Starting phenix.real_space_refine
on Fri Sep 11 16:26:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7d69_30591/09_2026/7d69_30591.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7d69_30591/09_2026/7d69_30591.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7d69_30591/09_2026/7d69_30591.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7d69_30591/09_2026/7d69_30591.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7d69_30591/09_2026/7d69_30591.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7d69_30591/09_2026/7d69_30591.map"
  }
  resolution = 3.57
  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=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     250      5.49       5
     S      13      5.16       5
     C    6015      2.51       5
     N    2012      2.21       5
     O    2567      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 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: 10857
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 716
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 3, 'TRANS': 86}
    Chain: "B"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "D"
      Number of atoms: 743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 743
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 1, 'TRANS': 94}
    Chain: "E"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 779
          Classifications: {'peptide': 99}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 95}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "F"
      Number of atoms: 621
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 621
          Classifications: {'peptide': 78}
          Incomplete info: {'n_c_alpha_c_only': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "H"
      Number of atoms: 743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 743
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 1, 'TRANS': 94}
    Chain: "C"
      Number of atoms: 754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 754
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "G"
      Number of atoms: 754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 754
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 2561
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 2561
          Classifications: {'DNA': 125}
          Link IDs: {'rna3p': 124}
    Chain: "J"
      Number of atoms: 2564
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 2564
          Classifications: {'DNA': 125}
          Link IDs: {'rna3p': 124}
  Time building chain proxies: 2.19, per 1000 atoms: 0.20
  Number of scatterers: 10857
  At special positions: 0
  Unit cell: (84, 121.8, 114.45, 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      13     16.00
     P     250     15.00
     O    2567      8.00
     N    2012      7.00
     C    6015      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: 0.85
  Conformation dependent library (CDL) restraints added in 228.0 milliseconds
  

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1368

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 6 sheets defined
      74.0% alpha, 1.9% beta
      121 base pairs and 227 stacking pairs defined.
    Time for finding SS restraints: 1.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 51 through 58
      removed outlier: 3.897A  pdb=" N   TYR A  55 " --> pdb=" O   GLU A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 78
    Processing helix  chain 'A' and resid 88 through 117
    Processing helix  chain 'A' and resid 123 through 133
    Processing helix  chain 'B' and resid 21 through 25
    Processing helix  chain 'B' and resid 26 through 37
    Processing helix  chain 'B' and resid 45 through 72
      removed outlier: 3.698A  pdb=" N   GLY B  72 " --> pdb=" O   TYR B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 90
    Processing helix  chain 'D' and resid 30 through 45
      removed outlier: 3.607A  pdb=" N   ILE D  43 " --> pdb=" O   ARG D  39 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   ARG D  44 " --> pdb=" O   SER D  40 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 54 through 84
    Processing helix  chain 'D' and resid 89 through 101
    Processing helix  chain 'D' and resid 103 through 122
    Processing helix  chain 'E' and resid 45 through 58
      removed outlier: 4.096A  pdb=" N   VAL E  49 " --> pdb=" O   GLY E  45 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   LYS E  50 " --> pdb=" O   MET E  46 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   SER E  58 " --> pdb=" O   LYS E  54 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 64 through 79
    Processing helix  chain 'E' and resid 88 through 117
    Processing helix  chain 'E' and resid 123 through 133
    Processing helix  chain 'F' and resid 21 through 25
    Processing helix  chain 'F' and resid 26 through 38
    Processing helix  chain 'F' and resid 44 through 72
      removed outlier: 4.273A  pdb=" N   GLN F  48 " --> pdb=" O   SER F  44 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ALA F  56 " --> pdb=" O   GLU F  52 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   GLY F  72 " --> pdb=" O   TYR F  68 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 78 through 88
    Processing helix  chain 'H' and resid 30 through 43
    Processing helix  chain 'H' and resid 54 through 84
    Processing helix  chain 'H' and resid 89 through 101
    Processing helix  chain 'H' and resid 103 through 122
    Processing helix  chain 'C' and resid 13 through 18
    Processing helix  chain 'C' and resid 23 through 34
    Processing helix  chain 'C' and resid 42 through 68
      removed outlier: 4.162A  pdb=" N   VAL C  46 " --> pdb=" O   SER C  42 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 87
      removed outlier: 3.604A  pdb=" N   ASP C  87 " --> pdb=" O   ALA C  83 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 87 through 94
    Processing helix  chain 'G' and resid 13 through 18
    Processing helix  chain 'G' and resid 23 through 34
    Processing helix  chain 'G' and resid 43 through 68
      removed outlier: 3.618A  pdb=" N   TYR G  47 " --> pdb=" O   ASP G  43 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 76 through 87
      removed outlier: 4.103A  pdb=" N   ASP G  87 " --> pdb=" O   ALA G  83 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 87 through 94
    Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87
      removed outlier: 7.028A  pdb=" N   ARG A  86 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 122
    Processing sheet with id=AA3, first strand: chain 'B' and resid 93 through 94
      removed outlier: 3.681A  pdb=" N   TYR B  94 " --> pdb=" O   THR G  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'E' and resid 86 through 87
      removed outlier: 7.127A  pdb=" N   ARG E  86 " --> pdb=" O   VAL F  77 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'E' and resid 121 through 122
    Processing sheet with id=AA6, first strand: chain 'F' and resid 92 through 94
      removed outlier: 6.189A  pdb=" N   THR F  92 " --> pdb=" O   THR C  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6

    392 hydrogen bonds defined for protein.
