Starting phenix.real_space_refine
on Tue Feb  3 13:58:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9u4l_63849/02_2026/9u4l_63849.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9u4l_63849/02_2026/9u4l_63849.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9u4l_63849/02_2026/9u4l_63849.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9u4l_63849/02_2026/9u4l_63849.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9u4l_63849/02_2026/9u4l_63849.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9u4l_63849/02_2026/9u4l_63849.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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=   1.000
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: 3
    Type Number    sf(0)   Gaussians
     C    2274      2.51       5
     N     546      2.21       5
     O     642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3462
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "D"
      Number of atoms: 577
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 577
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 3, 'TRANS': 65}
  Restraints were copied for chains:
    A, B, C, E, F
  Time building chain proxies: 0.36, per 1000 atoms: 0.10
  Number of scatterers: 3462
  At special positions: 0
  Unit cell: (89.472, 65.24, 53.124, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     642      8.00
     N     546      7.00
     C    2274      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.16
  Conformation dependent library (CDL) restraints added in 80.2 milliseconds
  

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  792

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 7 sheets defined
      0.0% alpha, 41.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28
      removed outlier: 6.406A  pdb=" N   GLN D  25 " --> pdb=" O   PHE C  26 " (cutoff:3.500A)
      removed outlier: 7.730A  pdb=" N   GLY C  28 " --> pdb=" O   GLN D  25 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   PHE D  27 " --> pdb=" O   GLY C  28 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 35
      removed outlier: 6.240A  pdb=" N   PHE A  32 " --> pdb=" O   GLU B  33 " (cutoff:3.500A)
      removed outlier: 7.696A  pdb=" N   ASP B  35 " --> pdb=" O   PHE A  32 " (cutoff:3.500A)
      removed outlier: 6.046A  pdb=" N   TYR A  34 " --> pdb=" O   ASP B  35 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   PHE B  32 " --> pdb=" O   GLU C  33 " (cutoff:3.500A)
      removed outlier: 7.791A  pdb=" N   ASP C  35 " --> pdb=" O   PHE B  32 " (cutoff:3.500A)
      removed outlier: 6.127A  pdb=" N   TYR B  34 " --> pdb=" O   ASP C  35 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   PHE D  32 " --> pdb=" O   GLU E  33 " (cutoff:3.500A)
      removed outlier: 7.683A  pdb=" N   ASP E  35 " --> pdb=" O   PHE D  32 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   TYR D  34 " --> pdb=" O   ASP E  35 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   PHE E  32 " --> pdb=" O   GLU F  33 " (cutoff:3.500A)
      removed outlier: 7.743A  pdb=" N   ASP F  35 " --> pdb=" O   PHE E  32 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   TYR E  34 " --> pdb=" O   ASP F  35 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 51
      removed outlier: 6.304A  pdb=" N   TYR A  48 " --> pdb=" O   ARG B  49 " (cutoff:3.500A)
      removed outlier: 7.921A  pdb=" N   SER B  51 " --> pdb=" O   TYR A  48 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   GLN A  50 " --> pdb=" O   SER B  51 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   TYR B  48 " --> pdb=" O   ARG C  49 " (cutoff:3.500A)
      removed outlier: 7.858A  pdb=" N   SER C  51 " --> pdb=" O   TYR B  48 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   GLN B  50 " --> pdb=" O   SER C  51 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   TYR D  48 " --> pdb=" O   ARG E  49 " (cutoff:3.500A)
      removed outlier: 7.919A  pdb=" N   SER E  51 " --> pdb=" O   TYR D  48 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   GLN D  50 " --> pdb=" O   SER E  51 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   TYR E  48 " --> pdb=" O   ARG F  49 " (cutoff:3.500A)
      removed outlier: 7.913A  pdb=" N   SER F  51 " --> pdb=" O   TYR E  48 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   GLN E  50 " --> pdb=" O   SER F  51 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 65
      removed outlier: 6.970A  pdb=" N   ILE A  61 " --> pdb=" O   GLY B  60 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   SER B  62 " --> pdb=" O   ILE A  61 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   GLU A  63 " --> pdb=" O   SER B  62 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   VAL B  64 " --> pdb=" O   GLU A  63 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   ARG A  65 " --> pdb=" O   VAL B  64 " (cutoff:3.500A)
      removed outlier: 9.111A  pdb=" N   ARG B  54 " --> pdb=" O   THR C  55 " (cutoff:3.500A)
      removed outlier: 10.010A  pdb=" N   LEU C  57 " --> pdb=" O   ARG B  54 " (cutoff:3.500A)
      removed outlier: 8.704A  pdb=" N   VAL B  56 " --> pdb=" O   LEU C  57 " (cutoff:3.500A)
      removed outlier: 10.017A  pdb=" N   SER C  59 " --> pdb=" O   VAL B  56 " (cutoff:3.500A)
      removed outlier: 8.784A  pdb=" N   ASP B  58 " --> pdb=" O   SER C  59 " (cutoff:3.500A)
      removed outlier: 9.680A  pdb=" N   ILE C  61 " --> pdb=" O   ASP B  58 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   GLY B  60 " --> pdb=" O   ILE C  61 " (cutoff:3.500A)
      removed outlier: 8.181A  pdb=" N   GLU C  63 " --> pdb=" O   GLY B  60 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   SER B  62 " --> pdb=" O   GLU C  63 " (cutoff:3.500A)
      removed outlier: 7.641A  pdb=" N   ARG C  65 " --> pdb=" O   SER B  62 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   VAL B  64 " --> pdb=" O   ARG C  65 " (cutoff:3.500A)
      removed outlier: 8.962A  pdb=" N   THR D  55 " --> pdb=" O   VAL C  56 " (cutoff:3.500A)
      removed outlier: 10.309A  pdb=" N   ASP C  58 " --> pdb=" O   THR D  55 " (cutoff:3.500A)
      removed outlier: 9.175A  pdb=" N   LEU D  57 " --> pdb=" O   ASP C  58 " (cutoff:3.500A)
      removed outlier: 10.536A  pdb=" N   GLY C  60 " --> pdb=" O   LEU D  57 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   SER D  59 " --> pdb=" O   GLY C  60 " (cutoff:3.500A)
      removed outlier: 7.474A  pdb=" N   SER C  62 " --> pdb=" O   SER D  59 " (cutoff:3.500A)
      removed outlier: 6.159A  pdb=" N   ILE D  61 " --> pdb=" O   SER C  62 " (cutoff:3.500A)
      removed outlier: 7.701A  pdb=" N   VAL C  64 " --> pdb=" O   ILE D  61 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   GLU D  63 " --> pdb=" O   VAL C  64 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   ILE D  61 " --> pdb=" O   GLY E  60 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   SER E  62 " --> pdb=" O   ILE D  61 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   GLU D  63 " --> pdb=" O   SER E  62 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   VAL E  64 " --> pdb=" O   GLU D  63 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   ARG D  65 " --> pdb=" O   VAL E  64 " (cutoff:3.500A)
      removed outlier: 9.111A  pdb=" N   ARG E  54 " --> pdb=" O   THR F  55 " (cutoff:3.500A)
      removed outlier: 10.023A  pdb=" N   LEU F  57 " --> pdb=" O   ARG E  54 " (cutoff:3.500A)
      removed outlier: 8.721A  pdb=" N   VAL E  56 " --> pdb=" O   LEU F  57 " (cutoff:3.500A)
      removed outlier: 10.052A  pdb=" N   SER F  59 " --> pdb=" O   VAL E  56 " (cutoff:3.500A)
      removed outlier: 8.828A  pdb=" N   ASP E  58 " --> pdb=" O   SER F  59 " (cutoff:3.500A)
      removed outlier: 9.743A  pdb=" N   ILE F  61 " --> pdb=" O   ASP E  58 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   GLY E  60 " --> pdb=" O   ILE F  61 " (cutoff:3.500A)
      removed outlier: 8.272A  pdb=" N   GLU F  63 " --> pdb=" O   GLY E  60 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   SER E  62 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 7.718A  pdb=" N   ARG F  65 " --> pdb=" O   SER E  62 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   VAL E  64 " --> pdb=" O   ARG F  65 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 71 through 77
      removed outlier: 6.550A  pdb=" N   VAL D  72 " --> pdb=" O   ILE C  73 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   LEU C  75 " --> pdb=" O   VAL D  72 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   PHE D  74 " --> pdb=" O   LEU C  75 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   VAL C  77 " --> pdb=" O   PHE D  74 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   ASP D  76 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   PHE D  71 " --> pdb=" O   VAL E  72 " (cutoff:3.500A)
      removed outlier: 7.813A  pdb=" N   PHE E  74 " --> pdb=" O   PHE D  71 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ILE D  73 " --> pdb=" O   PHE E  74 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   ASP E  76 " --> pdb=" O   ILE D  73 " (cutoff:3.500A)
      removed outlier: 6.019A  pdb=" N   LEU D  75 " --> pdb=" O   ASP E  76 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   PHE E  71 " --> pdb=" O   VAL F  72 " (cutoff:3.500A)
      removed outlier: 7.814A  pdb=" N   PHE F  74 " --> pdb=" O   PHE E  71 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ILE E  73 " --> pdb=" O   PHE F  74 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   ASP F  76 " --> pdb=" O   ILE E  73 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   LEU E  75 " --> pdb=" O   ASP F  76 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 87
    Processing sheet with id=AA7, first strand: chain 'E' and resid 86 through 87

    46 hydrogen bonds defined for protein.
