Starting phenix.real_space_refine
on Sat Sep 12 09:36:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pf6_13369/09_2026/7pf6_13369.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pf6_13369/09_2026/7pf6_13369.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pf6_13369/09_2026/7pf6_13369.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pf6_13369/09_2026/7pf6_13369.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pf6_13369/09_2026/7pf6_13369.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pf6_13369/09_2026/7pf6_13369.map"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     P     334      5.49       5
     S      10      5.16       5
     C    7420      2.51       5
     N    2528      2.21       5
     O    3178      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 13470
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 798
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 798
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "G"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 3405
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 167, 3405
          Classifications: {'DNA': 167}
          Link IDs: {'rna3p': 166}
    Chain: "J"
      Number of atoms: 3442
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 167, 3442
          Classifications: {'DNA': 167}
          Link IDs: {'rna3p': 166}
    Chain: "U"
      Number of atoms: 535
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 535
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 2, 'TRANS': 72}
  Time building chain proxies: 2.95, per 1000 atoms: 0.22
  Number of scatterers: 13470
  At special positions: 0
  Unit cell: (118.65, 149.1, 115.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     P     334     15.00
     O    3178      8.00
     N    2528      7.00
     C    7420      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: 0.84
  Conformation dependent library (CDL) restraints added in 376.8 milliseconds
  

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1566

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 10 sheets defined
      69.9% alpha, 2.8% beta
      167 base pairs and 282 stacking pairs defined.
    Time for finding SS restraints: 2.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.681A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.815A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.759A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 92
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.144A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
      removed outlier: 3.621A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ASN C  89 " --> pdb=" O   LEU C  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.514A  pdb=" N   ALA D 107 " --> pdb=" O   PRO D 103 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.619A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.689A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   GLY E 132 " --> pdb=" O   ARG E 128 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.834A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.470A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 101
      removed outlier: 3.513A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 123
      removed outlier: 3.856A  pdb=" N   ALA H 107 " --> pdb=" O   PRO H 103 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 38 through 51
      removed outlier: 3.835A  pdb=" N   LEU U  42 " --> pdb=" O   PRO U  38 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   SER U  50 " --> pdb=" O   ALA U  46 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   LYS U  51 " --> pdb=" O   VAL U  47 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 57 through 69
    Processing helix  chain 'U' and resid 75 through 90
      removed outlier: 3.884A  pdb=" N   GLY U  90 " --> pdb=" O   LEU U  86 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.952A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.789A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.492A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.023A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.367A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB1, first strand: chain 'U' and resid 92 through 94

    431 hydrogen bonds defined for protein.
    1281 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      428 hydrogen bonds
      852 hydrogen bond angles
      0 basepair planarities
      167 basepair parallelities
      282 stacking parallelities
  Total time for adding SS restraints: 2.75

  Time building geometry restraints manager: 1.25 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2463
        1.33 -     1.45: 4932
        1.45 -     1.57: 6305
        1.57 -     1.70: 666
        1.70 -     1.82: 20
  Bond restraints: 14386
  Sorted by residual:
  bond pdb=" C3'  DG J 610 "
       pdb=" O3'  DG J 610 "
    ideal  model  delta    sigma   weight residual
    1.435  1.524 -0.089 1.30e-02 5.92e+03 4.64e+01
  bond pdb=" C5'  DG J 611 "
       pdb=" C4'  DG J 611 "
    ideal  model  delta    sigma   weight residual
    1.512  1.542 -0.030 7.00e-03 2.04e+04 1.87e+01
  bond pdb=" C3'  DG J 610 "
       pdb=" C2'  DG J 610 "
    ideal  model  delta    sigma   weight residual
    1.516  1.549 -0.033 8.00e-03 1.56e+04 1.72e+01
  bond pdb=" C3'  DT I 167 "
       pdb=" O3'  DT I 167 "
    ideal  model  delta    sigma   weight residual
    1.435  1.488 -0.053 1.30e-02 5.92e+03 1.66e+01
  bond pdb=" C3'  DC I  31 "
       pdb=" C2'  DC I  31 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 8.00e-03 1.56e+04 1.33e+01