    1164 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      315 hydrogen bonds
      630 hydrogen bond angles
      0 basepair planarities
      121 basepair parallelities
      227 stacking parallelities
  Total time for adding SS restraints: 1.84

  Time building geometry restraints manager: 1.17 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: 1840
        1.33 -     1.45: 3827
        1.45 -     1.57: 5355
        1.57 -     1.68: 498
        1.68 -     1.80: 22
  Bond restraints: 11542
  Sorted by residual:
  bond pdb=" C3'  DG J  87 "
       pdb=" O3'  DG J  87 "
    ideal  model  delta    sigma   weight residual
    1.435  1.379  0.056 1.30e-02 5.92e+03 1.88e+01
  bond pdb=" C3'  DA I  22 "
       pdb=" O3'  DA I  22 "
    ideal  model  delta    sigma   weight residual
    1.435  1.382  0.053 1.30e-02 5.92e+03 1.64e+01
  bond pdb=" C3'  DT J  43 "
       pdb=" C2'  DT J  43 "
    ideal  model  delta    sigma   weight residual
    1.516  1.548 -0.032 8.00e-03 1.56e+04 1.57e+01
  bond pdb=" C3'  DG I  89 "
       pdb=" C2'  DG I  89 "
    ideal  model  delta    sigma   weight residual
    1.516  1.547 -0.031 8.00e-03 1.56e+04 1.52e+01
  bond pdb=" C3'  DG I  74 "
       pdb=" O3'  DG I  74 "
    ideal  model  delta    sigma   weight residual
    1.435  1.385  0.050 1.30e-02 5.92e+03 1.49e+01
  ... (remaining 11537 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 14743
        1.54 -     3.07: 1648
        3.07 -     4.61: 204
        4.61 -     6.14: 33
        6.14 -     7.68: 9
  Bond angle restraints: 16637
  Sorted by residual:
  angle pdb=" O4'  DA I 113 "
        pdb=" C1'  DA I 113 "
        pdb=" N9   DA I 113 "
      ideal   model   delta    sigma   weight residual
     108.00  104.02    3.98 7.00e-01 2.04e+00 3.23e+01
  angle pdb=" O4'  DG I  86 "
        pdb=" C1'  DG I  86 "
        pdb=" N9   DG I  86 "
      ideal   model   delta    sigma   weight residual
     108.00  111.97   -3.97 7.00e-01 2.04e+00 3.21e+01
  angle pdb=" O4'  DA J  76 "
        pdb=" C1'  DA J  76 "
        pdb=" N9   DA J  76 "
      ideal   model   delta    sigma   weight residual
     108.00  111.82   -3.82 7.00e-01 2.04e+00 2.98e+01
  angle pdb=" O4'  DA I  31 "
        pdb=" C1'  DA I  31 "
        pdb=" N9   DA I  31 "
      ideal   model   delta    sigma   weight residual
     108.00  104.29    3.71 7.00e-01 2.04e+00 2.80e+01
  angle pdb=" O5'  DC I   9 "
        pdb=" C5'  DC I   9 "
        pdb=" C4'  DC I   9 "
      ideal   model   delta    sigma   weight residual
     109.40  113.36   -3.96 8.00e-01 1.56e+00 2.46e+01
  ... (remaining 16632 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.69: 4776
       30.69 -    61.37: 1489
       61.37 -    92.05: 46
       92.05 -   122.74: 8
      122.74 -   153.42: 4
  Dihedral angle restraints: 6323
    sinusoidal: 4214
      harmonic: 2109
  Sorted by residual:
  dihedral pdb=" C4'  DT I 120 "
           pdb=" C3'  DT I 120 "
           pdb=" O3'  DT I 120 "
           pdb=" P    DC I 121 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   66.58  153.42     1      3.50e+01 8.16e-04 1.48e+01
  dihedral pdb=" C4'  DT J 114 "
           pdb=" C3'  DT J 114 "
           pdb=" O3'  DT J 114 "
           pdb=" P    DC J 115 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   76.89  143.11     1      3.50e+01 8.16e-04 1.41e+01
  dihedral pdb=" C4'  DC I 100 "
           pdb=" C3'  DC I 100 "
           pdb=" O3'  DC I 100 "
           pdb=" P    DT I 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   94.95  125.05     1      3.50e+01 8.16e-04 1.23e+01
  ... (remaining 6320 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1300
       0.062 -    0.123: 480
       0.123 -    0.185: 106
       0.185 -    0.246: 14
       0.246 -    0.308: 2
  Chirality restraints: 1902
  Sorted by residual:
  chirality pdb=" C3'  DT J 114 "
            pdb=" C4'  DT J 114 "
            pdb=" O3'  DT J 114 "
            pdb=" C2'  DT J 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.42   -0.31 2.00e-01 2.50e+01 2.37e+00
  chirality pdb=" C3'  DC I 100 "
            pdb=" C4'  DC I 100 "
            pdb=" O3'  DC I 100 "
            pdb=" C2'  DC I 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.48   -0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" C3'  DC I  37 "
            pdb=" C4'  DC I  37 "
            pdb=" O3'  DC I  37 "
            pdb=" C2'  DC I  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.50   -0.23 2.00e-01 2.50e+01 1.37e+00
  ... (remaining 1899 not shown)

  Planarity restraints: 1240
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I   9 "   -0.036 2.00e-02 2.50e+03   1.88e-02 7.92e+00
        pdb=" N1   DC I   9 "    0.039 2.00e-02 2.50e+03