    138 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: 0.29

  Time building geometry restraints manager: 0.23 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 558
        1.29 -     1.35: 522
        1.35 -     1.41: 468
        1.41 -     1.48: 522
        1.48 -     1.54: 1482
  Bond restraints: 3552
  Sorted by residual:
  bond pdb=" N   ARG E  21 "
       pdb=" CA  ARG E  21 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.02e+00
  bond pdb=" N   ARG C  21 "
       pdb=" CA  ARG C  21 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.89e+00
  bond pdb=" N   ARG D  21 "
       pdb=" CA  ARG D  21 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.87e+00
  bond pdb=" N   ARG F  21 "
       pdb=" CA  ARG F  21 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.85e+00
  bond pdb=" N   ARG B  21 "
       pdb=" CA  ARG B  21 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.83e+00
  ... (remaining 3547 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.69: 4110
        0.69 -     1.38: 564
        1.38 -     2.07: 62
        2.07 -     2.76: 16
        2.76 -     3.45: 42
  Bond angle restraints: 4794
  Sorted by residual:
  angle pdb=" N   GLY B  30 "
        pdb=" CA  GLY B  30 "
        pdb=" C   GLY B  30 "
      ideal   model   delta    sigma   weight residual
     110.60  114.05   -3.45 1.46e+00 4.69e-01 5.58e+00
  angle pdb=" N   GLY F  30 "
        pdb=" CA  GLY F  30 "
        pdb=" C   GLY F  30 "
      ideal   model   delta    sigma   weight residual
     110.60  114.05   -3.45 1.46e+00 4.69e-01 5.57e+00
  angle pdb=" N   GLY D  30 "
        pdb=" CA  GLY D  30 "
        pdb=" C   GLY D  30 "
      ideal   model   delta    sigma   weight residual
     110.60  114.03   -3.43 1.46e+00 4.69e-01 5.53e+00
  angle pdb=" N   GLY C  30 "
        pdb=" CA  GLY C  30 "
        pdb=" C   GLY C  30 "
      ideal   model   delta    sigma   weight residual
     110.60  114.02   -3.42 1.46e+00 4.69e-01 5.49e+00
  angle pdb=" N   GLY A  30 "
        pdb=" CA  GLY A  30 "
        pdb=" C   GLY A  30 "
      ideal   model   delta    sigma   weight residual
     110.60  114.01   -3.41 1.46e+00 4.69e-01 5.45e+00
  ... (remaining 4789 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.56: 1692
        9.56 -    19.11: 258
       19.11 -    28.67: 90
       28.67 -    38.22: 36
       38.22 -    47.78: 12
  Dihedral angle restraints: 2088
    sinusoidal: 870
      harmonic: 1218
  Sorted by residual:
  dihedral pdb=" CA  TYR C  47 "
           pdb=" CB  TYR C  47 "
           pdb=" CG  TYR C  47 "
           pdb=" CD1 TYR C  47 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -20.00   27.78  -47.78     2      2.00e+01 2.50e-03 6.58e+00
  dihedral pdb=" CA  TYR A  47 "
           pdb=" CB  TYR A  47 "
           pdb=" CG  TYR A  47 "
           pdb=" CD1 TYR A  47 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -20.00   27.74  -47.74     2      2.00e+01 2.50e-03 6.57e+00
  dihedral pdb=" CA  TYR F  47 "
           pdb=" CB  TYR F  47 "
           pdb=" CG  TYR F  47 "
           pdb=" CD1 TYR F  47 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -20.00   27.74  -47.74     2      2.00e+01 2.50e-03 6.57e+00
  ... (remaining 2085 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 264
       0.026 -    0.051: 183
       0.051 -    0.077: 23
       0.077 -    0.102: 29
       0.102 -    0.128: 23
  Chirality restraints: 522
  Sorted by residual:
  chirality pdb=" CA  ILE B  61 "
            pdb=" N   ILE B  61 "
            pdb=" C   ILE B  61 "
            pdb=" CB  ILE B  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.08e-01
  chirality pdb=" CA  ILE A  61 "
            pdb=" N   ILE A  61 "
            pdb=" C   ILE A  61 "
            pdb=" CB  ILE A  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.06e-01
  chirality pdb=" CA  ILE E  61 "
            pdb=" N   ILE E  61 "
            pdb=" C   ILE E  61 "
            pdb=" CB  ILE E  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.04e-01
  ... (remaining 519 not shown)

  Planarity restraints: 612
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU E  37 "    0.023 5.00e-02 4.00e+02   3.42e-02 1.87e+00
        pdb=" N   PRO E  38 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO E  38 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO E  38 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  37 "    0.023 5.00e-02 4.00e+02   3.42e-02 1.87e+00
        pdb=" N   PRO B  38 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO B  38 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B  38 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  37 "    0.023 5.00e-02 4.00e+02   3.41e-02 1.86e+00
        pdb=" N   PRO A  38 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A  38 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A  38 "    0.019 5.00e-02 4.00e+02
  ... (remaining 609 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 1188
        2.84 -     3.36: 2784
        3.36 -     3.87: 5706
        3.87 -     4.39: 6216
        4.39 -     4.90: 12587
  Nonbonded interactions: 28481
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP D  69 "
            pdb=" O   ASP C  67 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" OE1 GLU D  29 "
            pdb=" NH2 ARG E  49 "
     model   vdw
     2.335 3.120
  nonbonded pdb=" NH2 ARG D  49 "
            pdb=" OE1 GLU C  29 "
     model   vdw
     2.345 3.120
  nonbonded pdb=" OE1 GLU B  29 "
            pdb=" NH2 ARG C  49 "
     model   vdw
     2.382 3.120
  nonbonded pdb=" O   ASP E  67 "
            pdb=" OD1 ASP F  69 "
     model   vdw
     2.389 3.040
  ... (remaining 28476 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'D'
  selection = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             0.260
  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:             0.000
  Extract box with map and model:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     3.320
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:0.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    4.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
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      :  0.003   0.033   3552  Z= 0.165
  Angle     :  0.556   3.449   4794  Z= 0.322
  Chirality :  0.042   0.128    522
  Planarity :  0.004   0.034    612
  Dihedral  : 11.680  47.779   1296
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.96 %
    Favored  : 91.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.14 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.15 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D  68 
 TYR   0.006   0.001   TYR C  47 
 PHE   0.017   0.002   PHE A  23 
 HIS   0.001   0.000   HIS D  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 3552)
  covalent geometry    : angle       0.55618 ( 4794)
  hydrogen bonds       : bond        0.14952 (   46)
  hydrogen bonds       : angle       9.22995 (  138)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.077 
Fit side-chains
REVERT: D   24 ASP cc_start: 0.7883 (p0) cc_final: 0.7673 (p0)
REVERT: D   25 GLN cc_start: 0.8585 (mt0) cc_final: 0.8348 (mt0)
REVERT: D   61 ILE cc_start: 0.8932 (mm) cc_final: 0.8728 (mm)
REVERT: D   63 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7619 (mt-10)
REVERT: D   65 ARG cc_start: 0.6216 (mtt180) cc_final: 0.5794 (mtp85)
REVERT: D   78 LYS cc_start: 0.8638 (mttt) cc_final: 0.8245 (mttm)
REVERT: A   78 LYS cc_start: 0.8911 (mttt) cc_final: 0.8457 (mttm)
REVERT: A   80 PHE cc_start: 0.8433 (t80) cc_final: 0.6730 (p90)
REVERT: B   63 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7618 (mt-10)
REVERT: B   78 LYS cc_start: 0.8790 (mttt) cc_final: 0.8400 (mttm)
REVERT: C   58 ASP cc_start: 0.8197 (t0) cc_final: 0.7851 (t0)
REVERT: C   63 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7541 (mt-10)