  ... (remaining 14381 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.95: 20806
        5.95 -    11.89: 44
       11.89 -    17.84: 0
       17.84 -    23.79: 2
       23.79 -    29.73: 1
  Bond angle restraints: 20853
  Sorted by residual:
  angle pdb=" O3'  DG J 610 "
        pdb=" P    DG J 611 "
        pdb=" OP2  DG J 611 "
      ideal   model   delta    sigma   weight residual
     108.00   78.27   29.73 3.00e+00 1.11e-01 9.82e+01
  angle pdb=" O3'  DG J 610 "
        pdb=" P    DG J 611 "
        pdb=" OP1  DG J 611 "
      ideal   model   delta    sigma   weight residual
     108.00   85.49   22.51 3.00e+00 1.11e-01 5.63e+01
  angle pdb=" OP1  DG J 611 "
        pdb=" P    DG J 611 "
        pdb=" OP2  DG J 611 "
      ideal   model   delta    sigma   weight residual
     120.00  141.43  -21.43 3.00e+00 1.11e-01 5.10e+01
  angle pdb=" O4'  DG I 120 "
        pdb=" C4'  DG I 120 "
        pdb=" C3'  DG I 120 "
      ideal   model   delta    sigma   weight residual
     106.00  102.23    3.77 6.00e-01 2.78e+00 3.94e+01
  angle pdb=" O4'  DA I  40 "
        pdb=" C4'  DA I  40 "
        pdb=" C3'  DA I  40 "
      ideal   model   delta    sigma   weight residual
     106.00  102.25    3.75 6.00e-01 2.78e+00 3.92e+01
  ... (remaining 20848 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.71: 6024
       34.71 -    69.42: 1725
       69.42 -   104.13: 44
      104.13 -   138.84: 3
      138.84 -   173.55: 3
  Dihedral angle restraints: 7799
    sinusoidal: 5368
      harmonic: 2431
  Sorted by residual:
  dihedral pdb=" CA  GLN G  24 "
           pdb=" C   GLN G  24 "
           pdb=" N   PHE G  25 "
           pdb=" CA  PHE G  25 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.35   25.65     0      5.00e+00 4.00e-02 2.63e+01
  dihedral pdb=" CA  ILE H  54 "
           pdb=" C   ILE H  54 "
           pdb=" N   SER H  55 "
           pdb=" CA  SER H  55 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.42   21.58     0      5.00e+00 4.00e-02 1.86e+01
  dihedral pdb=" CA  ILE F  29 "
           pdb=" C   ILE F  29 "
           pdb=" N   THR F  30 "
           pdb=" CA  THR F  30 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.87  -21.13     0      5.00e+00 4.00e-02 1.79e+01
  ... (remaining 7796 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.382: 2375
       0.382 -    0.764: 0
       0.764 -    1.145: 0
       1.145 -    1.527: 0
       1.527 -    1.909: 1
  Chirality restraints: 2376
  Sorted by residual:
  chirality pdb=" P    DG J 611 "
            pdb=" OP1  DG J 611 "
            pdb=" OP2  DG J 611 "
            pdb=" O5'  DG J 611 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34    0.43    1.91 2.00e-01 2.50e+01 9.11e+01
  chirality pdb=" CG  LEU E 126 "
            pdb=" CB  LEU E 126 "
            pdb=" CD1 LEU E 126 "
            pdb=" CD2 LEU E 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.32   -0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CB  ILE G 111 "
            pdb=" CA  ILE G 111 "
            pdb=" CG1 ILE G 111 "
            pdb=" CG2 ILE G 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.55e+00
  ... (remaining 2373 not shown)

  Planarity restraints: 1478
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE G  79 "    0.046 5.00e-02 4.00e+02   6.87e-02 7.55e+00
        pdb=" N   PRO G  80 "   -0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO G  80 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO G  80 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I  30 "    0.034 2.00e-02 2.50e+03   1.75e-02 6.88e+00
        pdb=" N1   DC I  30 "   -0.033 2.00e-02 2.50e+03
        pdb=" C2   DC I  30 "   -0.001 2.00e-02 2.50e+03
        pdb=" O2   DC I  30 "   -0.010 2.00e-02 2.50e+03
        pdb=" N3   DC I  30 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DC I  30 "    0.012 2.00e-02 2.50e+03
        pdb=" N4   DC I  30 "    0.010 2.00e-02 2.50e+03
        pdb=" C5   DC I  30 "   -0.011 2.00e-02 2.50e+03
        pdb=" C6   DC I  30 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU H 102 "    0.042 5.00e-02 4.00e+02   6.34e-02 6.44e+00
        pdb=" N   PRO H 103 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO H 103 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO H 103 "    0.035 5.00e-02 4.00e+02
  ... (remaining 1475 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 2943
        2.79 -     3.32: 12785
        3.32 -     3.85: 29386
        3.85 -     4.37: 32078
        4.37 -     4.90: 44329
  Nonbonded interactions: 121521
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A  37 "
            pdb=" OP1  DC J 726 "
     model   vdw
     2.268 3.120
  nonbonded pdb=" OG  SER G  40 "
            pdb=" O   ARG G  42 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" OG  SER C  40 "
            pdb=" O   ARG C  42 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   GLU F  74 "
            pdb=" NH2 ARG H  92 "
     model   vdw
     2.313 3.120
  nonbonded pdb=" OG  SER F  47 "
            pdb=" OP1  DC J 662 "
     model   vdw
     2.314 3.040
  ... (remaining 121516 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     14.510
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
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      :  0.007   0.089  14386  Z= 0.633
  Angle     :  1.110  29.733  20853  Z= 0.848
  Chirality :  0.068   1.909   2376
  Planarity :  0.008   0.084   1478
  Dihedral  : 29.581 173.553   6233
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.26), residues: 825
  helix: -0.26 (0.20), residues: 573
