.025   0.004   TYR D 236 
 ARG   0.022   0.002   ARG B  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18097 (  656)
  hydrogen bonds       : angle       8.51332 ( 1872)
  covalent geometry    : bond        0.01399 (16888)
  covalent geometry    : angle       1.67513 (23040)
  Misc. bond           : bond        0.01034 (    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
  330 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 313
  time to evaluate  : 1.759 
Fit side-chains
REVERT: B  106 LYS cc_start: 0.7418 (mttt) cc_final: 0.7085 (mtmt)
REVERT: B  201 SER cc_start: 0.7911 (t) cc_final: 0.7677 (p)
REVERT: B  249 ASP cc_start: 0.6827 (m-30) cc_final: 0.6553 (t0)
REVERT: B  255 GLN cc_start: 0.7417 (pt0) cc_final: 0.7117 (pp30)
REVERT: B  392 MET cc_start: 0.8519 (mmm) cc_final: 0.7934 (mmm)
REVERT: B  394 MET cc_start: 0.6569 (mpp) cc_final: 0.5721 (mpp)
REVERT: B  428 GLU cc_start: 0.6028 (mp0) cc_final: 0.5637 (mp0)
REVERT: B  457 LYS cc_start: 0.7312 (ttpt) cc_final: 0.6825 (ttmm)
REVERT: B  476 LYS cc_start: 0.7055 (mttp) cc_final: 0.6851 (mptp)
REVERT: B  488 ASP cc_start: 0.6799 (m-30) cc_final: 0.6400 (m-30)
REVERT: B  492 HIS cc_start: 0.7138 (t-170) cc_final: 0.6854 (t-90)
REVERT: B  499 LYS cc_start: 0.7043 (tttp) cc_final: 0.6351 (ttpp)
REVERT: A  106 LYS cc_start: 0.7400 (mttt) cc_final: 0.7081 (mtmt)
REVERT: A  201 SER cc_start: 0.7911 (t) cc_final: 0.7666 (p)
REVERT: A  249 ASP cc_start: 0.6832 (m-30) cc_final: 0.6555 (t0)
REVERT: A  255 GLN cc_start: 0.7409 (pt0) cc_final: 0.7119 (pp30)
REVERT: A  392 MET cc_start: 0.8524 (mmm) cc_final: 0.8113 (mmm)
REVERT: A  394 MET cc_start: 0.6546 (mpp) cc_final: 0.5724 (mpp)
REVERT: A  428 GLU cc_start: 0.6063 (mp0) cc_final: 0.5676 (mp0)
REVERT: A  457 LYS cc_start: 0.7133 (ttpt) cc_final: 0.6706 (ttmm)
REVERT: A  476 LYS cc_start: 0.7000 (mttp) cc_final: 0.6791 (mptp)
REVERT: A  492 HIS cc_start: 0.7173 (t-170) cc_final: 0.6951 (t-90)
REVERT: A  499 LYS cc_start: 0.7029 (tttp) cc_final: 0.6343 (ttpp)
REVERT: C  106 LYS cc_start: 0.7398 (mttt) cc_final: 0.7079 (mtmt)
REVERT: C  201 SER cc_start: 0.7918 (t) cc_final: 0.7669 (p)
REVERT: C  249 ASP cc_start: 0.6807 (m-30) cc_final: 0.6536 (t0)
REVERT: C  255 GLN cc_start: 0.7407 (pt0) cc_final: 0.7173 (pp30)
REVERT: C  392 MET cc_start: 0.8514 (mmm) cc_final: 0.8103 (mmm)
REVERT: C  394 MET cc_start: 0.6454 (mpp) cc_final: 0.5673 (mpp)
REVERT: C  428 GLU cc_start: 0.6082 (mp0) cc_final: 0.5711 (mp0)
REVERT: C  457 LYS cc_start: 0.7138 (ttpt) cc_final: 0.6681 (ttmm)
REVERT: C  471 GLN cc_start: 0.7281 (mt0) cc_final: 0.7031 (mt0)
REVERT: C  476 LYS cc_start: 0.6905 (mttp) cc_final: 0.6699 (mptp)
REVERT: C  488 ASP cc_start: 0.6795 (m-30) cc_final: 0.6385 (m-30)
REVERT: C  492 HIS cc_start: 0.7136 (t-170) cc_final: 0.6842 (t-90)
REVERT: C  499 LYS cc_start: 0.7039 (tttp) cc_final: 0.6352 (ttpp)
REVERT: D  106 LYS cc_start: 0.7363 (mttt) cc_final: 0.7028 (mtmt)
REVERT: D  201 SER cc_start: 0.7915 (t) cc_final: 0.7679 (p)
REVERT: D  249 ASP cc_start: 0.6802 (m-30) cc_final: 0.6536 (t0)
REVERT: D  255 GLN cc_start: 0.7407 (pt0) cc_final: 0.7147 (pp30)
REVERT: D  392 MET cc_start: 0.8510 (mmm) cc_final: 0.7908 (mmm)
REVERT: D  394 MET cc_start: 0.6578 (mpp) cc_final: 0.5721 (mpp)
REVERT: D  428 GLU cc_start: 0.6063 (mp0) cc_final: 0.5691 (mp0)
REVERT: D  457 LYS cc_start: 0.7340 (ttpt) cc_final: 0.6866 (ttmm)
REVERT: D  471 GLN cc_start: 0.7287 (mt0) cc_final: 0.7042 (mt0)
REVERT: D  488 ASP cc_start: 0.6797 (m-30) cc_final: 0.6389 (m-30)
REVERT: D  492 HIS cc_start: 0.7194 (t-170) cc_final: 0.6914 (t-90)
REVERT: D  499 LYS cc_start: 0.7105 (tttp) cc_final: 0.6406 (ttpp)
  outliers start: 17
  outliers final: 4
  residues processed: 321
  average time/residue: 1.6299
  time to fit residues: 569.0217
Evaluate side-chains
  183 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 179
  time to evaluate  : 2.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain D residue  236 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 165 optimal weight:    0.9980
   chunk 148 optimal weight:    9.9990
   chunk 82 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 153 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9980
   chunk 93 optimal weight:    5.9990
   chunk 114 optimal weight:    0.9990
   chunk 177 optimal weight:    2.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
B  22 GLN
B 226 ASN
B 338 ASN
B 407 ASN
A  22 GLN
A 102 HIS
A 226 ASN
A 338 ASN
A 407 ASN
C  22 GLN
C 102 HIS
C 226 ASN
C 338 ASN
C 407 ASN
D  22 GLN
D 226 ASN
D 338 ASN
D 407 ASN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.130827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.110675 restraints weight = 18922.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 1.30
r_work: 0.3115 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  16892  Z= 0.136
  Angle     :  0.583   5.965  23040  Z= 0.299
  Chirality :  0.045   0.147   2328
  Planarity :  0.004   0.035   3052
  Dihedral  :  8.783 114.133   2260
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 10.51 %
    Favored  : 87.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.18), residues: 1980
  helix:  1.03 (0.20), residues: 688
  sheet:  0.32 (0.31), residues: 284
  loop : -0.34 (0.19), residues: 1008

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP C 303 
 HIS   0.005   0.001   HIS A 102 
 PHE   0.013   0.002   PHE C  57 
 TYR   0.017   0.001   TYR C 236 
 ARG   0.003   0.001   ARG C 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04707 (  656)
  hydrogen bonds       : angle       5.93537 ( 1872)
  covalent geometry    : bond        0.00336 (16888)
  covalent geometry    : angle       0.58280 (23040)
  Misc. bond           : bond        0.01836 (    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
  216 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 190
  time to evaluate  : 1.760 
Fit side-chains
REVERT: B   19 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.6773 (ttm-80)
REVERT: B  389 ASP cc_start: 0.6985 (OUTLIER) cc_final: 0.6425 (m-30)
REVERT: B  476 LYS cc_start: 0.8168 (mttp) cc_final: 0.7950 (mtpp)
REVERT: B  499 LYS cc_start: 0.7689 (tttp) cc_final: 0.7168 (ttpp)
REVERT: A   19 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.6761 (ttm-80)
REVERT: A  107 THR cc_start: 0.8112 (m) cc_final: 0.7753 (t)