REVERT: C   65 ARG cc_start: 0.6210 (mtt180) cc_final: 0.5938 (mtp85)
REVERT: C   76 ASP cc_start: 0.8334 (t0) cc_final: 0.8047 (t0)
REVERT: C   78 LYS cc_start: 0.8747 (mttt) cc_final: 0.8312 (mttm)
REVERT: E   34 TYR cc_start: 0.8339 (m-80) cc_final: 0.7779 (m-80)
REVERT: E   63 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7956 (mt-10)
REVERT: E   76 ASP cc_start: 0.8198 (t0) cc_final: 0.7997 (t0)
REVERT: E   78 LYS cc_start: 0.8606 (mttt) cc_final: 0.8181 (mttm)
REVERT: F   39 PHE cc_start: 0.8561 (t80) cc_final: 0.7934 (p90)
REVERT: F   58 ASP cc_start: 0.8103 (t0) cc_final: 0.7476 (t0)
REVERT: F   65 ARG cc_start: 0.6395 (mtt180) cc_final: 0.6128 (mtp85)
REVERT: F   71 PHE cc_start: 0.7745 (m-80) cc_final: 0.7496 (m-10)
REVERT: F   78 LYS cc_start: 0.8533 (mttt) cc_final: 0.8164 (mttp)
REVERT: F   80 PHE cc_start: 0.8078 (t80) cc_final: 0.7725 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.0550
  time to fit residues: 9.7295
Evaluate side-chains
  131 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 26 optimal weight:   20.0000
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:   40.0000
   chunk 32 optimal weight:    0.3980
   chunk 31 optimal weight:    8.9990
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:   20.0000
   chunk 30 optimal weight:    8.9990
   chunk 22 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   overall best weight:    5.4788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4636 r_free = 0.4636 target = 0.156922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.124290 restraints weight = 4962.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.126859 restraints weight = 2437.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.128489 restraints weight = 1652.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.129436 restraints weight = 1319.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.130065 restraints weight = 1164.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.4424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.3239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3552  Z= 0.188
  Angle     :  0.752   8.118   4794  Z= 0.362
  Chirality :  0.047   0.158    522
  Planarity :  0.005   0.037    612
  Dihedral  :  4.394  13.081    456
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 18.43 %
    Favored  : 79.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.07 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.09 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  68 
 TYR   0.012   0.002   TYR B  48 
 PHE   0.011   0.002   PHE C  74 
 HIS   0.001   0.000   HIS F  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 3552)
  covalent geometry    : angle       0.75184 ( 4794)
  hydrogen bonds       : bond        0.02656 (   46)
  hydrogen bonds       : angle       5.97052 (  138)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 149
  time to evaluate  : 0.079 
Fit side-chains
REVERT: D   58 ASP cc_start: 0.8231 (t0) cc_final: 0.7917 (t0)
REVERT: D   63 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7711 (mt-10)
REVERT: D   65 ARG cc_start: 0.6504 (mtt180) cc_final: 0.5749 (mtp85)
REVERT: D   74 PHE cc_start: 0.7363 (t80) cc_final: 0.7027 (t80)
REVERT: D   78 LYS cc_start: 0.8584 (mttt) cc_final: 0.8127 (mttm)
REVERT: A   39 PHE cc_start: 0.8824 (t80) cc_final: 0.8624 (t80)
REVERT: A   78 LYS cc_start: 0.8982 (mttt) cc_final: 0.8479 (mttm)
REVERT: A   80 PHE cc_start: 0.8429 (t80) cc_final: 0.6357 (p90)
REVERT: B   47 TYR cc_start: 0.8863 (t80) cc_final: 0.8499 (t80)
REVERT: B   59 SER cc_start: 0.8512 (p) cc_final: 0.8282 (p)
REVERT: B   63 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7745 (mt-10)
REVERT: B   74 PHE cc_start: 0.7571 (t80) cc_final: 0.7355 (t80)
REVERT: B   78 LYS cc_start: 0.8701 (mttt) cc_final: 0.8277 (mttm)
REVERT: C   25 GLN cc_start: 0.8967 (mt0) cc_final: 0.8732 (mt0)
REVERT: C   58 ASP cc_start: 0.8306 (t0) cc_final: 0.7700 (t0)
REVERT: C   63 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7552 (mt-10)
REVERT: C   65 ARG cc_start: 0.6131 (mtt180) cc_final: 0.5602 (mtp85)
REVERT: C   68 ARG cc_start: 0.6219 (mtt180) cc_final: 0.5971 (ptp-110)
REVERT: C   71 PHE cc_start: 0.7314 (m-80) cc_final: 0.7039 (m-10)
REVERT: C   74 PHE cc_start: 0.7558 (t80) cc_final: 0.7335 (t80)
REVERT: C   78 LYS cc_start: 0.8535 (mttt) cc_final: 0.8062 (mttm)
REVERT: E   58 ASP cc_start: 0.8223 (t0) cc_final: 0.7970 (t0)
REVERT: E   63 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7909 (mt-10)
REVERT: E   74 PHE cc_start: 0.7418 (t80) cc_final: 0.7153 (t80)
REVERT: E   78 LYS cc_start: 0.8503 (mttt) cc_final: 0.8087 (mttp)
REVERT: F   39 PHE cc_start: 0.8694 (t80) cc_final: 0.7721 (p90)
REVERT: F   47 TYR cc_start: 0.8808 (t80) cc_final: 0.8552 (t80)
REVERT: F   58 ASP cc_start: 0.8158 (t0) cc_final: 0.7742 (t0)
REVERT: F   59 SER cc_start: 0.8475 (p) cc_final: 0.8045 (p)
REVERT: F   61 ILE cc_start: 0.8545 (mm) cc_final: 0.8236 (mm)
REVERT: F   65 ARG cc_start: 0.6468 (mtt180) cc_final: 0.6082 (mtp85)
REVERT: F   78 LYS cc_start: 0.8474 (mttt) cc_final: 0.7967 (mmmt)
REVERT: F   80 PHE cc_start: 0.8320 (t80) cc_final: 0.8065 (t80)
  outliers start: 7
  outliers final: 6
  residues processed: 151
  average time/residue: 0.0587
  time to fit residues: 10.3807
Evaluate side-chains
  149 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 143
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue   59 SER
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain A residue   59 SER
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain E residue   22 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 17 optimal weight:   20.0000
   chunk 12 optimal weight:   20.0000
   chunk 6 optimal weight:    8.9990
   chunk 22 optimal weight:   40.0000
   chunk 31 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 13 optimal weight:    9.9990
   chunk 35 optimal weight:    7.9990
   chunk 25 optimal weight:   20.0000
   chunk 4 optimal weight:    7.9990
   overall best weight:    5.9988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4624 r_free = 0.4624 target = 0.155721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.122753 restraints weight = 4904.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.125454 restraints weight = 2357.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.127076 restraints weight = 1591.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.128045 restraints weight = 1281.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.128535 restraints weight = 1131.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.4369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.4046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3552  Z= 0.195
  Angle     :  0.725   8.091   4794  Z= 0.349
  Chirality :  0.045   0.146    522
  Planarity :  0.004   0.030    612
  Dihedral  :  4.328  12.943    456
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.70 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 18.18 %
    Favored  : 76.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.20 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.19 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  68 
 TYR   0.012   0.002   TYR B  48 
 PHE   0.014   0.002   PHE A  27 
 HIS   0.001   0.000   HIS B  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 3552)
  covalent geometry    : angle       0.72528 ( 4794)
  hydrogen bonds       : bond        0.02286 (   46)
  hydrogen bonds       : angle       5.47091 (  138)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 148
  time to evaluate  : 0.084 
Fit side-chains
REVERT: D   58 ASP cc_start: 0.8299 (t0) cc_final: 0.7893 (t0)
REVERT: D   63 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7854 (mt-10)
REVERT: D   65 ARG cc_start: 0.6618 (mtt180) cc_final: 0.5905 (mtp85)
REVERT: D   71 PHE cc_start: 0.7235 (m-80) cc_final: 0.6986 (m-10)