        pdb=" C2   DC I   9 "   -0.005 2.00e-02 2.50e+03
        pdb=" O2   DC I   9 "    0.009 2.00e-02 2.50e+03
        pdb=" N3   DC I   9 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DC I   9 "   -0.004 2.00e-02 2.50e+03
        pdb=" N4   DC I   9 "   -0.010 2.00e-02 2.50e+03
        pdb=" C5   DC I   9 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DC I   9 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J   9 "   -0.024 2.00e-02 2.50e+03   1.78e-02 7.11e+00
        pdb=" N1   DC J   9 "    0.044 2.00e-02 2.50e+03
        pdb=" C2   DC J   9 "   -0.017 2.00e-02 2.50e+03
        pdb=" O2   DC J   9 "    0.007 2.00e-02 2.50e+03
        pdb=" N3   DC J   9 "    0.001 2.00e-02 2.50e+03
        pdb=" C4   DC J   9 "   -0.003 2.00e-02 2.50e+03
        pdb=" N4   DC J   9 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5   DC J   9 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DC J   9 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  31 "   -0.038 2.00e-02 2.50e+03   1.60e-02 7.00e+00
        pdb=" N9   DA I  31 "    0.029 2.00e-02 2.50e+03
        pdb=" C8   DA I  31 "    0.014 2.00e-02 2.50e+03
        pdb=" N7   DA I  31 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5   DA I  31 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6   DA I  31 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I  31 "   -0.013 2.00e-02 2.50e+03
        pdb=" N1   DA I  31 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DA I  31 "    0.007 2.00e-02 2.50e+03
        pdb=" N3   DA I  31 "    0.008 2.00e-02 2.50e+03
        pdb=" C4   DA I  31 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1237 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 186
        2.63 -     3.20: 9662
        3.20 -     3.76: 21647
        3.76 -     4.33: 27367
        4.33 -     4.90: 38963
  Nonbonded interactions: 97825
  Sorted by model distance:
  nonbonded pdb=" OG  SER E  69 "
            pdb=" NH1 ARG E  73 "
     model   vdw
     2.062 3.120
  nonbonded pdb=" N   ASN D  55 "
            pdb=" OP1  DA I  12 "
     model   vdw
     2.134 3.120
  nonbonded pdb=" OG  SER C  41 "
            pdb=" OP1  DG J  98 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" OH  TYR F  68 "
            pdb=" OE2 GLU H  75 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" N2   DG I 114 "
            pdb=" O2   DT J  13 "
     model   vdw
     2.210 3.120
  ... (remaining 97820 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' and resid 51 through 140)
}
ncs_group {
  reference = (chain 'B' and (resid 20 through 96 or (resid 97 and (name N or name CA or name  \ 
C ))))
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}
ncs_group {
  reference = (chain 'I' and (resid 7 through 65 or resid 67 through 125))
  selection = (chain 'J' and (resid 1 through 59 or resid 61 through 119))
}

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:             0.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.150
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
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      :  0.010   0.083  11542  Z= 0.698
  Angle     :  0.995   7.680  16637  Z= 0.775
  Chirality :  0.065   0.308   1902
  Planarity :  0.005   0.042   1240
  Dihedral  : 28.860 153.423   4955
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 19.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.29), residues: 711
  helix: -0.22 (0.21), residues: 513
  sheet:  None (None), residues: 0
  loop : -2.04 (0.40), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A  64 
 TYR   0.020   0.003   TYR C  47 
 PHE   0.025   0.004   PHE C  94 
 HIS   0.016   0.002   HIS G  79 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00978 /  0.70 (11542)
  covalent geometry    : angle       0.99458 /  0.77 (16637)
  hydrogen bonds       : bond        0.09313 /  6.12 (  707)
  hydrogen bonds       : angle       4.46578 /  3.19 ( 1794)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
REVERT: A  138 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7768 (mp0)
REVERT: D   78 ASN cc_start: 0.8833 (t0) cc_final: 0.8304 (t0)
REVERT: D   82 ILE cc_start: 0.9136 (mt) cc_final: 0.8678 (mt)
REVERT: F   31 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.8032 (mmm160)
REVERT: F   87 LYS cc_start: 0.8948 (ttpt) cc_final: 0.8581 (ttmt)
REVERT: H   51 LEU cc_start: 0.7360 (pp) cc_final: 0.7110 (pp)
REVERT: C   96 ASN cc_start: 0.8080 (p0) cc_final: 0.7803 (p0)
REVERT: C  101 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7940 (mt-10)
REVERT: G   85 ARG cc_start: 0.7539 (mtt180) cc_final: 0.7336 (mtt180)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1518
  time to fit residues: 24.5432
Evaluate side-chains
  100 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:   20.0000