REVERT: A  389 ASP cc_start: 0.7006 (OUTLIER) cc_final: 0.6553 (m-30)
REVERT: A  476 LYS cc_start: 0.8172 (mttp) cc_final: 0.7966 (mtpp)
REVERT: A  499 LYS cc_start: 0.7685 (tttp) cc_final: 0.7155 (ttpp)
REVERT: C   19 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.6771 (ttm-80)
REVERT: C  107 THR cc_start: 0.8113 (m) cc_final: 0.7759 (t)
REVERT: C  389 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6545 (m-30)
REVERT: C  476 LYS cc_start: 0.8131 (mttp) cc_final: 0.7916 (mtpp)
REVERT: C  499 LYS cc_start: 0.7633 (tttp) cc_final: 0.7149 (ttpp)
REVERT: D   19 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.6773 (ttm-80)
REVERT: D  389 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6419 (m-30)
REVERT: D  499 LYS cc_start: 0.7637 (tttp) cc_final: 0.7151 (ttpp)
  outliers start: 26
  outliers final: 8
  residues processed: 212
  average time/residue: 1.4062
  time to fit residues: 329.0058
Evaluate side-chains
  165 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 149
  time to evaluate  : 1.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain A residue   19 ARG
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain C residue   19 ARG
Chi-restraints excluded: chain C residue  180 ASP
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  389 ASP
Chi-restraints excluded: chain D residue   19 ARG
Chi-restraints excluded: chain D residue  180 ASP
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  389 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 34 optimal weight:    7.9990
   chunk 50 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9990
   chunk 42 optimal weight:    8.9990
   chunk 147 optimal weight:    3.9990
   chunk 182 optimal weight:    4.9990
   chunk 163 optimal weight:    6.9990
   chunk 117 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 179 optimal weight:    6.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
B  63 HIS
B 226 ASN
B 338 ASN
B 369 ASN
A  63 HIS
A 102 HIS
A 226 ASN
A 338 ASN
A 369 ASN
C  63 HIS
C 102 HIS
C 226 ASN
C 338 ASN
C 369 ASN
D  63 HIS
D 226 ASN
D 338 ASN
D 369 ASN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.125393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.104968 restraints weight = 19074.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 1.32
r_work: 0.3025 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.2914 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.2522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.080  16892  Z= 0.248
  Angle     :  0.689   7.752  23040  Z= 0.349
  Chirality :  0.049   0.153   2328
  Planarity :  0.005   0.041   3052
  Dihedral  :  9.692 135.254   2260
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.43 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 11.04 %
    Favored  : 86.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.18), residues: 1980
  helix:  0.73 (0.20), residues: 684
  sheet:  0.54 (0.32), residues: 272
  loop : -0.40 (0.19), residues: 1024

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D 183 
 HIS   0.007   0.002   HIS C 372 
 PHE   0.015   0.003   PHE C 136 
 TYR   0.021   0.002   TYR B 236 
 ARG   0.004   0.001   ARG D 382 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05788 (  656)
  hydrogen bonds       : angle       6.18463 ( 1872)
  covalent geometry    : bond        0.00626 (16888)
  covalent geometry    : angle       0.68910 (23040)
  Misc. bond           : bond        0.03432 (    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
  206 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 162
  time to evaluate  : 1.994 
Fit side-chains
REVERT: B   12 MET cc_start: 0.8641 (mtm) cc_final: 0.8275 (mtm)
REVERT: B   19 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7003 (ttm-80)
REVERT: B  101 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7603 (tp30)
REVERT: B  107 THR cc_start: 0.8260 (m) cc_final: 0.7863 (t)
REVERT: B  191 GLU cc_start: 0.8122 (pm20) cc_final: 0.7920 (pm20)
REVERT: B  424 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.6811 (tm-30)
REVERT: B  437 ASP cc_start: 0.7401 (m-30) cc_final: 0.6824 (m-30)
REVERT: B  499 LYS cc_start: 0.7761 (tttp) cc_final: 0.7242 (ttpp)
REVERT: A   12 MET cc_start: 0.8641 (mtm) cc_final: 0.8221 (mtm)
REVERT: A   19 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.6938 (ttm-80)
REVERT: A  101 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7591 (tp30)
REVERT: A  107 THR cc_start: 0.8269 (m) cc_final: 0.7857 (t)
REVERT: A  424 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.6799 (tm-30)
REVERT: A  437 ASP cc_start: 0.7388 (m-30) cc_final: 0.7015 (m-30)
REVERT: A  499 LYS cc_start: 0.7772 (tttp) cc_final: 0.7247 (ttpp)
REVERT: C   12 MET cc_start: 0.8647 (mtm) cc_final: 0.8267 (mtm)
REVERT: C   19 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.6950 (ttm-80)
REVERT: C  101 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7603 (tp30)
REVERT: C  107 THR cc_start: 0.8259 (m) cc_final: 0.7855 (t)
REVERT: C  437 ASP cc_start: 0.7424 (m-30) cc_final: 0.7062 (m-30)
REVERT: C  499 LYS cc_start: 0.7743 (tttp) cc_final: 0.7248 (ttpp)
REVERT: D   12 MET cc_start: 0.8653 (mtm) cc_final: 0.8289 (mtm)
REVERT: D   19 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.6986 (ttm-80)
REVERT: D  101 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7583 (tp30)
REVERT: D  107 THR cc_start: 0.8262 (m) cc_final: 0.7854 (t)
REVERT: D  191 GLU cc_start: 0.8137 (pm20) cc_final: 0.7937 (pm20)
REVERT: D  424 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.6809 (tm-30)
REVERT: D  437 ASP cc_start: 0.7390 (m-30) cc_final: 0.7014 (m-30)
REVERT: D  499 LYS cc_start: 0.7768 (tttp) cc_final: 0.7245 (ttpp)
  outliers start: 44
  outliers final: 18
  residues processed: 194
  average time/residue: 1.3559
  time to fit residues: 291.4239
Evaluate side-chains
  174 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 145
  time to evaluate  : 1.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  344 GLU
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain B residue  424 GLN
Chi-restraints excluded: chain A residue   19 ARG
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  424 GLN
Chi-restraints excluded: chain C residue   19 ARG
Chi-restraints excluded: chain C residue  101 GLU
Chi-restraints excluded: chain C residue  128 ASP
Chi-restraints excluded: chain C residue  180 ASP