REVERT: D   74 PHE cc_start: 0.7472 (t80) cc_final: 0.7114 (t80)
REVERT: D   78 LYS cc_start: 0.8450 (mttt) cc_final: 0.8027 (mttp)
REVERT: A   24 ASP cc_start: 0.7797 (p0) cc_final: 0.6981 (t0)
REVERT: A   39 PHE cc_start: 0.8676 (t80) cc_final: 0.8413 (t80)
REVERT: A   47 TYR cc_start: 0.8659 (t80) cc_final: 0.8455 (t80)
REVERT: A   65 ARG cc_start: 0.5515 (ttp80) cc_final: 0.5288 (mtp85)
REVERT: A   68 ARG cc_start: 0.7643 (ptp90) cc_final: 0.7220 (mtp85)
REVERT: A   76 ASP cc_start: 0.8374 (t0) cc_final: 0.8049 (t0)
REVERT: A   78 LYS cc_start: 0.8952 (mttt) cc_final: 0.8458 (mttm)
REVERT: A   80 PHE cc_start: 0.8404 (t80) cc_final: 0.6124 (p90)
REVERT: B   47 TYR cc_start: 0.8851 (t80) cc_final: 0.8410 (t80)
REVERT: B   59 SER cc_start: 0.8570 (p) cc_final: 0.8333 (p)
REVERT: B   63 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7679 (mt-10)
REVERT: B   74 PHE cc_start: 0.7726 (t80) cc_final: 0.7457 (t80)
REVERT: B   78 LYS cc_start: 0.8673 (mttt) cc_final: 0.8228 (mttm)
REVERT: C   40 LEU cc_start: 0.8818 (mt) cc_final: 0.8585 (mt)
REVERT: C   63 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7800 (mt-10)
REVERT: C   65 ARG cc_start: 0.6218 (mtt180) cc_final: 0.5863 (mtp85)
REVERT: C   71 PHE cc_start: 0.7410 (m-80) cc_final: 0.7189 (m-10)
REVERT: C   78 LYS cc_start: 0.8611 (mttt) cc_final: 0.8128 (mttm)
REVERT: E   63 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7996 (mt-10)
REVERT: E   68 ARG cc_start: 0.6195 (mtt180) cc_final: 0.5772 (mtp85)
REVERT: E   74 PHE cc_start: 0.7569 (t80) cc_final: 0.7351 (t80)
REVERT: E   78 LYS cc_start: 0.8513 (mttt) cc_final: 0.8107 (mttp)
REVERT: E   80 PHE cc_start: 0.8568 (t80) cc_final: 0.8329 (t80)
REVERT: F   39 PHE cc_start: 0.8739 (t80) cc_final: 0.7687 (p90)
REVERT: F   47 TYR cc_start: 0.8788 (t80) cc_final: 0.8553 (t80)
REVERT: F   58 ASP cc_start: 0.8078 (t0) cc_final: 0.7709 (t0)
REVERT: F   59 SER cc_start: 0.8552 (p) cc_final: 0.8112 (p)
REVERT: F   65 ARG cc_start: 0.6681 (mtt180) cc_final: 0.6372 (mtp85)
REVERT: F   68 ARG cc_start: 0.5859 (mtt180) cc_final: 0.4133 (mmp-170)
REVERT: F   78 LYS cc_start: 0.8510 (mttt) cc_final: 0.8036 (mmmt)
  outliers start: 21
  outliers final: 19
  residues processed: 152
  average time/residue: 0.0547
  time to fit residues: 9.7603
Evaluate side-chains
  165 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 146
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   41 SER
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue   59 SER
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain A residue   59 SER
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   88 LYS
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain C residue   22 LEU
Chi-restraints excluded: chain C residue   41 SER
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   86 THR
Chi-restraints excluded: chain E residue   22 LEU
Chi-restraints excluded: chain E residue   43 THR
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   43 THR
Chi-restraints excluded: chain F residue   86 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 25 optimal weight:   20.0000
   chunk 7 optimal weight:   20.0000
   chunk 11 optimal weight:   20.0000
   chunk 3 optimal weight:    6.9990
   chunk 26 optimal weight:    6.9990
   chunk 35 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 17 optimal weight:   20.0000
   chunk 20 optimal weight:   20.0000
   chunk 15 optimal weight:    9.9990
   chunk 2 optimal weight:    5.9990
   overall best weight:    6.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.153761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.120133 restraints weight = 4818.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.122670 restraints weight = 2374.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.124268 restraints weight = 1623.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.125118 restraints weight = 1310.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.125206 restraints weight = 1169.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.4334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.4436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   3552  Z= 0.213
  Angle     :  0.742   8.645   4794  Z= 0.350
  Chirality :  0.045   0.145    522
  Planarity :  0.004   0.025    612
  Dihedral  :  4.304  12.238    456
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.44 %
    Favored  : 88.56 %
  Rotamer:
    Outliers :  7.58 %
    Allowed  : 17.68 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.32 (0.34), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.28 (0.26), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D  68 
 TYR   0.013   0.002   TYR A  48 
 PHE   0.025   0.002   PHE B  80 
 HIS   0.001   0.000   HIS F  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 3552)
  covalent geometry    : angle       0.74193 ( 4794)
  hydrogen bonds       : bond        0.02156 (   46)
  hydrogen bonds       : angle       5.02817 (  138)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 152
  time to evaluate  : 0.159 
Fit side-chains
REVERT: D   39 PHE cc_start: 0.9098 (t80) cc_final: 0.8878 (t80)
REVERT: D   58 ASP cc_start: 0.8301 (t0) cc_final: 0.8070 (t0)
REVERT: D   63 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7777 (mt-10)
REVERT: D   65 ARG cc_start: 0.6723 (mtt180) cc_final: 0.5946 (mtp85)
REVERT: D   74 PHE cc_start: 0.7533 (t80) cc_final: 0.7156 (t80)
REVERT: D   78 LYS cc_start: 0.8488 (mttt) cc_final: 0.8018 (mttp)
REVERT: A   24 ASP cc_start: 0.7908 (p0) cc_final: 0.7109 (t0)
REVERT: A   39 PHE cc_start: 0.8317 (t80) cc_final: 0.8097 (t80)
REVERT: A   68 ARG cc_start: 0.7700 (ptp90) cc_final: 0.7473 (mtp85)
REVERT: A   76 ASP cc_start: 0.8481 (t0) cc_final: 0.8145 (t0)
REVERT: A   78 LYS cc_start: 0.8945 (mttt) cc_final: 0.8464 (mttm)
REVERT: A   80 PHE cc_start: 0.8459 (t80) cc_final: 0.6592 (p90)
REVERT: B   47 TYR cc_start: 0.8893 (t80) cc_final: 0.8426 (t80)
REVERT: B   63 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7669 (mt-10)
REVERT: B   68 ARG cc_start: 0.7463 (ptp90) cc_final: 0.7076 (ptp-110)
REVERT: B   74 PHE cc_start: 0.7658 (t80) cc_final: 0.7361 (t80)
REVERT: B   78 LYS cc_start: 0.8663 (mttt) cc_final: 0.8209 (mttm)
REVERT: C   39 PHE cc_start: 0.8815 (t80) cc_final: 0.8592 (t80)
REVERT: C   58 ASP cc_start: 0.8388 (t0) cc_final: 0.7841 (t0)
REVERT: C   59 SER cc_start: 0.8839 (p) cc_final: 0.8286 (p)
REVERT: C   61 ILE cc_start: 0.8900 (mm) cc_final: 0.8631 (mm)
REVERT: C   63 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7748 (mt-10)
REVERT: C   65 ARG cc_start: 0.6228 (mtt180) cc_final: 0.5859 (mtp85)
REVERT: C   68 ARG cc_start: 0.6814 (mtp85) cc_final: 0.6498 (ptp-110)
REVERT: C   78 LYS cc_start: 0.8616 (mttt) cc_final: 0.8162 (mttm)
REVERT: C   80 PHE cc_start: 0.8210 (t80) cc_final: 0.7966 (t80)
REVERT: E   63 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7936 (mt-10)
REVERT: E   68 ARG cc_start: 0.6140 (mtt180) cc_final: 0.5470 (mtp85)
REVERT: E   74 PHE cc_start: 0.7570 (t80) cc_final: 0.7344 (t80)
REVERT: E   78 LYS cc_start: 0.8490 (mttt) cc_final: 0.8074 (mttp)
REVERT: E   80 PHE cc_start: 0.8603 (t80) cc_final: 0.8372 (t80)
REVERT: F   39 PHE cc_start: 0.8759 (t80) cc_final: 0.7681 (p90)
REVERT: F   58 ASP cc_start: 0.8121 (t0) cc_final: 0.7717 (t0)
REVERT: F   59 SER cc_start: 0.8708 (p) cc_final: 0.8286 (p)
REVERT: F   61 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7578 (mm)
REVERT: F   65 ARG cc_start: 0.6618 (mtt180) cc_final: 0.6362 (mtp85)
REVERT: F   67 ASP cc_start: 0.8558 (t0) cc_final: 0.8343 (t0)
REVERT: F   68 ARG cc_start: 0.5828 (mtt180) cc_final: 0.4210 (mmp-170)
REVERT: F   76 ASP cc_start: 0.8222 (t0) cc_final: 0.7970 (t0)
REVERT: F   78 LYS cc_start: 0.8359 (mttt) cc_final: 0.7920 (mmmt)
REVERT: F   80 PHE cc_start: 0.8486 (t80) cc_final: 0.8267 (t80)