  sheet:  None (None), residues: 0
  loop : -0.72 (0.32), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG H  99 
 TYR   0.034   0.004   TYR E  54 
 PHE   0.032   0.003   PHE E 104 
 HIS   0.007   0.002   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00737 /  0.63 (14386)
  covalent geometry    : angle       1.11039 /  0.85 (20853)
  hydrogen bonds       : bond        0.11346 /  7.63 (  859)
  hydrogen bonds       : angle       4.71288 /  3.46 ( 2133)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.6986 (mm) cc_final: 0.5837 (mm)
REVERT: A   90 MET cc_start: 0.8665 (mmp) cc_final: 0.8320 (mmp)
REVERT: A   93 GLN cc_start: 0.8953 (tt0) cc_final: 0.8694 (tp40)
REVERT: A   94 GLU cc_start: 0.8981 (mp0) cc_final: 0.8595 (pm20)
REVERT: B   68 ASP cc_start: 0.9022 (m-30) cc_final: 0.8784 (m-30)
REVERT: C   62 ILE cc_start: 0.9108 (pt) cc_final: 0.8908 (pt)
REVERT: C   73 ASN cc_start: 0.8677 (t0) cc_final: 0.8361 (p0)
REVERT: D  108 LYS cc_start: 0.9237 (mppt) cc_final: 0.8997 (mtmm)
REVERT: E  104 PHE cc_start: 0.8634 (m-80) cc_final: 0.8386 (m-80)
REVERT: F   62 LEU cc_start: 0.9648 (mt) cc_final: 0.9444 (mt)
REVERT: F   63 GLU cc_start: 0.8443 (tm-30) cc_final: 0.7914 (tm-30)
REVERT: G   36 LYS cc_start: 0.9070 (mppt) cc_final: 0.8656 (mppt)
REVERT: G   64 GLU cc_start: 0.8945 (tp30) cc_final: 0.8717 (tp30)
REVERT: G   95 LYS cc_start: 0.8706 (mmmt) cc_final: 0.8448 (mmmt)
REVERT: H   47 GLN cc_start: 0.9116 (mt0) cc_final: 0.8805 (mt0)
REVERT: H   85 LYS cc_start: 0.9417 (mppt) cc_final: 0.9120 (tptp)
REVERT: H  106 LEU cc_start: 0.9607 (tp) cc_final: 0.9403 (tp)
REVERT: H  113 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8417 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.1133
  time to fit residues: 29.0953
Evaluate side-chains
  120 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:   20.0000
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:   20.0000
   chunk 106 optimal weight:    6.9990
   overall best weight:    1.4984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  93 GLN
E 108 ASN
** G  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  84 GLN
** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.055298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.045825 restraints weight = 120887.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.046960 restraints weight = 74248.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.047721 restraints weight = 53092.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.048219 restraints weight = 41975.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.048576 restraints weight = 35682.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.1115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  14386  Z= 0.177
  Angle     :  0.823  24.116  20853  Z= 0.458
  Chirality :  0.068   2.156   2376
  Planarity :  0.006   0.062   1478
  Dihedral  : 33.048 178.074   4581
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 14.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 10.39 %
    Favored  : 88.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.27), residues: 825
  helix:  0.50 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop : -0.65 (0.34), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  31 
 TYR   0.025   0.002   TYR F  88 
 PHE   0.015   0.002   PHE H  65 
 HIS   0.008   0.001   HIS D 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.18 (14386)
  covalent geometry    : angle       0.82256 /  0.46 (20853)
  hydrogen bonds       : bond        0.06184 /  4.20 (  859)
  hydrogen bonds       : angle       3.85755 /  2.78 ( 2133)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 142
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.6978 (mm) cc_final: 0.5748 (mm)
REVERT: B   85 ASP cc_start: 0.8547 (m-30) cc_final: 0.8344 (m-30)
REVERT: D   46 LYS cc_start: 0.8801 (mmtt) cc_final: 0.7987 (mmmt)
REVERT: E   77 ASP cc_start: 0.9214 (m-30) cc_final: 0.8584 (t0)
REVERT: E   93 GLN cc_start: 0.7864 (tp-100) cc_final: 0.7651 (tp40)
REVERT: E  108 ASN cc_start: 0.8946 (m-40) cc_final: 0.8713 (m110)
REVERT: F   63 GLU cc_start: 0.8408 (tm-30) cc_final: 0.7997 (tm-30)
REVERT: G   95 LYS cc_start: 0.8641 (mmmt) cc_final: 0.8419 (mmmt)
REVERT: H   47 GLN cc_start: 0.9114 (mt0) cc_final: 0.8717 (mt0)
REVERT: H  113 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8547 (mm-30)
  outliers start: 11
  outliers final: 5
  residues processed: 148
  average time/residue: 0.1081
  time to fit residues: 24.0254
Evaluate side-chains
  120 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 115
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain D residue  105 GLU
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   68 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 109 optimal weight:   20.0000
   chunk 58 optimal weight:    9.9990
   chunk 17 optimal weight:   20.0000
   chunk 54 optimal weight:    0.9990
   chunk 98 optimal weight:   30.0000
   chunk 64 optimal weight:    0.8980
   chunk 11 optimal weight:    5.9990
   chunk 24 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    2.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E  55 GLN
** G  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  95 GLN
** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.054558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.045147 restraints weight = 122336.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.046280 restraints weight = 73881.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.047041 restraints weight = 52454.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.047543 restraints weight = 41185.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.047894 restraints weight = 34855.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.1493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14386  Z= 0.182
  Angle     :  0.783  25.385  20853  Z= 0.438