   overall best weight:    0.9582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  44 GLN
** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  79 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 = 0.4193 r_free = 0.4193 target = 0.180615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.122992 restraints weight = 14734.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.123569 restraints weight = 9967.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.124218 restraints weight = 9290.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.124652 restraints weight = 8822.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.124857 restraints weight = 8781.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.1155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.118  11542  Z= 0.174
  Angle     :  0.781   8.996  16637  Z= 0.433
  Chirality :  0.056   0.398   1902
  Planarity :  0.006   0.061   1240
  Dihedral  : 32.560 161.477   3513
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 14.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 14.24 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.28), residues: 711
  helix:  0.51 (0.20), residues: 521
  sheet:  None (None), residues: 0
  loop : -1.43 (0.41), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 132 
 TYR   0.021   0.002   TYR E  55 
 PHE   0.025   0.002   PHE G  60 
 HIS   0.013   0.002   HIS G  79 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00335 /  0.17 (11542)
  covalent geometry    : angle       0.78063 /  0.43 (16637)
  hydrogen bonds       : bond        0.05363 /  3.64 (  707)
  hydrogen bonds       : angle       3.72493 /  2.66 ( 1794)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   31 ARG cc_start: 0.8322 (mmm-85) cc_final: 0.8020 (mmm160)
REVERT: F   51 ARG cc_start: 0.8284 (mtt180) cc_final: 0.7986 (mtt-85)
REVERT: F   87 LYS cc_start: 0.8879 (ttpt) cc_final: 0.8494 (ttmt)
REVERT: H   84 LYS cc_start: 0.8133 (mmtt) cc_final: 0.7926 (mmtt)
REVERT: C   96 ASN cc_start: 0.8093 (p0) cc_final: 0.7807 (p0)
REVERT: C  101 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7863 (mt-10)
  outliers start: 9
  outliers final: 2
  residues processed: 114
  average time/residue: 0.1262
  time to fit residues: 19.4429
Evaluate side-chains
  97 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain G residue   82 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 78 optimal weight:   40.0000
   chunk 74 optimal weight:   30.0000
   chunk 53 optimal weight:    2.9990
   chunk 90 optimal weight:   50.0000
   chunk 2 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 51 optimal weight:   10.0000
   chunk 88 optimal weight:   30.0000
   chunk 67 optimal weight:    2.9990
   chunk 91 optimal weight:   50.0000
   overall best weight:    2.7588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  44 GLN
** C  79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  30 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.178372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.121680 restraints weight = 14955.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.121744 restraints weight = 11179.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.122611 restraints weight = 10252.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.123169 restraints weight = 9077.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.123484 restraints weight = 8749.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.1452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  11542  Z= 0.221
  Angle     :  0.772   8.423  16637  Z= 0.422
  Chirality :  0.052   0.360   1902
  Planarity :  0.005   0.053   1240
  Dihedral  : 32.473 174.446   3513
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 15.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 17.15 %
    Favored  : 79.45 %
  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:  0.15 (0.29), residues: 711
  helix:  0.63 (0.21), residues: 524
  sheet:  None (None), residues: 0
  loop : -1.22 (0.42), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 132 
 TYR   0.022   0.002   TYR E  55 
 PHE   0.016   0.002   PHE G  60 
 HIS   0.011   0.002   HIS G  79 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00478 /  0.22 (11542)
  covalent geometry    : angle       0.77160 /  0.42 (16637)
  hydrogen bonds       : bond        0.05145 /  3.50 (  707)
  hydrogen bonds       : angle       3.55473 /  2.54 ( 1794)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   35 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8467 (tpp80)
REVERT: E   62 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8137 (mm)
REVERT: F   31 ARG cc_start: 0.8323 (mmm-85) cc_final: 0.8050 (mmm160)