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  344 GLU
Chi-restraints excluded: chain C residue  389 ASP
Chi-restraints excluded: chain D residue   19 ARG
Chi-restraints excluded: chain D residue  101 GLU
Chi-restraints excluded: chain D residue  128 ASP
Chi-restraints excluded: chain D residue  180 ASP
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  344 GLU
Chi-restraints excluded: chain D residue  389 ASP
Chi-restraints excluded: chain D residue  424 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 149 optimal weight:    0.9980
   chunk 49 optimal weight:    5.9990
   chunk 161 optimal weight:    0.8980
   chunk 108 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   chunk 135 optimal weight:    2.9990
   chunk 189 optimal weight:    9.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
B 226 ASN
A 226 ASN
C 226 ASN
D 226 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.128758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.108524 restraints weight = 18880.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 1.30
r_work: 0.3079 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2970 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.2628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  16892  Z= 0.135
  Angle     :  0.564   6.858  23040  Z= 0.285
  Chirality :  0.045   0.144   2328
  Planarity :  0.004   0.043   3052
  Dihedral  :  8.901 124.970   2260
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 12.32 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.19), residues: 1980
  helix:  0.93 (0.20), residues: 684
  sheet:  0.64 (0.33), residues: 276
  loop : -0.29 (0.19), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 183 
 HIS   0.003   0.001   HIS C 372 
 PHE   0.012   0.002   PHE C 136 
 TYR   0.017   0.002   TYR A 236 
 ARG   0.003   0.000   ARG D 382 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04444 (  656)
  hydrogen bonds       : angle       5.83366 ( 1872)
  covalent geometry    : bond        0.00338 (16888)
  covalent geometry    : angle       0.56426 (23040)
  Misc. bond           : bond        0.00516 (    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
  199 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 166
  time to evaluate  : 1.810 
Fit side-chains
REVERT: B  101 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7235 (tp30)
REVERT: B  107 THR cc_start: 0.8181 (m) cc_final: 0.7830 (t)
REVERT: B  191 GLU cc_start: 0.8090 (pm20) cc_final: 0.7867 (pm20)
REVERT: B  424 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.6722 (tm-30)
REVERT: B  437 ASP cc_start: 0.7390 (m-30) cc_final: 0.6772 (m-30)
REVERT: B  499 LYS cc_start: 0.7722 (tttp) cc_final: 0.7209 (ttpp)
REVERT: A   12 MET cc_start: 0.8470 (mtm) cc_final: 0.8241 (mtm)
REVERT: A   59 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8145 (t0)
REVERT: A  107 THR cc_start: 0.8189 (m) cc_final: 0.7840 (t)
REVERT: A  424 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.6739 (tm-30)
REVERT: A  437 ASP cc_start: 0.7404 (m-30) cc_final: 0.6814 (m-30)
REVERT: A  499 LYS cc_start: 0.7728 (tttp) cc_final: 0.7222 (ttpp)
REVERT: C   59 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8154 (t0)
REVERT: C  101 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7296 (tp30)
REVERT: C  107 THR cc_start: 0.8180 (m) cc_final: 0.7825 (t)
REVERT: C  437 ASP cc_start: 0.7391 (m-30) cc_final: 0.6774 (m-30)
REVERT: C  499 LYS cc_start: 0.7737 (tttp) cc_final: 0.7232 (ttpp)
REVERT: D  101 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7264 (tp30)
REVERT: D  107 THR cc_start: 0.8188 (m) cc_final: 0.7835 (t)
REVERT: D  424 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.6703 (tm-30)
REVERT: D  437 ASP cc_start: 0.7401 (m-30) cc_final: 0.6767 (m-30)
REVERT: D  499 LYS cc_start: 0.7686 (tttp) cc_final: 0.7168 (ttpp)
  outliers start: 33
  outliers final: 16
  residues processed: 191
  average time/residue: 1.4306
  time to fit residues: 301.7390
Evaluate side-chains
  176 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 152
  time to evaluate  : 1.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  344 GLU
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain B residue  424 GLN
Chi-restraints excluded: chain A residue   59 ASP
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  424 GLN
Chi-restraints excluded: chain C residue   59 ASP
Chi-restraints excluded: chain C residue  101 GLU
Chi-restraints excluded: chain C residue  180 ASP
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  344 GLU
Chi-restraints excluded: chain C residue  389 ASP
Chi-restraints excluded: chain D residue  101 GLU
Chi-restraints excluded: chain D residue  180 ASP
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  344 GLU
Chi-restraints excluded: chain D residue  389 ASP
Chi-restraints excluded: chain D residue  424 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 159 optimal weight:    4.9990
   chunk 186 optimal weight:    1.9990
   chunk 101 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 127 optimal weight:    6.9990
   chunk 77 optimal weight:    0.7980
   chunk 83 optimal weight:    6.9990
   chunk 148 optimal weight:    2.9990
   chunk 181 optimal weight:    5.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
B 226 ASN
A 226 ASN
C 226 ASN
D 226 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.128422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.108352 restraints weight = 19093.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 1.27
r_work: 0.3089 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.2722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  16892  Z= 0.147
  Angle     :  0.575   6.887  23040  Z= 0.289
  Chirality :  0.045   0.142   2328
  Planarity :  0.004   0.044   3052
  Dihedral  :  8.844 124.251   2260
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 12.73 %
    Favored  : 84.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.19), residues: 1980
  helix:  0.97 (0.20), residues: 684
  sheet:  0.58 (0.33), residues: 276
  loop : -0.28 (0.19), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 183 
 HIS   0.003   0.001   HIS B  63 
 PHE   0.014   0.002   PHE D 136 
 TYR   0.018   0.002   TYR B 236 
 ARG   0.003   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04530 (  656)
  hydrogen bonds       : angle       5.80582 ( 1872)