  Chirality :  0.065   2.079   2376
  Planarity :  0.005   0.055   1478
  Dihedral  : 32.942 175.033   4581
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 15.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 13.56 %
    Favored  : 84.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.27), residues: 825
  helix:  0.68 (0.21), residues: 591
  sheet:  None (None), residues: 0
  loop : -0.68 (0.35), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG A 116 
 TYR   0.040   0.003   TYR F  88 
 PHE   0.034   0.002   PHE E 104 
 HIS   0.006   0.001   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.18 (14386)
  covalent geometry    : angle       0.78305 /  0.44 (20853)
  hydrogen bonds       : bond        0.06584 /  4.46 (  859)
  hydrogen bonds       : angle       3.72529 /  2.68 ( 2133)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 130
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.9535 (OUTLIER) cc_final: 0.9183 (mp10)
REVERT: A  120 MET cc_start: 0.2943 (mtt) cc_final: 0.2623 (mtt)
REVERT: B   85 ASP cc_start: 0.8566 (m-30) cc_final: 0.8324 (m-30)
REVERT: D   46 LYS cc_start: 0.8812 (mmtt) cc_final: 0.8024 (mmmt)
REVERT: E   77 ASP cc_start: 0.9184 (m-30) cc_final: 0.8663 (t70)
REVERT: E  104 PHE cc_start: 0.8967 (m-80) cc_final: 0.8578 (m-80)
REVERT: E  108 ASN cc_start: 0.8862 (m-40) cc_final: 0.8645 (m110)
REVERT: F   63 GLU cc_start: 0.8491 (tm-30) cc_final: 0.7974 (tm-30)
REVERT: G   36 LYS cc_start: 0.8885 (mppt) cc_final: 0.8606 (mmtm)
REVERT: G   57 TYR cc_start: 0.8832 (t80) cc_final: 0.8476 (t80)
REVERT: G   95 LYS cc_start: 0.8753 (mmmt) cc_final: 0.8454 (mmmt)
REVERT: H   47 GLN cc_start: 0.9067 (mt0) cc_final: 0.8796 (mt0)
REVERT: H  113 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8668 (mm-30)
  outliers start: 13
  outliers final: 7
  residues processed: 138
  average time/residue: 0.1109
  time to fit residues: 22.8933
Evaluate side-chains
  114 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain B residue   68 ASP
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain D residue  105 GLU
Chi-restraints excluded: chain E residue   48 LEU
Chi-restraints excluded: chain F residue   43 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 109 optimal weight:   20.0000
   chunk 43 optimal weight:    3.9990
   chunk 87 optimal weight:   30.0000
   chunk 49 optimal weight:    0.9980
   chunk 95 optimal weight:   30.0000
   chunk 61 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 11 optimal weight:   10.0000
   chunk 31 optimal weight:    0.7980
   chunk 68 optimal weight:    3.9990
   chunk 108 optimal weight:    7.9990
   overall best weight:    2.7586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E  55 GLN
** G  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.053892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.044638 restraints weight = 121492.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.045735 restraints weight = 73098.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.046461 restraints weight = 52039.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.046975 restraints weight = 41101.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.047312 restraints weight = 34623.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.1781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14386  Z= 0.191
  Angle     :  0.779  25.612  20853  Z= 0.433
  Chirality :  0.065   2.072   2376
  Planarity :  0.005   0.052   1478
  Dihedral  : 32.959 174.403   4581
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 16.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 15.87 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.41 (0.28), residues: 825
  helix:  0.74 (0.21), residues: 593
  sheet:  None (None), residues: 0
  loop : -0.75 (0.35), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E  53 
 TYR   0.048   0.003   TYR F  88 
 PHE   0.018   0.002   PHE E 104 
 HIS   0.008   0.002   HIS H 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.19 (14386)
  covalent geometry    : angle       0.77914 /  0.43 (20853)
  hydrogen bonds       : bond        0.06896 /  4.66 (  859)
  hydrogen bonds       : angle       3.69693 /  2.66 ( 2133)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.9563 (OUTLIER) cc_final: 0.9215 (mp10)
REVERT: B   85 ASP cc_start: 0.8634 (m-30) cc_final: 0.8377 (m-30)
REVERT: D   46 LYS cc_start: 0.8778 (mmtt) cc_final: 0.7962 (mmmt)
REVERT: D  108 LYS cc_start: 0.9192 (mppt) cc_final: 0.8675 (mmtm)
REVERT: E   77 ASP cc_start: 0.9108 (m-30) cc_final: 0.8588 (t70)
REVERT: E   93 GLN cc_start: 0.7634 (tp-100) cc_final: 0.7353 (tp40)
REVERT: E  104 PHE cc_start: 0.8976 (m-80) cc_final: 0.8594 (m-80)
REVERT: E  108 ASN cc_start: 0.8797 (m-40) cc_final: 0.8551 (m110)
REVERT: F   63 GLU cc_start: 0.8514 (tm-30) cc_final: 0.7976 (tm-30)
REVERT: F   74 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8533 (tm-30)
REVERT: G   36 LYS cc_start: 0.8896 (mppt) cc_final: 0.8677 (mmtm)
REVERT: G   57 TYR cc_start: 0.8882 (t80) cc_final: 0.8566 (t80)
REVERT: G   95 LYS cc_start: 0.8827 (mmmt) cc_final: 0.8515 (mmmt)
REVERT: H   47 GLN cc_start: 0.9056 (mt0) cc_final: 0.8763 (mt0)
REVERT: H  109 HIS cc_start: 0.9424 (m170) cc_final: 0.8973 (m90)
  outliers start: 13
  outliers final: 9