REVERT: F   87 LYS cc_start: 0.8927 (ttpt) cc_final: 0.8560 (ttmt)
REVERT: H   84 LYS cc_start: 0.8200 (mmtt) cc_final: 0.7908 (mmtt)
REVERT: C   96 ASN cc_start: 0.8108 (p0) cc_final: 0.7860 (p0)
REVERT: C  101 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7898 (mt-10)
REVERT: G   81 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8292 (tp)
  outliers start: 21
  outliers final: 12
  residues processed: 112
  average time/residue: 0.1151
  time to fit residues: 17.9158
Evaluate side-chains
  106 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain B residue   35 ARG
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain D residue  121 THR
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain F residue   44 SER
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue   82 THR
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain G residue   81 LEU
Chi-restraints excluded: chain G residue   82 THR
Chi-restraints excluded: chain G residue   89 GLU
Chi-restraints excluded: chain G residue  104 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 75 optimal weight:   30.0000
   chunk 82 optimal weight:   30.0000
   chunk 9 optimal weight:    0.9990
   chunk 57 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 89 optimal weight:   30.0000
   chunk 59 optimal weight:    6.9990
   chunk 19 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   overall best weight:    1.5384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  80 GLN
E  44 GLN
** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  30 HIS
** C  79 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 = 0.4191 r_free = 0.4191 target = 0.180504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.122749 restraints weight = 14986.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.124963 restraints weight = 10205.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.125190 restraints weight = 8940.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.125471 restraints weight = 8434.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.125926 restraints weight = 7719.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11542  Z= 0.164
  Angle     :  0.696  10.072  16637  Z= 0.389
  Chirality :  0.049   0.321   1902
  Planarity :  0.004   0.047   1240
  Dihedral  : 32.282 178.609   3513
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 18.93 %
    Favored  : 78.48 %
  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:  0.71 (0.29), residues: 711
  helix:  1.09 (0.21), residues: 520
  sheet:  None (None), residues: 0
  loop : -1.15 (0.41), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 132 
 TYR   0.014   0.002   TYR E  55 
 PHE   0.014   0.002   PHE G  60 
 HIS   0.010   0.002   HIS G  79 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.16 (11542)
  covalent geometry    : angle       0.69623 /  0.39 (16637)
  hydrogen bonds       : bond        0.04502 /  3.07 (  707)
  hydrogen bonds       : angle       3.40675 /  2.42 ( 1794)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   35 ARG cc_start: 0.8657 (ttm170) cc_final: 0.8316 (tpp80)
REVERT: D   82 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8693 (mp)
REVERT: D  119 LYS cc_start: 0.8627 (ttmt) cc_final: 0.8044 (tmmt)
REVERT: E   62 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7859 (mm)
REVERT: F   87 LYS cc_start: 0.8885 (ttpt) cc_final: 0.8491 (ttmt)
REVERT: H   84 LYS cc_start: 0.8204 (mmtt) cc_final: 0.7885 (mmtt)
REVERT: C   96 ASN cc_start: 0.8075 (p0) cc_final: 0.7841 (p0)
REVERT: C  101 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7844 (mt-10)
  outliers start: 16
  outliers final: 10
  residues processed: 115
  average time/residue: 0.1288
  time to fit residues: 19.8601
Evaluate side-chains
  106 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain D residue   82 ILE
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain E residue  116 HIS
Chi-restraints excluded: chain F residue   44 SER
Chi-restraints excluded: chain H residue   54 SER
Chi-restraints excluded: chain H residue  105 ILE
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain G residue   82 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 87 optimal weight:   30.0000
   chunk 46 optimal weight:    2.9990
   chunk 59 optimal weight:    7.9990
   chunk 63 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 81 optimal weight:   40.0000
   chunk 10 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 75 optimal weight:   30.0000
   chunk 14 optimal weight:    1.9990