  outliers start: 30
  outliers final: 24
  residues processed: 160
  average time/residue: 0.0560
  time to fit residues: 10.6372
Evaluate side-chains
  174 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 149
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   41 SER
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue   59 SER
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain A residue   41 SER
Chi-restraints excluded: chain A residue   59 SER
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   88 LYS
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain C residue   22 LEU
Chi-restraints excluded: chain C residue   41 SER
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   86 THR
Chi-restraints excluded: chain E residue   22 LEU
Chi-restraints excluded: chain E residue   41 SER
Chi-restraints excluded: chain E residue   43 THR
Chi-restraints excluded: chain E residue   59 SER
Chi-restraints excluded: chain E residue   86 THR
Chi-restraints excluded: chain F residue   43 THR
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain F residue   86 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 14 optimal weight:    9.9990
   chunk 34 optimal weight:    0.0570
   chunk 4 optimal weight:   30.0000
   chunk 15 optimal weight:   10.0000
   chunk 5 optimal weight:   20.0000
   chunk 11 optimal weight:   20.0000
   chunk 26 optimal weight:    8.9990
   chunk 28 optimal weight:    8.9990
   chunk 19 optimal weight:   20.0000
   chunk 6 optimal weight:   10.0000
   overall best weight:    7.6108

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4581 r_free = 0.4581 target = 0.151994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.118919 restraints weight = 4908.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.121448 restraints weight = 2398.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.122960 restraints weight = 1641.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.123884 restraints weight = 1334.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.124155 restraints weight = 1186.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.4349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.4768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   3552  Z= 0.231
  Angle     :  0.753   9.195   4794  Z= 0.355
  Chirality :  0.045   0.142    522
  Planarity :  0.004   0.028    612
  Dihedral  :  4.273  11.809    456
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.69 %
    Favored  : 88.31 %
  Rotamer:
    Outliers :  9.09 %
    Allowed  : 18.69 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.33 (0.34), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.29 (0.26), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  68 
 TYR   0.015   0.002   TYR A  48 
 PHE   0.019   0.002   PHE B  80 
 HIS   0.002   0.001   HIS F  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 ( 3552)
  covalent geometry    : angle       0.75328 ( 4794)
  hydrogen bonds       : bond        0.02133 (   46)
  hydrogen bonds       : angle       5.01196 (  138)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 148
  time to evaluate  : 0.079 
Fit side-chains
REVERT: D   63 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7844 (mt-10)
REVERT: D   65 ARG cc_start: 0.6852 (mtt180) cc_final: 0.6570 (mtp85)
REVERT: D   74 PHE cc_start: 0.7588 (t80) cc_final: 0.7239 (t80)
REVERT: D   78 LYS cc_start: 0.8513 (mttt) cc_final: 0.8033 (mttp)
REVERT: A   39 PHE cc_start: 0.8422 (t80) cc_final: 0.8185 (t80)
REVERT: A   68 ARG cc_start: 0.7525 (ptp90) cc_final: 0.7306 (mtp85)
REVERT: A   76 ASP cc_start: 0.8531 (t0) cc_final: 0.8248 (t0)
REVERT: A   78 LYS cc_start: 0.8919 (mttt) cc_final: 0.8460 (mttm)
REVERT: A   80 PHE cc_start: 0.8513 (t80) cc_final: 0.6537 (p90)
REVERT: B   63 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7704 (mt-10)
REVERT: B   74 PHE cc_start: 0.7626 (t80) cc_final: 0.7278 (t80)
REVERT: B   78 LYS cc_start: 0.8668 (mttt) cc_final: 0.8207 (mttm)
REVERT: C   58 ASP cc_start: 0.8397 (t0) cc_final: 0.7897 (t0)
REVERT: C   59 SER cc_start: 0.8863 (p) cc_final: 0.8291 (p)
REVERT: C   61 ILE cc_start: 0.8899 (mm) cc_final: 0.8624 (mm)
REVERT: C   63 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7789 (mt-10)
REVERT: C   74 PHE cc_start: 0.7611 (t80) cc_final: 0.7341 (t80)
REVERT: C   78 LYS cc_start: 0.8575 (mttt) cc_final: 0.8048 (mttm)
REVERT: E   63 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8051 (mt-10)
REVERT: E   68 ARG cc_start: 0.5977 (mtt180) cc_final: 0.5536 (mtp85)
REVERT: E   74 PHE cc_start: 0.7609 (t80) cc_final: 0.7364 (t80)
REVERT: E   78 LYS cc_start: 0.8461 (mttt) cc_final: 0.8034 (mttp)
REVERT: F   39 PHE cc_start: 0.8766 (t80) cc_final: 0.7684 (p90)
REVERT: F   58 ASP cc_start: 0.8118 (t0) cc_final: 0.7756 (t0)
REVERT: F   59 SER cc_start: 0.8730 (p) cc_final: 0.8291 (p)
REVERT: F   65 ARG cc_start: 0.6779 (mtt180) cc_final: 0.6486 (mtp85)
REVERT: F   68 ARG cc_start: 0.5889 (mtt180) cc_final: 0.3873 (mmp-170)
REVERT: F   76 ASP cc_start: 0.8306 (t0) cc_final: 0.8040 (t0)
REVERT: F   78 LYS cc_start: 0.8351 (mttt) cc_final: 0.7913 (mmmt)
REVERT: F   80 PHE cc_start: 0.8505 (t80) cc_final: 0.8294 (t80)
  outliers start: 36
  outliers final: 29
  residues processed: 159
  average time/residue: 0.0520
  time to fit residues: 9.7852
Evaluate side-chains
  176 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 147
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue   41 SER
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue   59 SER
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain A residue   41 SER
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   59 SER
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   88 LYS
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain C residue   22 LEU
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   86 THR
Chi-restraints excluded: chain E residue   22 LEU
Chi-restraints excluded: chain E residue   41 SER
Chi-restraints excluded: chain E residue   43 THR
Chi-restraints excluded: chain E residue   59 SER
Chi-restraints excluded: chain E residue   86 THR
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   43 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 34 optimal weight:    0.5980
   chunk 30 optimal weight:    9.9990
   chunk 21 optimal weight:    3.9990
   chunk 33 optimal weight:    7.9990
   chunk 10 optimal weight:    0.0870
   chunk 9 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 31 optimal weight:   10.0000
   chunk 11 optimal weight:   20.0000
   chunk 15 optimal weight:    5.9990
   chunk 20 optimal weight:    9.9990
   overall best weight:    3.7364

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4748 r_free = 0.4748 target = 0.164411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.131274 restraints weight = 4701.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.134353 restraints weight = 2267.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.136156 restraints weight = 1494.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.137187 restraints weight = 1181.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.137716 restraints weight = 1039.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.4482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.4938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3552  Z= 0.142
  Angle     :  0.700   8.788   4794  Z= 0.328
  Chirality :  0.044   0.162    522
  Planarity :  0.003   0.028    612
  Dihedral  :  4.043  11.661    456
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.20 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 24.49 %
    Favored  : 70.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.27 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.25 (0.26), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  68 
 TYR   0.010   0.001   TYR B  47 