  residues processed: 133
  average time/residue: 0.1057
  time to fit residues: 21.1865
Evaluate side-chains
  121 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain D residue  105 GLU
Chi-restraints excluded: chain E residue   48 LEU
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain H residue   66 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 107 optimal weight:    0.0270
   chunk 28 optimal weight:    4.9990
   chunk 80 optimal weight:   20.0000
   chunk 16 optimal weight:    8.9990
   chunk 48 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.7644

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 109 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.055626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.046235 restraints weight = 121532.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.047389 restraints weight = 72221.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.048140 restraints weight = 50763.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.048677 restraints weight = 39813.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.049027 restraints weight = 33420.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  14386  Z= 0.151
  Angle     :  0.759  25.868  20853  Z= 0.422
  Chirality :  0.064   2.023   2376
  Planarity :  0.005   0.055   1478
  Dihedral  : 32.895 173.159   4581
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 16.45 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.28), residues: 825
  helix:  0.79 (0.21), residues: 592
  sheet:  None (None), residues: 0
  loop : -0.59 (0.36), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 116 
 TYR   0.048   0.003   TYR F  88 
 PHE   0.022   0.002   PHE E 104 
 HIS   0.009   0.001   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.15 (14386)
  covalent geometry    : angle       0.75946 /  0.42 (20853)
  hydrogen bonds       : bond        0.04984 /  3.36 (  859)
  hydrogen bonds       : angle       3.50716 /  2.52 ( 2133)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 128
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.9529 (OUTLIER) cc_final: 0.9116 (mp10)
REVERT: A  105 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8063 (mt-10)
REVERT: B   85 ASP cc_start: 0.8522 (m-30) cc_final: 0.8274 (m-30)
REVERT: D   46 LYS cc_start: 0.8636 (mmtt) cc_final: 0.7837 (mmmt)
REVERT: D  108 LYS cc_start: 0.9154 (mppt) cc_final: 0.8576 (mmtm)
REVERT: E   77 ASP cc_start: 0.9153 (m-30) cc_final: 0.8647 (t0)
REVERT: E  104 PHE cc_start: 0.8973 (m-80) cc_final: 0.8551 (m-80)
REVERT: F   63 GLU cc_start: 0.8520 (tm-30) cc_final: 0.7939 (tm-30)
REVERT: F   74 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8495 (tm-30)
REVERT: G   36 LYS cc_start: 0.8809 (mppt) cc_final: 0.8538 (mmtm)
REVERT: G   57 TYR cc_start: 0.8904 (t80) cc_final: 0.8518 (t80)
REVERT: G   95 LYS cc_start: 0.8862 (mmmt) cc_final: 0.8528 (mmmt)
REVERT: H   47 GLN cc_start: 0.9073 (mt0) cc_final: 0.8778 (mt0)
REVERT: H   99 ARG cc_start: 0.9519 (mmm-85) cc_final: 0.9305 (mtp85)
  outliers start: 12
  outliers final: 7
  residues processed: 135
  average time/residue: 0.1077
  time to fit residues: 21.7143
Evaluate side-chains
  123 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain D residue  105 GLU
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain F residue   43 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 39 optimal weight:    8.9990
   chunk 8 optimal weight:    4.9990
   chunk 32 optimal weight:    6.9990
   chunk 24 optimal weight:    0.6980
   chunk 34 optimal weight:    0.4980
   chunk 48 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 95 optimal weight:   30.0000
   chunk 85 optimal weight:   30.0000
   chunk 41 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   overall best weight:    1.4384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.054960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.045851 restraints weight = 115510.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.047020 restraints weight = 68573.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.047802 restraints weight = 47851.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.048321 restraints weight = 37066.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.048712 restraints weight = 30913.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14386  Z= 0.161
  Angle     :  0.761  25.682  20853  Z= 0.422
  Chirality :  0.063   2.029   2376
  Planarity :  0.005   0.058   1478
  Dihedral  : 32.795 172.331   4581
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 15.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 19.19 %
    Favored  : 79.22 %
  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:  0.63 (0.28), residues: 825
  helix:  0.88 (0.21), residues: 592
  sheet:  None (None), residues: 0
  loop : -0.58 (0.36), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  79 
 TYR   0.053   0.002   TYR F  88 
 PHE   0.013   0.001   PHE E 104 
 HIS   0.006   0.001   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.16 (14386)
  covalent geometry    : angle       0.76132 /  0.42 (20853)
  hydrogen bonds       : bond        0.05496 /  3.71 (  859)
  hydrogen bonds       : angle       3.52657 /  2.54 ( 2133)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.9535 (OUTLIER) cc_final: 0.9165 (mp10)
REVERT: A  105 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8158 (mt-10)
REVERT: B   85 ASP cc_start: 0.8475 (m-30) cc_final: 0.8190 (m-30)
REVERT: D   46 LYS cc_start: 0.8622 (mmtt) cc_final: 0.7842 (mmmt)
REVERT: D  108 LYS cc_start: 0.9202 (mppt) cc_final: 0.8617 (mmtm)