  covalent geometry    : bond        0.00370 (16888)
  covalent geometry    : angle       0.57491 (23040)
  Misc. bond           : bond        0.02027 (    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: 39
    poor density    : 168
  time to evaluate  : 2.021 
Fit side-chains
REVERT: B  101 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7312 (tp30)
REVERT: B  107 THR cc_start: 0.8218 (m) cc_final: 0.7861 (t)
REVERT: B  191 GLU cc_start: 0.8069 (pm20) cc_final: 0.7854 (pm20)
REVERT: B  424 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.6823 (tm-30)
REVERT: B  437 ASP cc_start: 0.7409 (m-30) cc_final: 0.7029 (m-30)
REVERT: B  499 LYS cc_start: 0.7705 (tttp) cc_final: 0.7206 (ttpp)
REVERT: A   59 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8209 (t0)
REVERT: A  101 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7287 (tp30)
REVERT: A  107 THR cc_start: 0.8215 (m) cc_final: 0.7860 (t)
REVERT: A  191 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7697 (pm20)
REVERT: A  249 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7417 (t0)
REVERT: A  424 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.6801 (tm-30)
REVERT: A  437 ASP cc_start: 0.7392 (m-30) cc_final: 0.7006 (m-30)
REVERT: A  499 LYS cc_start: 0.7714 (tttp) cc_final: 0.7231 (ttpp)
REVERT: C   59 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8214 (t0)
REVERT: C  101 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7319 (tp30)
REVERT: C  107 THR cc_start: 0.8199 (m) cc_final: 0.7858 (t)
REVERT: C  191 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7723 (pm20)
REVERT: C  249 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7433 (t0)
REVERT: C  437 ASP cc_start: 0.7403 (m-30) cc_final: 0.6725 (m-30)
REVERT: C  499 LYS cc_start: 0.7739 (tttp) cc_final: 0.7248 (ttpp)
REVERT: D  101 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7270 (tp30)
REVERT: D  107 THR cc_start: 0.8212 (m) cc_final: 0.7850 (t)
REVERT: D  191 GLU cc_start: 0.8106 (pm20) cc_final: 0.7889 (pm20)
REVERT: D  249 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7456 (t0)
REVERT: D  424 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.6798 (tm-30)
REVERT: D  437 ASP cc_start: 0.7381 (m-30) cc_final: 0.6998 (m-30)
REVERT: D  499 LYS cc_start: 0.7702 (tttp) cc_final: 0.7199 (ttpp)
  outliers start: 39
  outliers final: 17
  residues processed: 196
  average time/residue: 1.7245
  time to fit residues: 375.6156
Evaluate side-chains
  191 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 160
  time to evaluate  : 3.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  344 GLU
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain B residue  424 GLN
Chi-restraints excluded: chain A residue   59 ASP
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  424 GLN
Chi-restraints excluded: chain C residue   59 ASP
Chi-restraints excluded: chain C residue  101 GLU
Chi-restraints excluded: chain C residue  180 ASP
Chi-restraints excluded: chain C residue  191 GLU
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  249 ASP
Chi-restraints excluded: chain C residue  344 GLU
Chi-restraints excluded: chain C residue  389 ASP
Chi-restraints excluded: chain D residue  101 GLU
Chi-restraints excluded: chain D residue  180 ASP
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  249 ASP
Chi-restraints excluded: chain D residue  344 GLU
Chi-restraints excluded: chain D residue  361 THR
Chi-restraints excluded: chain D residue  389 ASP
Chi-restraints excluded: chain D residue  424 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 138 optimal weight:    2.9990
   chunk 86 optimal weight:    0.0170
   chunk 123 optimal weight:    7.9990
   chunk 134 optimal weight:    0.8980
   chunk 100 optimal weight:    6.9990
   chunk 40 optimal weight:    0.6980
   chunk 144 optimal weight:   10.0000
   chunk 194 optimal weight:    0.8980
   chunk 145 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0010
   overall best weight:    0.5024

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

Flipped N/Q/H residues before XYZ refinement:
B 226 ASN
A 226 ASN
C 226 ASN
D 102 HIS
D 226 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.132882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.112772 restraints weight = 18935.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 1.33
r_work: 0.3148 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.2883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  16892  Z= 0.093
  Angle     :  0.510   6.574  23040  Z= 0.253
  Chirality :  0.042   0.134   2328
  Planarity :  0.004   0.045   3052
  Dihedral  :  7.814 109.958   2260
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 12.85 %
    Favored  : 85.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.19), residues: 1980
  helix:  1.33 (0.20), residues: 680
  sheet:  0.68 (0.33), residues: 276
  loop : -0.18 (0.19), residues: 1024

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 183 
 HIS   0.004   0.001   HIS C  89 
 PHE   0.011   0.001   PHE B 473 
 TYR   0.014   0.001   TYR B 236 
 ARG   0.003   0.000   ARG D 382 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03397 (  656)
  hydrogen bonds       : angle       5.42287 ( 1872)
  covalent geometry    : bond        0.00222 (16888)
  covalent geometry    : angle       0.50997 (23040)
  Misc. bond           : bond        0.00916 (    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
  222 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 193
  time to evaluate  : 2.425 
Fit side-chains
REVERT: B  107 THR cc_start: 0.8127 (m) cc_final: 0.7777 (t)
REVERT: B  249 ASP cc_start: 0.7807 (m-30) cc_final: 0.7469 (t0)
REVERT: B  424 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.6681 (tm-30)
REVERT: B  437 ASP cc_start: 0.7331 (m-30) cc_final: 0.6680 (m-30)
REVERT: B  499 LYS cc_start: 0.7743 (tttp) cc_final: 0.7191 (ttpp)
REVERT: A  107 THR cc_start: 0.8145 (m) cc_final: 0.7809 (t)
REVERT: A  249 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7435 (t0)
REVERT: A  424 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.6707 (tm-30)
REVERT: A  437 ASP cc_start: 0.7303 (m-30) cc_final: 0.6649 (m-30)
REVERT: A  499 LYS cc_start: 0.7769 (tttp) cc_final: 0.7210 (ttpp)
REVERT: C  107 THR cc_start: 0.8112 (m) cc_final: 0.7765 (t)
REVERT: C  249 ASP cc_start: 0.7754 (m-30) cc_final: 0.7481 (t0)