   overall best weight:    1.3784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  79 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.180615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.123074 restraints weight = 14956.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.124786 restraints weight = 10375.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.125145 restraints weight = 9451.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.125505 restraints weight = 8669.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.126367 restraints weight = 7918.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.2084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11542  Z= 0.159
  Angle     :  0.684   8.258  16637  Z= 0.383
  Chirality :  0.047   0.309   1902
  Planarity :  0.005   0.076   1240
  Dihedral  : 32.165 179.784   3513
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 18.77 %
    Favored  : 77.99 %
  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:  0.91 (0.29), residues: 711
  helix:  1.26 (0.21), residues: 520
  sheet:  None (None), residues: 0
  loop : -1.18 (0.41), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F  36 
 TYR   0.011   0.001   TYR E 102 
 PHE   0.015   0.002   PHE G  60 
 HIS   0.008   0.002   HIS G  79 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.16 (11542)
  covalent geometry    : angle       0.68438 /  0.38 (16637)
  hydrogen bonds       : bond        0.04436 /  3.01 (  707)
  hydrogen bonds       : angle       3.36880 /  2.39 ( 1794)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 THR cc_start: 0.7754 (p) cc_final: 0.7544 (p)
REVERT: B   35 ARG cc_start: 0.8646 (ttm170) cc_final: 0.8390 (tpp80)
REVERT: D   85 ARG cc_start: 0.8291 (mtm110) cc_final: 0.8010 (mtm110)
REVERT: D  119 LYS cc_start: 0.8660 (ttmt) cc_final: 0.8087 (tmmt)
REVERT: F   87 LYS cc_start: 0.8874 (ttpt) cc_final: 0.8498 (ttmt)
REVERT: H   84 LYS cc_start: 0.8210 (mmtt) cc_final: 0.7849 (mmtt)
REVERT: C   96 ASN cc_start: 0.8059 (p0) cc_final: 0.7820 (p0)
REVERT: C  101 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7832 (mt-10)
REVERT: G   81 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8268 (tp)
  outliers start: 20
  outliers final: 15
  residues processed: 109
  average time/residue: 0.1320
  time to fit residues: 19.1377
Evaluate side-chains
  108 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain D residue  121 THR
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue   66 LEU
Chi-restraints excluded: chain E residue  116 HIS
Chi-restraints excluded: chain F residue   44 SER
Chi-restraints excluded: chain H residue   83 SER
Chi-restraints excluded: chain H residue  105 ILE
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue   82 THR
Chi-restraints excluded: chain G residue   81 LEU
Chi-restraints excluded: chain G residue   82 THR
Chi-restraints excluded: chain G residue   89 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 76 optimal weight:   30.0000
   chunk 61 optimal weight:    0.3980
   chunk 75 optimal weight:   30.0000
   chunk 68 optimal weight:   50.0000
   chunk 39 optimal weight:    7.9990
   chunk 58 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 50 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.1984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 116 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 = 0.4198 r_free = 0.4198 target = 0.181379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.123573 restraints weight = 14996.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.125122 restraints weight = 10510.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.125505 restraints weight = 9503.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.126087 restraints weight = 8720.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.126273 restraints weight = 8343.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.2294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11542  Z= 0.149
  Angle     :  0.664  11.835  16637  Z= 0.373
  Chirality :  0.046   0.280   1902
  Planarity :  0.004   0.053   1240
  Dihedral  : 32.073 179.356   3513
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 13.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 19.74 %
    Favored  : 76.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.30), residues: 711
  helix:  1.48 (0.21), residues: 520
  sheet:  None (None), residues: 0
  loop : -1.10 (0.41), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  31 
 TYR   0.010   0.001   TYR E 102 
 PHE   0.013   0.002   PHE G  60 
 HIS   0.008   0.001   HIS G  79 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.15 (11542)
  covalent geometry    : angle       0.66433 /  0.37 (16637)
  hydrogen bonds       : bond        0.04267 /  2.90 (  707)
  hydrogen bonds       : angle       3.28859 /  2.33 ( 1794)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
REVERT: B   31 ARG cc_start: 0.7897 (mtp85) cc_final: 0.7510 (mtp85)