REVERT: E   77 ASP cc_start: 0.9163 (m-30) cc_final: 0.8650 (t0)
REVERT: E  104 PHE cc_start: 0.9013 (m-80) cc_final: 0.8608 (m-80)
REVERT: E  108 ASN cc_start: 0.9090 (m-40) cc_final: 0.8835 (m110)
REVERT: F   63 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8000 (tm-30)
REVERT: F   74 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8512 (tm-30)
REVERT: G   36 LYS cc_start: 0.8835 (mppt) cc_final: 0.8548 (mmtm)
REVERT: G   95 LYS cc_start: 0.8864 (mmmt) cc_final: 0.8581 (mmmt)
REVERT: H   47 GLN cc_start: 0.9066 (mt0) cc_final: 0.8774 (mt0)
REVERT: H   99 ARG cc_start: 0.9535 (mmm-85) cc_final: 0.9301 (mtp85)
  outliers start: 11
  outliers final: 8
  residues processed: 136
  average time/residue: 0.1130
  time to fit residues: 22.8536
Evaluate side-chains
  129 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 120
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain D residue  105 GLU
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   43 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 51 optimal weight:    6.9990
   chunk 96 optimal weight:   20.0000
   chunk 98 optimal weight:   30.0000
   chunk 22 optimal weight:   10.0000
   chunk 103 optimal weight:   20.0000
   chunk 50 optimal weight:    5.9990
   chunk 73 optimal weight:   20.0000
   chunk 57 optimal weight:    6.9990
   chunk 12 optimal weight:    4.9990
   chunk 90 optimal weight:   30.0000
   chunk 106 optimal weight:    5.9990
   overall best weight:    6.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 GLN
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.049614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.040862 restraints weight = 124897.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.041900 restraints weight = 75620.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.042575 restraints weight = 53566.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.043060 restraints weight = 42126.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.043376 restraints weight = 35279.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.2928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.075  14386  Z= 0.328
  Angle     :  0.935  27.160  20853  Z= 0.510
  Chirality :  0.069   2.040   2376
  Planarity :  0.007   0.070   1478
  Dihedral  : 33.087 171.662   4581
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 30.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.77 %
    Favored  : 77.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.27), residues: 825
  helix:  0.04 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -1.02 (0.35), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E  53 
 TYR   0.052   0.004   TYR F  88 
 PHE   0.022   0.003   PHE F 100 
 HIS   0.012   0.003   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00610 /  0.33 (14386)
  covalent geometry    : angle       0.93522 /  0.51 (20853)
  hydrogen bonds       : bond        0.13891 /  9.28 (  859)
  hydrogen bonds       : angle       4.34725 /  3.15 ( 2133)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 111
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.9569 (OUTLIER) cc_final: 0.9344 (mp10)
REVERT: C   84 GLN cc_start: 0.6528 (OUTLIER) cc_final: 0.4626 (tm-30)
REVERT: C   91 GLU cc_start: 0.7483 (tp30) cc_final: 0.7019 (tp30)
REVERT: D   42 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.7712 (t80)
REVERT: E   77 ASP cc_start: 0.9197 (m-30) cc_final: 0.8655 (t0)
REVERT: E  108 ASN cc_start: 0.9095 (m-40) cc_final: 0.8839 (m110)
REVERT: F   63 GLU cc_start: 0.8537 (tm-30) cc_final: 0.7941 (tm-30)
REVERT: F   74 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8599 (tm-30)
REVERT: G   95 LYS cc_start: 0.8939 (mmmt) cc_final: 0.8687 (mmmt)
REVERT: H   47 GLN cc_start: 0.9055 (mt0) cc_final: 0.8703 (mt0)
REVERT: H   99 ARG cc_start: 0.9588 (mmm-85) cc_final: 0.9181 (mmm-85)
  outliers start: 22
  outliers final: 17
  residues processed: 124
  average time/residue: 0.0991
  time to fit residues: 18.7463
Evaluate side-chains
  120 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue  106 ASP
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   68 ASP
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   84 GLN
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   42 TYR
Chi-restraints excluded: chain D residue   52 THR
Chi-restraints excluded: chain D residue   69 ILE
Chi-restraints excluded: chain D residue  105 GLU
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain E residue  130 ILE
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   68 ASP
Chi-restraints excluded: chain H residue   66 VAL
Chi-restraints excluded: chain U residue   93 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 98 optimal weight:   30.0000
   chunk 96 optimal weight:   20.0000
   chunk 20 optimal weight:    0.3980
   chunk 78 optimal weight:   20.0000
   chunk 86 optimal weight:   20.0000
   chunk 24 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 92 optimal weight:   20.0000
   chunk 107 optimal weight:   30.0000
   chunk 45 optimal weight:    1.9990
   overall best weight:    2.6788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 112 GLN
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.051747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.042763 restraints weight = 124294.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.043815 restraints weight = 74552.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.044530 restraints weight = 52677.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.045003 restraints weight = 41350.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.045316 restraints weight = 34876.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.2872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  14386  Z= 0.198