REVERT: C  424 GLN cc_start: 0.7623 (tp40) cc_final: 0.7308 (tm-30)
REVERT: C  437 ASP cc_start: 0.7290 (m-30) cc_final: 0.6595 (m-30)
REVERT: C  499 LYS cc_start: 0.7778 (tttp) cc_final: 0.7225 (ttpp)
REVERT: D  107 THR cc_start: 0.8120 (m) cc_final: 0.7774 (t)
REVERT: D  249 ASP cc_start: 0.7756 (m-30) cc_final: 0.7471 (t0)
REVERT: D  424 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.6692 (tm-30)
REVERT: D  437 ASP cc_start: 0.7312 (m-30) cc_final: 0.6641 (m-30)
REVERT: D  499 LYS cc_start: 0.7742 (tttp) cc_final: 0.7182 (ttpp)
  outliers start: 29
  outliers final: 12
  residues processed: 212
  average time/residue: 1.3793
  time to fit residues: 326.8367
Evaluate side-chains
  188 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 172
  time to evaluate  : 1.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain B residue  424 GLN
Chi-restraints excluded: chain A residue   59 ASP
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  424 GLN
Chi-restraints excluded: chain C residue   59 ASP
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  389 ASP
Chi-restraints excluded: chain D residue  150 THR
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  389 ASP
Chi-restraints excluded: chain D residue  424 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 163 optimal weight:    3.9990
   chunk 195 optimal weight:    7.9990
   chunk 145 optimal weight:    2.9990
   chunk 148 optimal weight:    0.9990
   chunk 104 optimal weight:    5.9990
   chunk 29 optimal weight:    6.9990
   chunk 152 optimal weight:   10.0000
   chunk 100 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
B 102 HIS
B 226 ASN
B 235 HIS
B 338 ASN
B 439 ASN
A 226 ASN
A 235 HIS
A 338 ASN
A 439 ASN
C 102 HIS
C 226 ASN
C 235 HIS
C 338 ASN
C 439 ASN
D 102 HIS
D 226 ASN
D 235 HIS
D 338 ASN
D 439 ASN

Total number of N/Q/H flips: 19

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.127511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.107586 restraints weight = 19184.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 1.26
r_work: 0.3069 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.2863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068  16892  Z= 0.192
  Angle     :  0.614   7.008  23040  Z= 0.308
  Chirality :  0.046   0.146   2328
  Planarity :  0.005   0.047   3052
  Dihedral  :  9.104 125.464   2260
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 12.03 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.19), residues: 1980
  helix:  0.99 (0.20), residues: 684
  sheet:  0.51 (0.33), residues: 276
  loop : -0.25 (0.19), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 183 
 HIS   0.004   0.001   HIS A  75 
 PHE   0.016   0.002   PHE B 136 
 TYR   0.019   0.002   TYR D 236 
 ARG   0.003   0.001   ARG C  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04904 (  656)
  hydrogen bonds       : angle       5.86256 ( 1872)
  covalent geometry    : bond        0.00486 (16888)
  covalent geometry    : angle       0.61380 (23040)
  Misc. bond           : bond        0.02745 (    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
  207 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 155
  time to evaluate  : 1.769 
Fit side-chains
REVERT: B  101 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7345 (tp30)
REVERT: B  107 THR cc_start: 0.8227 (m) cc_final: 0.7861 (t)
REVERT: B  249 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7437 (t0)
REVERT: B  424 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.6776 (tm-30)
REVERT: B  437 ASP cc_start: 0.7450 (m-30) cc_final: 0.7164 (m-30)
REVERT: B  458 ARG cc_start: 0.8184 (mtp180) cc_final: 0.7935 (mtm180)
REVERT: B  488 ASP cc_start: 0.7581 (m-30) cc_final: 0.7343 (m-30)
REVERT: B  499 LYS cc_start: 0.7654 (tttp) cc_final: 0.7162 (ttpp)
REVERT: A   12 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8250 (mtm)
REVERT: A  107 THR cc_start: 0.8218 (m) cc_final: 0.7851 (t)
REVERT: A  191 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7732 (pm20)
REVERT: A  249 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7500 (t0)
REVERT: A  424 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.6761 (tm-30)
REVERT: A  437 ASP cc_start: 0.7450 (m-30) cc_final: 0.7164 (m-30)
REVERT: A  458 ARG cc_start: 0.8257 (mtm-85) cc_final: 0.7869 (mtm180)
REVERT: A  488 ASP cc_start: 0.7580 (m-30) cc_final: 0.7359 (m-30)
REVERT: A  499 LYS cc_start: 0.7690 (tttp) cc_final: 0.7187 (ttpp)
REVERT: C  101 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7360 (tp30)
REVERT: C  107 THR cc_start: 0.8203 (m) cc_final: 0.7838 (t)
REVERT: C  191 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7701 (pm20)
REVERT: C  249 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7484 (t0)
REVERT: C  437 ASP cc_start: 0.7427 (m-30) cc_final: 0.7119 (m-30)
REVERT: C  458 ARG cc_start: 0.8183 (mtp180) cc_final: 0.7939 (mtm180)
REVERT: C  488 ASP cc_start: 0.7575 (m-30) cc_final: 0.7338 (m-30)
REVERT: C  499 LYS cc_start: 0.7684 (tttp) cc_final: 0.7185 (ttpp)
REVERT: D   12 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8245 (mtm)
REVERT: D  101 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7336 (tp30)
REVERT: D  107 THR cc_start: 0.8210 (m) cc_final: 0.7843 (t)
REVERT: D  191 GLU cc_start: 0.8062 (pm20) cc_final: 0.7860 (pm20)
REVERT: D  249 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7495 (t0)
REVERT: D  424 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.6757 (tm-30)
REVERT: D  437 ASP cc_start: 0.7457 (m-30) cc_final: 0.7168 (m-30)
REVERT: D  458 ARG cc_start: 0.8194 (mtp180) cc_final: 0.7944 (mtm180)
REVERT: D  488 ASP cc_start: 0.7578 (m-30) cc_final: 0.7344 (m-30)
REVERT: D  499 LYS cc_start: 0.7661 (tttp) cc_final: 0.7153 (ttpp)
  outliers start: 52
  outliers final: 20
  residues processed: 193
  average time/residue: 1.4164
  time to fit residues: 301.4581
Evaluate side-chains
  183 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 149
  time to evaluate  : 1.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  249 ASP
Chi-restraints excluded: chain B residue  344 GLU
Chi-restraints excluded: chain B residue  361 THR
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain B residue  392 MET
Chi-restraints excluded: chain B residue  424 GLN
Chi-restraints excluded: chain A residue   12 MET