REVERT: B   35 ARG cc_start: 0.8548 (ttm170) cc_final: 0.7926 (ttm170)
REVERT: D   82 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8671 (mp)
REVERT: D  119 LYS cc_start: 0.8646 (ttmt) cc_final: 0.8078 (tmmt)
REVERT: F   31 ARG cc_start: 0.8297 (mmm-85) cc_final: 0.8036 (mmm160)
REVERT: F   51 ARG cc_start: 0.8506 (mtt-85) cc_final: 0.8253 (mtt-85)
REVERT: F   87 LYS cc_start: 0.8866 (ttpt) cc_final: 0.8497 (ttmt)
REVERT: H   84 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7701 (mmtt)
REVERT: C   96 ASN cc_start: 0.8046 (p0) cc_final: 0.7773 (p0)
REVERT: C  101 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7732 (mt-10)
REVERT: G   81 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8250 (tp)
  outliers start: 21
  outliers final: 16
  residues processed: 113
  average time/residue: 0.1361
  time to fit residues: 20.5967
Evaluate side-chains
  110 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain D residue   82 ILE
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue  116 HIS
Chi-restraints excluded: chain H residue   63 SER
Chi-restraints excluded: chain H residue  105 ILE
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue   27 ILE
Chi-restraints excluded: chain C residue   82 THR
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain G residue   81 LEU
Chi-restraints excluded: chain G residue   82 THR
Chi-restraints excluded: chain G residue   89 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 76 optimal weight:   30.0000
   chunk 53 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 55 optimal weight:   10.0000
   chunk 51 optimal weight:    7.9990
   chunk 4 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   chunk 61 optimal weight:    7.9990
   chunk 50 optimal weight:    7.9990
   overall best weight:    2.1786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  54 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.179776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.122105 restraints weight = 15088.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.123736 restraints weight = 10354.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.124094 restraints weight = 9464.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.124671 restraints weight = 8594.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.124784 restraints weight = 8232.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  11542  Z= 0.188
  Angle     :  0.680  11.058  16637  Z= 0.376
  Chirality :  0.046   0.281   1902
  Planarity :  0.005   0.058   1240
  Dihedral  : 32.086 178.540   3513
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 13.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 19.74 %
    Favored  : 76.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.30), residues: 711
  helix:  1.37 (0.21), residues: 521
  sheet:  None (None), residues: 0
  loop : -1.13 (0.41), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F  36 
 TYR   0.013   0.001   TYR E 102 
 PHE   0.011   0.002   PHE E  68 
 HIS   0.007   0.002   HIS G  79 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00399 /  0.19 (11542)
  covalent geometry    : angle       0.67962 /  0.38 (16637)
  hydrogen bonds       : bond        0.04444 /  3.01 (  707)
  hydrogen bonds       : angle       3.33490 /  2.36 ( 1794)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
REVERT: B   31 ARG cc_start: 0.7931 (mtp85) cc_final: 0.7546 (mtp85)
REVERT: B   35 ARG cc_start: 0.8524 (ttm170) cc_final: 0.7955 (ttm170)
REVERT: D   82 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8752 (mp)
REVERT: D  119 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8057 (tmmt)
REVERT: F   87 LYS cc_start: 0.8876 (ttpt) cc_final: 0.8497 (ttmt)
REVERT: H   84 LYS cc_start: 0.8171 (mmtt) cc_final: 0.7717 (mmtt)
REVERT: C   62 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7478 (mm-30)
REVERT: C   96 ASN cc_start: 0.8075 (p0) cc_final: 0.7840 (p0)
REVERT: C  101 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7745 (mt-10)
REVERT: G   81 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8272 (tp)
  outliers start: 24
  outliers final: 20
  residues processed: 113
  average time/residue: 0.1202
  time to fit residues: 18.5797
Evaluate side-chains
  111 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain D residue   82 ILE
Chi-restraints excluded: chain D residue  121 THR
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue  116 HIS
Chi-restraints excluded: chain F residue   44 SER
Chi-restraints excluded: chain F residue   58 LEU
Chi-restraints excluded: chain H residue   63 SER
Chi-restraints excluded: chain H residue  105 ILE
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue   27 ILE
Chi-restraints excluded: chain C residue   82 THR