  Angle     :  0.824  26.975  20853  Z= 0.453
  Chirality :  0.066   2.013   2376
  Planarity :  0.006   0.063   1478
  Dihedral  : 33.191 172.599   4581
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 20.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 21.21 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.16 (0.27), residues: 825
  helix:  0.34 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -1.03 (0.35), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 116 
 TYR   0.056   0.003   TYR F  88 
 PHE   0.052   0.003   PHE E 104 
 HIS   0.007   0.002   HIS D  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.20 (14386)
  covalent geometry    : angle       0.82397 /  0.45 (20853)
  hydrogen bonds       : bond        0.07068 /  4.73 (  859)
  hydrogen bonds       : angle       3.95192 /  2.85 ( 2133)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   91 GLU cc_start: 0.7308 (tp30) cc_final: 0.6881 (tp30)
REVERT: D   42 TYR cc_start: 0.8015 (OUTLIER) cc_final: 0.7428 (t80)
REVERT: D  108 LYS cc_start: 0.9139 (mppt) cc_final: 0.8569 (mmtm)
REVERT: E   77 ASP cc_start: 0.9215 (m-30) cc_final: 0.8711 (t70)
REVERT: E   79 LYS cc_start: 0.8034 (tmtt) cc_final: 0.7448 (tmtt)
REVERT: E  108 ASN cc_start: 0.9004 (m-40) cc_final: 0.8745 (m110)
REVERT: F   63 GLU cc_start: 0.8511 (tm-30) cc_final: 0.7858 (tm-30)
REVERT: F   74 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8389 (tm-30)
REVERT: G   95 LYS cc_start: 0.8939 (mmmt) cc_final: 0.8693 (mmmt)
REVERT: H   47 GLN cc_start: 0.9014 (mt0) cc_final: 0.8665 (mt0)
REVERT: H   99 ARG cc_start: 0.9534 (mmm-85) cc_final: 0.9277 (mtp85)
  outliers start: 15
  outliers final: 11
  residues processed: 129
  average time/residue: 0.1120
  time to fit residues: 21.6610
Evaluate side-chains
  122 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   42 TYR
Chi-restraints excluded: chain D residue  105 GLU
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain E residue  130 ILE
Chi-restraints excluded: chain U residue   63 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 45 optimal weight:    0.1980
   chunk 15 optimal weight:    0.6980
   chunk 47 optimal weight:    9.9990
   chunk 66 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 105 optimal weight:    2.9990
   chunk 74 optimal weight:   30.0000
   chunk 75 optimal weight:   20.0000
   chunk 87 optimal weight:   30.0000
   chunk 84 optimal weight:   20.0000
   overall best weight:    2.3786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.051891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.042860 restraints weight = 124004.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.043954 restraints weight = 73531.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.044678 restraints weight = 51529.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.045161 restraints weight = 40246.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.045490 restraints weight = 33863.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.2973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14386  Z= 0.189
  Angle     :  0.819  26.513  20853  Z= 0.449
  Chirality :  0.065   2.012   2376
  Planarity :  0.005   0.062   1478
  Dihedral  : 32.985 172.245   4581
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 20.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 21.65 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.27), residues: 825
  helix:  0.44 (0.21), residues: 592
  sheet:  None (None), residues: 0
  loop : -1.03 (0.35), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 116 
 TYR   0.042   0.002   TYR F  88 
 PHE   0.034   0.002   PHE E 104 
 HIS   0.009   0.002   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.19 (14386)
  covalent geometry    : angle       0.81918 /  0.45 (20853)
  hydrogen bonds       : bond        0.06835 /  4.57 (  859)
  hydrogen bonds       : angle       3.84290 /  2.77 ( 2133)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8445 (pt0)
REVERT: A  105 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8241 (mt-10)
REVERT: C   91 GLU cc_start: 0.7337 (tp30) cc_final: 0.6869 (tp30)
REVERT: D   42 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.7351 (t80)
REVERT: D  108 LYS cc_start: 0.9127 (mppt) cc_final: 0.8549 (mmtm)
REVERT: E   77 ASP cc_start: 0.9220 (m-30) cc_final: 0.8693 (t0)
REVERT: E   79 LYS cc_start: 0.8118 (tmtt) cc_final: 0.7545 (tmtt)
REVERT: E  104 PHE cc_start: 0.9013 (m-80) cc_final: 0.8660 (m-80)
REVERT: E  108 ASN cc_start: 0.8989 (m-40) cc_final: 0.8776 (m110)
REVERT: F   63 GLU cc_start: 0.8509 (tm-30) cc_final: 0.7831 (tm-30)
REVERT: F   74 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8437 (tm-30)
REVERT: G   95 LYS cc_start: 0.8940 (mmmt) cc_final: 0.8715 (mmmt)
REVERT: H   47 GLN cc_start: 0.9011 (mt0) cc_final: 0.8669 (mt0)
REVERT: H   71 GLU cc_start: 0.7916 (tt0) cc_final: 0.7543 (tm-30)
  outliers start: 12
  outliers final: 11
  residues processed: 125
  average time/residue: 0.1105
  time to fit residues: 20.8331
Evaluate side-chains
  125 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   42 TYR
Chi-restraints excluded: chain D residue  105 GLU
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain E residue  130 ILE
Chi-restraints excluded: chain F residue   34 ILE
Chi-restraints excluded: chain U residue   63 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9990