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  424 GLN
Chi-restraints excluded: chain C residue  101 GLU
Chi-restraints excluded: chain C residue  180 ASP
Chi-restraints excluded: chain C residue  191 GLU
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  249 ASP
Chi-restraints excluded: chain C residue  344 GLU
Chi-restraints excluded: chain C residue  361 THR
Chi-restraints excluded: chain C residue  389 ASP
Chi-restraints excluded: chain C residue  392 MET
Chi-restraints excluded: chain D residue   12 MET
Chi-restraints excluded: chain D residue  101 GLU
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  249 ASP
Chi-restraints excluded: chain D residue  344 GLU
Chi-restraints excluded: chain D residue  361 THR
Chi-restraints excluded: chain D residue  389 ASP
Chi-restraints excluded: chain D residue  424 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 126 optimal weight:    6.9990
   chunk 98 optimal weight:    3.9990
   chunk 148 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   chunk 73 optimal weight:    3.9990
   chunk 147 optimal weight:    1.9990
   chunk 183 optimal weight:    1.9990
   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 226 ASN
A 226 ASN
C 226 ASN
D 226 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.129673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.109354 restraints weight = 19003.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 1.32
r_work: 0.3095 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  16892  Z= 0.128
  Angle     :  0.552   6.756  23040  Z= 0.277
  Chirality :  0.044   0.140   2328
  Planarity :  0.004   0.047   3052
  Dihedral  :  8.564 119.979   2260
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 12.44 %
    Favored  : 84.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.19), residues: 1980
  helix:  1.08 (0.20), residues: 680
  sheet:  0.53 (0.33), residues: 276
  loop : -0.21 (0.19), residues: 1024

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 183 
 HIS   0.004   0.001   HIS B 235 
 PHE   0.013   0.001   PHE D 136 
 TYR   0.016   0.001   TYR A 236 
 ARG   0.003   0.000   ARG D 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04136 (  656)
  hydrogen bonds       : angle       5.68771 ( 1872)
  covalent geometry    : bond        0.00321 (16888)
  covalent geometry    : angle       0.55175 (23040)
  Misc. bond           : bond        0.01245 (    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: 44
    poor density    : 160
  time to evaluate  : 1.799 
Fit side-chains
REVERT: B  107 THR cc_start: 0.8217 (m) cc_final: 0.7867 (t)
REVERT: B  249 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7465 (t0)
REVERT: B  424 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.6805 (tm-30)
REVERT: B  437 ASP cc_start: 0.7408 (m-30) cc_final: 0.6897 (m-30)
REVERT: B  458 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7879 (mtm180)
REVERT: B  488 ASP cc_start: 0.7615 (m-30) cc_final: 0.7397 (m-30)
REVERT: B  499 LYS cc_start: 0.7704 (tttp) cc_final: 0.7125 (ttpp)
REVERT: A   12 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8169 (mtm)
REVERT: A  107 THR cc_start: 0.8202 (m) cc_final: 0.7856 (t)
REVERT: A  191 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7695 (pm20)
REVERT: A  249 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7500 (t0)
REVERT: A  424 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.6767 (tm-30)
REVERT: A  437 ASP cc_start: 0.7420 (m-30) cc_final: 0.6774 (m-30)
REVERT: A  458 ARG cc_start: 0.8282 (mtm-85) cc_final: 0.7897 (mtm180)
REVERT: A  488 ASP cc_start: 0.7639 (m-30) cc_final: 0.7431 (m-30)
REVERT: A  499 LYS cc_start: 0.7693 (tttp) cc_final: 0.7136 (ttpp)
REVERT: C   59 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8105 (t0)
REVERT: C  107 THR cc_start: 0.8199 (m) cc_final: 0.7848 (t)
REVERT: C  191 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7790 (pm20)
REVERT: C  249 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7444 (t0)
REVERT: C  437 ASP cc_start: 0.7394 (m-30) cc_final: 0.6848 (m-30)
REVERT: C  458 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7893 (mtm180)
REVERT: C  488 ASP cc_start: 0.7624 (m-30) cc_final: 0.7419 (m-30)
REVERT: C  499 LYS cc_start: 0.7710 (tttp) cc_final: 0.7142 (ttpp)
REVERT: D   12 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8194 (mtm)
REVERT: D  107 THR cc_start: 0.8213 (m) cc_final: 0.7862 (t)
REVERT: D  249 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7471 (t0)
REVERT: D  424 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.6781 (tm-30)
REVERT: D  437 ASP cc_start: 0.7400 (m-30) cc_final: 0.6869 (m-30)
REVERT: D  458 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7891 (mtm180)
REVERT: D  488 ASP cc_start: 0.7625 (m-30) cc_final: 0.7421 (m-30)
REVERT: D  499 LYS cc_start: 0.7705 (tttp) cc_final: 0.7116 (ttpp)
  outliers start: 44
  outliers final: 16
  residues processed: 192
  average time/residue: 1.4223
  time to fit residues: 306.2684
Evaluate side-chains
  191 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 160
  time to evaluate  : 2.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  249 ASP
Chi-restraints excluded: chain B residue  344 GLU
Chi-restraints excluded: chain B residue  361 THR
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain B residue  424 GLN
Chi-restraints excluded: chain B residue  458 ARG
Chi-restraints excluded: chain A residue   12 MET
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  424 GLN
Chi-restraints excluded: chain C residue   59 ASP
Chi-restraints excluded: chain C residue  191 GLU
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  249 ASP
Chi-restraints excluded: chain C residue  344 GLU
Chi-restraints excluded: chain C residue  361 THR
Chi-restraints excluded: chain C residue  389 ASP
Chi-restraints excluded: chain C residue  392 MET
Chi-restraints excluded: chain C residue  458 ARG
Chi-restraints excluded: chain D residue   12 MET
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  249 ASP
Chi-restraints excluded: chain D residue  344 GLU
Chi-restraints excluded: chain D residue  389 ASP
Chi-restraints excluded: chain D residue  424 GLN
Chi-restraints excluded: chain D residue  458 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 179 optimal weight:    0.3980
   chunk 10 optimal weight:    3.9990