 PHE   0.013   0.002   PHE B  80 
 HIS   0.001   0.001   HIS F  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 3552)
  covalent geometry    : angle       0.70022 ( 4794)
  hydrogen bonds       : bond        0.01786 (   46)
  hydrogen bonds       : angle       4.85559 (  138)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 146
  time to evaluate  : 0.083 
Fit side-chains
REVERT: D   63 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7865 (mt-10)
REVERT: D   74 PHE cc_start: 0.7527 (t80) cc_final: 0.7198 (t80)
REVERT: D   78 LYS cc_start: 0.8493 (mttt) cc_final: 0.8005 (mttp)
REVERT: A   24 ASP cc_start: 0.7822 (p0) cc_final: 0.6933 (t0)
REVERT: A   78 LYS cc_start: 0.8903 (mttt) cc_final: 0.8438 (mttm)
REVERT: A   80 PHE cc_start: 0.8514 (t80) cc_final: 0.6504 (p90)
REVERT: B   47 TYR cc_start: 0.8751 (t80) cc_final: 0.8277 (t80)
REVERT: B   63 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7710 (mt-10)
REVERT: B   65 ARG cc_start: 0.7387 (mtp85) cc_final: 0.6974 (mtp85)
REVERT: B   68 ARG cc_start: 0.7397 (ptp90) cc_final: 0.7123 (ptp-110)
REVERT: B   74 PHE cc_start: 0.7652 (t80) cc_final: 0.7297 (t80)
REVERT: B   78 LYS cc_start: 0.8628 (mttt) cc_final: 0.8164 (mttm)
REVERT: C   59 SER cc_start: 0.8906 (p) cc_final: 0.8292 (p)
REVERT: C   61 ILE cc_start: 0.8898 (mm) cc_final: 0.8646 (mm)
REVERT: C   63 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7776 (mt-10)
REVERT: C   74 PHE cc_start: 0.7531 (t80) cc_final: 0.7266 (t80)
REVERT: C   78 LYS cc_start: 0.8565 (mttt) cc_final: 0.8031 (mttm)
REVERT: E   63 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7930 (mt-10)
REVERT: E   68 ARG cc_start: 0.6020 (mtt180) cc_final: 0.5413 (mtp85)
REVERT: E   74 PHE cc_start: 0.7528 (t80) cc_final: 0.7312 (t80)
REVERT: E   78 LYS cc_start: 0.8329 (mttt) cc_final: 0.7946 (mttp)
REVERT: F   39 PHE cc_start: 0.8780 (t80) cc_final: 0.7729 (p90)
REVERT: F   47 TYR cc_start: 0.8900 (t80) cc_final: 0.8651 (t80)
REVERT: F   58 ASP cc_start: 0.8235 (t0) cc_final: 0.7823 (t0)
REVERT: F   59 SER cc_start: 0.8531 (p) cc_final: 0.8117 (p)
REVERT: F   65 ARG cc_start: 0.6705 (mtt180) cc_final: 0.6494 (mtp85)
REVERT: F   68 ARG cc_start: 0.5881 (mtt180) cc_final: 0.4157 (mmp-170)
REVERT: F   78 LYS cc_start: 0.8343 (mttt) cc_final: 0.7890 (mmmt)
  outliers start: 19
  outliers final: 14
  residues processed: 152
  average time/residue: 0.0749
  time to fit residues: 13.1855
Evaluate side-chains
  154 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 140
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   41 SER
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue   88 LYS
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain C residue   22 LEU
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain E residue   22 LEU
Chi-restraints excluded: chain E residue   86 THR
Chi-restraints excluded: chain F residue   22 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 6 optimal weight:    9.9990
   chunk 22 optimal weight:   30.0000
   chunk 8 optimal weight:    5.9990
   chunk 3 optimal weight:    8.9990
   chunk 13 optimal weight:   20.0000
   chunk 2 optimal weight:    9.9990
   chunk 11 optimal weight:   20.0000
   chunk 4 optimal weight:    7.9990
   chunk 35 optimal weight:    7.9990
   chunk 30 optimal weight:   10.0000
   chunk 25 optimal weight:    8.9990
   overall best weight:    7.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4604 r_free = 0.4604 target = 0.151567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.119148 restraints weight = 5051.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.121823 restraints weight = 2399.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.123365 restraints weight = 1610.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.124310 restraints weight = 1299.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.124845 restraints weight = 1150.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.4330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.5230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   3552  Z= 0.240
  Angle     :  0.782   8.923   4794  Z= 0.374
  Chirality :  0.045   0.146    522
  Planarity :  0.004   0.030    612
  Dihedral  :  4.283  12.920    456
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.19 %
    Favored  : 87.81 %
  Rotamer:
    Outliers :  7.83 %
    Allowed  : 21.97 %
    Favored  : 70.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.32 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.28 (0.26), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  21 
 TYR   0.016   0.002   TYR C  48 
 PHE   0.022   0.002   PHE A  39 
 HIS   0.002   0.001   HIS F  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00536 ( 3552)
  covalent geometry    : angle       0.78246 ( 4794)
  hydrogen bonds       : bond        0.01571 (   46)
  hydrogen bonds       : angle       4.79947 (  138)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 146
  time to evaluate  : 0.082 
Fit side-chains
REVERT: D   63 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7820 (mt-10)
REVERT: D   74 PHE cc_start: 0.7529 (t80) cc_final: 0.7158 (t80)
REVERT: D   78 LYS cc_start: 0.8381 (mttt) cc_final: 0.7895 (mttp)
REVERT: A   76 ASP cc_start: 0.8559 (t0) cc_final: 0.8334 (t0)
REVERT: A   78 LYS cc_start: 0.8912 (mttt) cc_final: 0.8435 (mttm)
REVERT: A   80 PHE cc_start: 0.8557 (t80) cc_final: 0.6579 (p90)
REVERT: B   47 TYR cc_start: 0.8784 (t80) cc_final: 0.8239 (t80)
REVERT: B   63 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7810 (mt-10)
REVERT: B   65 ARG cc_start: 0.7326 (mtp85) cc_final: 0.6995 (mtp85)
REVERT: B   74 PHE cc_start: 0.7598 (t80) cc_final: 0.7239 (t80)
REVERT: B   78 LYS cc_start: 0.8652 (mttt) cc_final: 0.8162 (mttm)
REVERT: C   39 PHE cc_start: 0.8913 (t80) cc_final: 0.8593 (t80)
REVERT: C   59 SER cc_start: 0.8986 (p) cc_final: 0.8631 (p)
REVERT: C   61 ILE cc_start: 0.8840 (mm) cc_final: 0.8630 (mm)
REVERT: C   63 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7780 (mt-10)
REVERT: C   65 ARG cc_start: 0.7634 (mtp85) cc_final: 0.7184 (mtp85)
REVERT: C   78 LYS cc_start: 0.8522 (mttt) cc_final: 0.7987 (mttp)
REVERT: E   63 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7783 (mt-10)
REVERT: E   74 PHE cc_start: 0.7603 (t80) cc_final: 0.7377 (t80)
REVERT: E   78 LYS cc_start: 0.8270 (mttt) cc_final: 0.7865 (mttp)
REVERT: F   39 PHE cc_start: 0.8757 (t80) cc_final: 0.7668 (p90)
REVERT: F   58 ASP cc_start: 0.8128 (t0) cc_final: 0.7693 (t0)
REVERT: F   59 SER cc_start: 0.8594 (p) cc_final: 0.8188 (p)
REVERT: F   65 ARG cc_start: 0.6735 (mtt180) cc_final: 0.6461 (mtp85)
REVERT: F   68 ARG cc_start: 0.5857 (mtt180) cc_final: 0.3896 (mmp-170)
REVERT: F   76 ASP cc_start: 0.8299 (t0) cc_final: 0.8053 (t0)
REVERT: F   78 LYS cc_start: 0.8295 (mttt) cc_final: 0.7894 (mmmt)
  outliers start: 31
  outliers final: 28
  residues processed: 155
  average time/residue: 0.0630
  time to fit residues: 11.4448
Evaluate side-chains
  170 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 142
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue   41 SER
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue   59 SER
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain A residue   41 SER
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   59 SER
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue   88 LYS
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain C residue   22 LEU
Chi-restraints excluded: chain C residue   41 SER
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   86 THR
Chi-restraints excluded: chain E residue   22 LEU
Chi-restraints excluded: chain E residue   41 SER
Chi-restraints excluded: chain E residue   43 THR
Chi-restraints excluded: chain E residue   59 SER
Chi-restraints excluded: chain E residue   86 THR