   chunk 75 optimal weight:   30.0000
   chunk 6 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 88 optimal weight:   40.0000
   chunk 93 optimal weight:   20.0000
   chunk 100 optimal weight:   20.0000
   chunk 108 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.9784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  84 ASN
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.053421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.044264 restraints weight = 121667.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.045367 restraints weight = 72864.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.046113 restraints weight = 51447.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.046580 restraints weight = 40273.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.046928 restraints weight = 34161.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.3068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  14386  Z= 0.166
  Angle     :  0.814  26.265  20853  Z= 0.447
  Chirality :  0.065   2.003   2376
  Planarity :  0.005   0.058   1478
  Dihedral  : 32.828 170.581   4581
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 17.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 21.93 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.04 (0.27), residues: 825
  helix:  0.50 (0.21), residues: 594
  sheet:  None (None), residues: 0
  loop : -1.02 (0.35), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E  52 
 TYR   0.062   0.003   TYR F  88 
 PHE   0.043   0.002   PHE E 104 
 HIS   0.009   0.002   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.17 (14386)
  covalent geometry    : angle       0.81430 /  0.45 (20853)
  hydrogen bonds       : bond        0.05136 /  3.47 (  859)
  hydrogen bonds       : angle       3.76339 /  2.74 ( 2133)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 130
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8438 (pt0)
REVERT: A  105 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8269 (mt-10)
REVERT: C   91 GLU cc_start: 0.7242 (tp30) cc_final: 0.6790 (tp30)
REVERT: D   42 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.7306 (t80)
REVERT: D   46 LYS cc_start: 0.8564 (mmtt) cc_final: 0.7482 (mmmt)
REVERT: D  108 LYS cc_start: 0.9084 (mppt) cc_final: 0.8563 (mmtm)
REVERT: E   77 ASP cc_start: 0.9192 (m-30) cc_final: 0.8616 (t0)
REVERT: E   79 LYS cc_start: 0.8010 (tmtt) cc_final: 0.7348 (tmtt)
REVERT: E   97 GLU cc_start: 0.7573 (pt0) cc_final: 0.7162 (mt-10)
REVERT: E  104 PHE cc_start: 0.8964 (m-80) cc_final: 0.8665 (m-80)
REVERT: F   63 GLU cc_start: 0.8495 (tm-30) cc_final: 0.7802 (tm-30)
REVERT: F   74 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8434 (tm-30)
REVERT: F   86 VAL cc_start: 0.8608 (t) cc_final: 0.8362 (t)
REVERT: G   95 LYS cc_start: 0.8956 (mmmt) cc_final: 0.8595 (mmmt)
REVERT: H   47 GLN cc_start: 0.8974 (mt0) cc_final: 0.8592 (mt0)
REVERT: H   71 GLU cc_start: 0.7910 (tt0) cc_final: 0.7533 (tm-30)
REVERT: H   99 ARG cc_start: 0.9528 (mmm-85) cc_final: 0.9270 (mtp85)
  outliers start: 14
  outliers final: 11
  residues processed: 137
  average time/residue: 0.1230
  time to fit residues: 24.7043
Evaluate side-chains
  132 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   42 TYR
Chi-restraints excluded: chain D residue  105 GLU
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain E residue  130 ILE
Chi-restraints excluded: chain F residue   88 TYR
Chi-restraints excluded: chain U residue   63 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 98 optimal weight:   30.0000
   chunk 57 optimal weight:   10.0000
   chunk 50 optimal weight:    0.0370
   chunk 74 optimal weight:   30.0000
   chunk 27 optimal weight:    9.9990
   chunk 56 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 73 optimal weight:   20.0000
   chunk 1 optimal weight:    5.9990
   chunk 42 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   overall best weight:    1.9864

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.052825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.043707 restraints weight = 124111.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.044797 restraints weight = 75223.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.045539 restraints weight = 53341.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.046010 restraints weight = 41828.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.046360 restraints weight = 35367.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.3188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  14386  Z= 0.179
  Angle     :  0.809  26.062  20853  Z= 0.444
  Chirality :  0.064   2.016   2376
  Planarity :  0.005   0.063   1478
  Dihedral  : 32.722 169.470   4581
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 19.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 23.52 %
    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:  0.12 (0.28), residues: 825
  helix:  0.54 (0.21), residues: 592
  sheet:  None (None), residues: 0
  loop : -0.91 (0.36), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 116 
 TYR   0.059   0.002   TYR F  88 
 PHE   0.035   0.002   PHE E 104 
 HIS   0.004   0.001   HIS D  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.18 (14386)
  covalent geometry    : angle       0.80855 /  0.44 (20853)
  hydrogen bonds       : bond        0.06219 /  4.17 (  859)
  hydrogen bonds       : angle       3.77400 /  2.75 ( 2133)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2232.38 seconds
wall clock time: 39 minutes 21.72 seconds (2361.72 seconds total)