   chunk 137 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 79 optimal weight:    0.0770
   chunk 148 optimal weight:   20.0000
   chunk 159 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 107 optimal weight:    3.9990
   chunk 46 optimal weight:   10.0000
   overall best weight:    1.2140

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

Flipped N/Q/H residues before XYZ refinement:
B 226 ASN
A 226 ASN
C 226 ASN
D 226 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.130307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.109994 restraints weight = 19067.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 1.33
r_work: 0.3103 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.2994 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.2948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  16892  Z= 0.120
  Angle     :  0.543   6.650  23040  Z= 0.273
  Chirality :  0.044   0.138   2328
  Planarity :  0.004   0.046   3052
  Dihedral  :  8.440 119.448   2260
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 12.85 %
    Favored  : 84.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.19), residues: 1980
  helix:  1.14 (0.20), residues: 680
  sheet:  0.39 (0.32), residues: 304
  loop : -0.05 (0.19), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 183 
 HIS   0.004   0.001   HIS B 235 
 PHE   0.012   0.001   PHE D 136 
 TYR   0.017   0.001   TYR D 236 
 ARG   0.003   0.000   ARG D 382 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04011 (  656)
  hydrogen bonds       : angle       5.62365 ( 1872)
  covalent geometry    : bond        0.00299 (16888)
  covalent geometry    : angle       0.54327 (23040)
  Misc. bond           : bond        0.01577 (    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
  201 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 164
  time to evaluate  : 1.916 
Fit side-chains
REVERT: B   59 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.8066 (t0)
REVERT: B  107 THR cc_start: 0.8210 (m) cc_final: 0.7853 (t)
REVERT: B  249 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7505 (t0)
REVERT: B  424 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.6847 (tm-30)
REVERT: B  437 ASP cc_start: 0.7407 (m-30) cc_final: 0.7107 (m-30)
REVERT: B  458 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7882 (mtm180)
REVERT: B  488 ASP cc_start: 0.7627 (m-30) cc_final: 0.7409 (m-30)
REVERT: B  499 LYS cc_start: 0.7716 (tttp) cc_final: 0.7135 (ttpp)
REVERT: A   12 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8170 (mtm)
REVERT: A   59 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.8038 (t0)
REVERT: A  107 THR cc_start: 0.8203 (m) cc_final: 0.7853 (t)
REVERT: A  191 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7786 (pm20)
REVERT: A  249 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7517 (t0)
REVERT: A  424 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.6809 (tm-30)
REVERT: A  437 ASP cc_start: 0.7389 (m-30) cc_final: 0.6961 (m-30)
REVERT: A  458 ARG cc_start: 0.8285 (mtm-85) cc_final: 0.7880 (mtm180)
REVERT: A  488 ASP cc_start: 0.7620 (m-30) cc_final: 0.7408 (m-30)
REVERT: A  499 LYS cc_start: 0.7709 (tttp) cc_final: 0.7136 (ttpp)
REVERT: C  107 THR cc_start: 0.8191 (m) cc_final: 0.7836 (t)
REVERT: C  191 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7792 (pm20)
REVERT: C  249 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7473 (t0)
REVERT: C  437 ASP cc_start: 0.7380 (m-30) cc_final: 0.6832 (m-30)
REVERT: C  458 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7899 (mtm180)
REVERT: C  488 ASP cc_start: 0.7644 (m-30) cc_final: 0.7436 (m-30)
REVERT: C  499 LYS cc_start: 0.7730 (tttp) cc_final: 0.7150 (ttpp)
REVERT: D   12 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8161 (mtm)
REVERT: D   59 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.8036 (t0)
REVERT: D  107 THR cc_start: 0.8211 (m) cc_final: 0.7859 (t)
REVERT: D  249 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7475 (t0)
REVERT: D  424 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.6824 (tm-30)
REVERT: D  437 ASP cc_start: 0.7400 (m-30) cc_final: 0.7103 (m-30)
REVERT: D  458 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7898 (mtm180)
REVERT: D  488 ASP cc_start: 0.7657 (m-30) cc_final: 0.7442 (m-30)
REVERT: D  499 LYS cc_start: 0.7694 (tttp) cc_final: 0.7118 (ttpp)
  outliers start: 37
  outliers final: 17
  residues processed: 188
  average time/residue: 1.8657
  time to fit residues: 386.5778
Evaluate side-chains
  197 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 163
  time to evaluate  : 2.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  249 ASP
Chi-restraints excluded: chain B residue  344 GLU
Chi-restraints excluded: chain B residue  361 THR
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain B residue  424 GLN
Chi-restraints excluded: chain B residue  458 ARG
Chi-restraints excluded: chain A residue   12 MET
Chi-restraints excluded: chain A residue   59 ASP
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  424 GLN
Chi-restraints excluded: chain C residue  180 ASP
Chi-restraints excluded: chain C residue  191 GLU
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  249 ASP
Chi-restraints excluded: chain C residue  344 GLU
Chi-restraints excluded: chain C residue  361 THR
Chi-restraints excluded: chain C residue  389 ASP
Chi-restraints excluded: chain C residue  458 ARG
Chi-restraints excluded: chain D residue   12 MET
Chi-restraints excluded: chain D residue   59 ASP
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  249 ASP
Chi-restraints excluded: chain D residue  344 GLU
Chi-restraints excluded: chain D residue  389 ASP
Chi-restraints excluded: chain D residue  424 GLN
Chi-restraints excluded: chain D residue  458 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 171 optimal weight:    0.5980
   chunk 101 optimal weight:    3.9990
   chunk 75 optimal weight:    0.8980
   chunk 172 optimal weight:    0.8980
   chunk 168 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   chunk 46 optimal weight:    7.9990
   chunk 20 optimal weight:    0.1980
   chunk 103 optimal weight:    0.9980
   chunk 178 optimal weight:    7.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 226 ASN
A 102 HIS
A 226 ASN
C 226 ASN