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   43 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 8 optimal weight:   20.0000
   chunk 22 optimal weight:    7.9990
   chunk 6 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 11 optimal weight:    8.9990
   chunk 2 optimal weight:   20.0000
   chunk 29 optimal weight:    8.9990
   chunk 15 optimal weight:    5.9990
   overall best weight:    7.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4598 r_free = 0.4598 target = 0.151092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.118913 restraints weight = 5019.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.121608 restraints weight = 2348.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.123232 restraints weight = 1561.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.124129 restraints weight = 1250.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.124672 restraints weight = 1108.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.4322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.5366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   3552  Z= 0.232
  Angle     :  0.815   9.621   4794  Z= 0.379
  Chirality :  0.046   0.143    522
  Planarity :  0.004   0.026    612
  Dihedral  :  4.328  13.291    456
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.70 %
    Favored  : 89.30 %
  Rotamer:
    Outliers :  7.58 %
    Allowed  : 23.74 %
    Favored  : 68.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.37 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.33 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  21 
 TYR   0.015   0.002   TYR A  48 
 PHE   0.018   0.002   PHE A  27 
 HIS   0.002   0.001   HIS F  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 ( 3552)
  covalent geometry    : angle       0.81472 ( 4794)
  hydrogen bonds       : bond        0.01530 (   46)
  hydrogen bonds       : angle       4.72537 (  138)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 144
  time to evaluate  : 0.082 
Fit side-chains
REVERT: D   63 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7791 (mt-10)
REVERT: D   74 PHE cc_start: 0.7520 (t80) cc_final: 0.7218 (t80)
REVERT: D   78 LYS cc_start: 0.8385 (mttt) cc_final: 0.7886 (mttp)
REVERT: A   78 LYS cc_start: 0.8897 (mttt) cc_final: 0.8422 (mttm)
REVERT: B   47 TYR cc_start: 0.8785 (t80) cc_final: 0.8291 (t80)
REVERT: B   65 ARG cc_start: 0.7371 (mtp85) cc_final: 0.7037 (mtp85)
REVERT: B   68 ARG cc_start: 0.7016 (ptp-110) cc_final: 0.6783 (ptp-170)
REVERT: B   74 PHE cc_start: 0.7578 (t80) cc_final: 0.7202 (t80)
REVERT: B   78 LYS cc_start: 0.8638 (mttt) cc_final: 0.8220 (mttm)
REVERT: C   40 LEU cc_start: 0.8718 (mm) cc_final: 0.8510 (mt)
REVERT: C   59 SER cc_start: 0.8979 (p) cc_final: 0.8655 (p)
REVERT: C   63 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7806 (mt-10)
REVERT: C   65 ARG cc_start: 0.7686 (mtp85) cc_final: 0.7086 (mtp85)
REVERT: C   78 LYS cc_start: 0.8508 (mttt) cc_final: 0.7962 (mttp)
REVERT: E   63 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7695 (mt-10)
REVERT: E   68 ARG cc_start: 0.5793 (mtp85) cc_final: 0.5350 (mtp85)
REVERT: E   78 LYS cc_start: 0.8270 (mttt) cc_final: 0.7934 (mttp)
REVERT: F   39 PHE cc_start: 0.8786 (t80) cc_final: 0.7648 (p90)
REVERT: F   58 ASP cc_start: 0.8162 (t0) cc_final: 0.7708 (t0)
REVERT: F   59 SER cc_start: 0.8535 (p) cc_final: 0.8116 (p)
REVERT: F   65 ARG cc_start: 0.6715 (mtt180) cc_final: 0.6375 (mtp85)
REVERT: F   68 ARG cc_start: 0.5755 (mtt180) cc_final: 0.3832 (mmp-170)
REVERT: F   76 ASP cc_start: 0.8371 (t0) cc_final: 0.8104 (t0)
REVERT: F   78 LYS cc_start: 0.8263 (mttt) cc_final: 0.7877 (mmmt)
  outliers start: 30
  outliers final: 28
  residues processed: 151
  average time/residue: 0.0568
  time to fit residues: 10.1182
Evaluate side-chains
  169 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 141
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   41 SER
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue   59 SER
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain A residue   41 SER
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   59 SER
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   88 LYS
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain C residue   22 LEU
Chi-restraints excluded: chain C residue   41 SER
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   86 THR
Chi-restraints excluded: chain E residue   22 LEU
Chi-restraints excluded: chain E residue   41 SER
Chi-restraints excluded: chain E residue   43 THR
Chi-restraints excluded: chain E residue   59 SER
Chi-restraints excluded: chain E residue   61 ILE
Chi-restraints excluded: chain E residue   86 THR
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   43 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 34 optimal weight:   30.0000
   chunk 26 optimal weight:   20.0000
   chunk 14 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    8.9990
   chunk 7 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 20 optimal weight:    6.9990
   overall best weight:    6.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4613 r_free = 0.4613 target = 0.152395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.119798 restraints weight = 4885.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.122456 restraints weight = 2318.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.124049 restraints weight = 1565.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.124927 restraints weight = 1263.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.125470 restraints weight = 1127.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.4340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.5470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   3552  Z= 0.214
  Angle     :  0.811   9.881   4794  Z= 0.378
  Chirality :  0.046   0.156    522
  Planarity :  0.004   0.027    612
  Dihedral  :  4.316  14.671    456
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.19 %
    Favored  : 87.81 %
  Rotamer:
    Outliers :  7.32 %
    Allowed  : 25.00 %
    Favored  : 67.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.38 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.33 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  68 
 TYR   0.013   0.002   TYR A  48 
 PHE   0.029   0.002   PHE B  80 
 HIS   0.002   0.001   HIS F  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 ( 3552)
  covalent geometry    : angle       0.81083 ( 4794)
  hydrogen bonds       : bond        0.01441 (   46)
  hydrogen bonds       : angle       4.70932 (  138)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 142
  time to evaluate  : 0.136 
Fit side-chains
REVERT: D   63 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7858 (mt-10)
REVERT: D   74 PHE cc_start: 0.7543 (t80) cc_final: 0.7270 (t80)
REVERT: D   78 LYS cc_start: 0.8493 (mttt) cc_final: 0.8020 (mttp)
REVERT: A   78 LYS cc_start: 0.8852 (mttt) cc_final: 0.8394 (mttm)
REVERT: B   47 TYR cc_start: 0.8805 (t80) cc_final: 0.8276 (t80)
REVERT: B   65 ARG cc_start: 0.7451 (mtp85) cc_final: 0.7178 (mtp85)
REVERT: B   68 ARG cc_start: 0.7209 (ptp-110) cc_final: 0.6961 (ptp-170)
REVERT: B   74 PHE cc_start: 0.7638 (t80) cc_final: 0.7392 (t80)
REVERT: B   78 LYS cc_start: 0.8700 (mttt) cc_final: 0.8286 (mttm)
REVERT: C   40 LEU cc_start: 0.8786 (mm) cc_final: 0.8546 (mt)
REVERT: C   59 SER cc_start: 0.8928 (p) cc_final: 0.8670 (p)
REVERT: C   63 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7861 (mt-10)
REVERT: C   65 ARG cc_start: 0.7681 (mtp85) cc_final: 0.7142 (mtp85)
REVERT: C   78 LYS cc_start: 0.8610 (mttt) cc_final: 0.8081 (mttp)
REVERT: E   63 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7869 (mt-10)
REVERT: E   68 ARG cc_start: 0.5926 (mtp85) cc_final: 0.5492 (mtp85)
REVERT: E   78 LYS cc_start: 0.8350 (mttt) cc_final: 0.8011 (mttp)
REVERT: F   39 PHE cc_start: 0.8770 (t80) cc_final: 0.7667 (p90)