D 226 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.132554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.113220 restraints weight = 18997.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 1.24
r_work: 0.3148 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3044 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.3012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  16892  Z= 0.099
  Angle     :  0.520   6.493  23040  Z= 0.260
  Chirality :  0.043   0.138   2328
  Planarity :  0.004   0.045   3052
  Dihedral  :  8.012 112.674   2260
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 13.08 %
    Favored  : 84.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.19), residues: 1980
  helix:  1.27 (0.20), residues: 680
  sheet:  0.44 (0.32), residues: 304
  loop :  0.00 (0.19), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 183 
 HIS   0.005   0.001   HIS A 102 
 PHE   0.011   0.001   PHE C 136 
 TYR   0.015   0.001   TYR D 236 
 ARG   0.003   0.000   ARG D 382 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03581 (  656)
  hydrogen bonds       : angle       5.46331 ( 1872)
  covalent geometry    : bond        0.00242 (16888)
  covalent geometry    : angle       0.51971 (23040)
  Misc. bond           : bond        0.01272 (    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
  206 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 173
  time to evaluate  : 2.151 
Fit side-chains
REVERT: B  107 THR cc_start: 0.8155 (m) cc_final: 0.7808 (t)
REVERT: B  249 ASP cc_start: 0.7794 (m-30) cc_final: 0.7376 (t0)
REVERT: B  424 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.6767 (tm-30)
REVERT: B  437 ASP cc_start: 0.7344 (m-30) cc_final: 0.6833 (m-30)
REVERT: B  499 LYS cc_start: 0.7637 (tttp) cc_final: 0.7095 (ttpp)
REVERT: A   12 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8121 (mtm)
REVERT: A  107 THR cc_start: 0.8123 (m) cc_final: 0.7782 (t)
REVERT: A  249 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7346 (t0)
REVERT: A  392 MET cc_start: 0.8455 (mmm) cc_final: 0.8239 (mmm)
REVERT: A  424 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.6748 (tm-30)
REVERT: A  437 ASP cc_start: 0.7338 (m-30) cc_final: 0.6653 (m-30)
REVERT: A  458 ARG cc_start: 0.8254 (mtm-85) cc_final: 0.7852 (mtm180)
REVERT: A  499 LYS cc_start: 0.7649 (tttp) cc_final: 0.7113 (ttpp)
REVERT: C  107 THR cc_start: 0.8145 (m) cc_final: 0.7800 (t)
REVERT: C  191 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7805 (pm20)
REVERT: C  249 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7427 (t0)
REVERT: C  424 GLN cc_start: 0.7652 (tp40) cc_final: 0.7339 (tm-30)
REVERT: C  437 ASP cc_start: 0.7312 (m-30) cc_final: 0.6993 (m-30)
REVERT: C  499 LYS cc_start: 0.7658 (tttp) cc_final: 0.7123 (ttpp)
REVERT: D   12 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8100 (mtm)
REVERT: D  107 THR cc_start: 0.8132 (m) cc_final: 0.7786 (t)
REVERT: D  249 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7457 (t0)
REVERT: D  424 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.6740 (tm-30)
REVERT: D  437 ASP cc_start: 0.7362 (m-30) cc_final: 0.6829 (m-30)
REVERT: D  499 LYS cc_start: 0.7632 (tttp) cc_final: 0.7080 (ttpp)
  outliers start: 33
  outliers final: 20
  residues processed: 195
  average time/residue: 1.3432
  time to fit residues: 290.4615
Evaluate side-chains
  195 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 166
  time to evaluate  : 1.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  344 GLU
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain B residue  424 GLN
Chi-restraints excluded: chain A residue   12 MET
Chi-restraints excluded: chain A residue   59 ASP
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  424 GLN
Chi-restraints excluded: chain C residue   59 ASP
Chi-restraints excluded: chain C residue  180 ASP
Chi-restraints excluded: chain C residue  191 GLU
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  249 ASP
Chi-restraints excluded: chain C residue  344 GLU
Chi-restraints excluded: chain C residue  389 ASP
Chi-restraints excluded: chain D residue   12 MET
Chi-restraints excluded: chain D residue   59 ASP
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  249 ASP
Chi-restraints excluded: chain D residue  344 GLU
Chi-restraints excluded: chain D residue  361 THR
Chi-restraints excluded: chain D residue  389 ASP
Chi-restraints excluded: chain D residue  424 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 118 optimal weight:   10.0000
   chunk 28 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   chunk 181 optimal weight:    2.9990
   chunk 69 optimal weight:   10.0000
   chunk 86 optimal weight:    5.9990
   chunk 109 optimal weight:   10.0000
   chunk 113 optimal weight:    1.9990
   chunk 177 optimal weight:    0.3980
   chunk 9 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    2.2788

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

Flipped N/Q/H residues before XYZ refinement:
B 226 ASN
A 226 ASN
C 226 ASN
C 338 ASN
D 226 ASN
D 338 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.128023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.108136 restraints weight = 19123.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 1.26
r_work: 0.3076 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 3.01 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.2938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  16892  Z= 0.176
  Angle     :  0.605   6.896  23040  Z= 0.303
  Chirality :  0.046   0.144   2328
  Planarity :  0.005   0.048   3052
  Dihedral  :  9.006 125.247   2260
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 12.91 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.19), residues: 1980
  helix:  0.98 (0.20), residues: 684
  sheet:  0.33 (0.31), residues: 304
  loop : -0.08 (0.19), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D 183 
 HIS   0.005   0.001   HIS B 235 
 PHE   0.015   0.002   PHE B 136 
 TYR   0.019   0.002   TYR C 236 
 ARG   0.003   0.000   ARG B 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04709 (  656)
  hydrogen bonds       : angle       5.80078 ( 1872)
  covalent geometry    : bond        0.00445 (16888)
  covalent geometry    : angle       0.60499 (23040)
  Misc. bond           : bond        0.02697 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11100.79 seconds
wall clock time: 194 minutes 28.13 seconds (11668.13 seconds total)