REVERT: F   58 ASP cc_start: 0.8112 (t0) cc_final: 0.7723 (t0)
REVERT: F   59 SER cc_start: 0.8591 (p) cc_final: 0.8197 (p)
REVERT: F   68 ARG cc_start: 0.5722 (mtt180) cc_final: 0.3718 (mmp-170)
REVERT: F   76 ASP cc_start: 0.8458 (t0) cc_final: 0.8206 (t0)
REVERT: F   78 LYS cc_start: 0.8352 (mttt) cc_final: 0.7999 (mmmt)
  outliers start: 29
  outliers final: 26
  residues processed: 149
  average time/residue: 0.0668
  time to fit residues: 11.7963
Evaluate side-chains
  165 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   41 SER
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue   59 SER
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain A residue   41 SER
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   59 SER
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   88 LYS
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain C residue   22 LEU
Chi-restraints excluded: chain C residue   41 SER
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain E residue   22 LEU
Chi-restraints excluded: chain E residue   41 SER
Chi-restraints excluded: chain E residue   43 THR
Chi-restraints excluded: chain E residue   86 THR
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   43 THR
Chi-restraints excluded: chain F residue   86 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 17 optimal weight:    6.9990
   chunk 21 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 32 optimal weight:    8.9990
   chunk 18 optimal weight:    5.9990
   chunk 16 optimal weight:   30.0000
   chunk 35 optimal weight:    8.9990
   chunk 28 optimal weight:    7.9990
   chunk 33 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    5.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4626 r_free = 0.4626 target = 0.153479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.120841 restraints weight = 4895.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.123453 restraints weight = 2390.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.125027 restraints weight = 1639.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.125970 restraints weight = 1326.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.126468 restraints weight = 1180.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.4383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.5596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3552  Z= 0.185
  Angle     :  0.798   9.844   4794  Z= 0.372
  Chirality :  0.045   0.148    522
  Planarity :  0.004   0.027    612
  Dihedral  :  4.259  17.513    456
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.44 %
    Favored  : 88.56 %
  Rotamer:
    Outliers :  6.31 %
    Allowed  : 26.01 %
    Favored  : 67.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.36 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.32 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  21 
 TYR   0.011   0.002   TYR B  47 
 PHE   0.027   0.002   PHE B  80 
 HIS   0.003   0.001   HIS B  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 3552)
  covalent geometry    : angle       0.79787 ( 4794)
  hydrogen bonds       : bond        0.01511 (   46)
  hydrogen bonds       : angle       4.70565 (  138)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 143
  time to evaluate  : 0.137 
Fit side-chains
REVERT: D   63 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7846 (mt-10)
REVERT: D   65 ARG cc_start: 0.7389 (mtp85) cc_final: 0.6622 (mtp85)
REVERT: D   74 PHE cc_start: 0.7646 (t80) cc_final: 0.7408 (t80)
REVERT: D   78 LYS cc_start: 0.8443 (mttt) cc_final: 0.8013 (mttp)
REVERT: A   78 LYS cc_start: 0.8844 (mttt) cc_final: 0.8445 (mttm)
REVERT: B   47 TYR cc_start: 0.8785 (t80) cc_final: 0.8330 (t80)
REVERT: B   65 ARG cc_start: 0.7468 (mtp85) cc_final: 0.7183 (mtp85)
REVERT: B   74 PHE cc_start: 0.7653 (t80) cc_final: 0.7368 (t80)
REVERT: B   78 LYS cc_start: 0.8585 (mttt) cc_final: 0.8168 (mttm)
REVERT: C   40 LEU cc_start: 0.8758 (mm) cc_final: 0.8470 (mt)
REVERT: C   59 SER cc_start: 0.8900 (p) cc_final: 0.8645 (p)
REVERT: C   63 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7877 (mt-10)
REVERT: C   65 ARG cc_start: 0.7689 (mtp85) cc_final: 0.7122 (mtp85)
REVERT: C   78 LYS cc_start: 0.8627 (mttt) cc_final: 0.8099 (mttm)
REVERT: E   68 ARG cc_start: 0.5893 (mtp85) cc_final: 0.5450 (mtp85)
REVERT: E   78 LYS cc_start: 0.8349 (mttt) cc_final: 0.8004 (mttp)
REVERT: F   39 PHE cc_start: 0.8778 (t80) cc_final: 0.7686 (p90)
REVERT: F   58 ASP cc_start: 0.8059 (t0) cc_final: 0.7692 (t0)
REVERT: F   59 SER cc_start: 0.8518 (p) cc_final: 0.8143 (p)
REVERT: F   68 ARG cc_start: 0.5791 (mtt180) cc_final: 0.3763 (mmp-170)
REVERT: F   76 ASP cc_start: 0.8435 (t0) cc_final: 0.8199 (t0)
REVERT: F   78 LYS cc_start: 0.8337 (mttt) cc_final: 0.8015 (mmmt)
  outliers start: 25
  outliers final: 24
  residues processed: 149
  average time/residue: 0.0636
  time to fit residues: 11.2323
Evaluate side-chains
  166 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 142
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   41 SER
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue   59 SER
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain A residue   41 SER
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   59 SER
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   88 LYS
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain C residue   22 LEU
Chi-restraints excluded: chain C residue   41 SER
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain E residue   22 LEU
Chi-restraints excluded: chain E residue   41 SER
Chi-restraints excluded: chain E residue   43 THR
Chi-restraints excluded: chain E residue   59 SER
Chi-restraints excluded: chain E residue   86 THR
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   43 THR
Chi-restraints excluded: chain F residue   86 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 2 optimal weight:   20.0000
   chunk 14 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 27 optimal weight:    6.9990
   chunk 30 optimal weight:    9.9990
   chunk 10 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 18 optimal weight:    5.9990
   chunk 26 optimal weight:   10.0000
   overall best weight:    5.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4612 r_free = 0.4612 target = 0.151035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.118325 restraints weight = 4983.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.121011 restraints weight = 2338.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.122644 restraints weight = 1568.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.123561 restraints weight = 1263.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.124000 restraints weight = 1124.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.4368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.5677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3552  Z= 0.186
  Angle     :  0.801   9.932   4794  Z= 0.373
  Chirality :  0.045   0.146    522
  Planarity :  0.004   0.026    612
  Dihedral  :  4.265  20.525    456
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.69 %
    Favored  : 88.31 %
  Rotamer:
    Outliers :  6.31 %
    Allowed  : 25.76 %
    Favored  : 67.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.36 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.32 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  21 
 TYR   0.011   0.002   TYR C  48 
 PHE   0.029   0.002   PHE B  80 
 HIS   0.002   0.001   HIS B  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 3552)
  covalent geometry    : angle       0.80143 ( 4794)
  hydrogen bonds       : bond        0.01446 (   46)
  hydrogen bonds       : angle       4.69899 (  138)

===============================================================================
Job complete
usr+sys time: 574.54 seconds
wall clock time: 10 minutes 34.09 seconds (634.09 seconds total)