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain G residue   81 LEU
Chi-restraints excluded: chain G residue   82 THR
Chi-restraints excluded: chain G residue   89 GLU
Chi-restraints excluded: chain G residue   98 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 78 optimal weight:   40.0000
   chunk 42 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 63 optimal weight:    0.6980
   chunk 24 optimal weight:    7.9990
   chunk 30 optimal weight:    0.7980
   chunk 84 optimal weight:   30.0000
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 111 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.182526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.124231 restraints weight = 15007.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.126384 restraints weight = 10179.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.126505 restraints weight = 8810.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.127225 restraints weight = 8527.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.127247 restraints weight = 8011.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  11542  Z= 0.135
  Angle     :  0.633  11.243  16637  Z= 0.360
  Chirality :  0.044   0.281   1902
  Planarity :  0.004   0.044   1240
  Dihedral  : 31.805 179.300   3513
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 20.71 %
    Favored  : 76.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.47 (0.30), residues: 711
  helix:  1.69 (0.22), residues: 520
  sheet:  None (None), residues: 0
  loop : -1.00 (0.41), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F  36 
 TYR   0.010   0.001   TYR D  33 
 PHE   0.016   0.002   PHE G  60 
 HIS   0.007   0.001   HIS G  79 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00236 /  0.14 (11542)
  covalent geometry    : angle       0.63336 /  0.36 (16637)
  hydrogen bonds       : bond        0.04160 /  2.84 (  707)
  hydrogen bonds       : angle       3.22207 /  2.27 ( 1794)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: B   31 ARG cc_start: 0.7842 (mtp85) cc_final: 0.7546 (mtp85)
REVERT: B   35 ARG cc_start: 0.8440 (ttm170) cc_final: 0.8025 (ttm170)
REVERT: D   82 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8643 (mp)
REVERT: D   85 ARG cc_start: 0.8193 (mtm110) cc_final: 0.7965 (mtm110)
REVERT: D  119 LYS cc_start: 0.8653 (ttmt) cc_final: 0.8044 (tmmt)
REVERT: F   87 LYS cc_start: 0.8846 (ttpt) cc_final: 0.8450 (ttmt)
REVERT: H   84 LYS cc_start: 0.8077 (mmtt) cc_final: 0.7591 (mmtt)
REVERT: H  104 GLU cc_start: 0.7554 (tp30) cc_final: 0.6982 (tp30)
REVERT: H  107 ARG cc_start: 0.7866 (ttp80) cc_final: 0.7458 (tmm-80)
REVERT: C   62 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7426 (mm-30)
REVERT: C   96 ASN cc_start: 0.8037 (p0) cc_final: 0.7793 (p0)
  outliers start: 19
  outliers final: 11
  residues processed: 114
  average time/residue: 0.1284
  time to fit residues: 19.8273
Evaluate side-chains
  103 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain D residue   82 ILE
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue  116 HIS
Chi-restraints excluded: chain H residue   63 SER
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain G residue   82 THR
Chi-restraints excluded: chain G residue   89 GLU
Chi-restraints excluded: chain G residue   98 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9990
   chunk 63 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9990
   chunk 10 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   chunk 83 optimal weight:   30.0000
   chunk 21 optimal weight:    0.8980
   chunk 58 optimal weight:    5.9990
   chunk 72 optimal weight:   30.0000
   overall best weight:    0.8984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 116 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 = 0.4209 r_free = 0.4209 target = 0.182677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.124604 restraints weight = 14929.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.126862 restraints weight = 10155.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.126688 restraints weight = 9036.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.127278 restraints weight = 8424.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.127778 restraints weight = 7591.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.2799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11542  Z= 0.141
  Angle     :  0.636  12.161  16637  Z= 0.359
  Chirality :  0.043   0.282   1902
  Planarity :  0.004   0.044   1240
  Dihedral  : 31.709 179.215   3513
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 14.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 22.01 %
    Favored  : 75.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.51 (0.30), residues: 711
  helix:  1.74 (0.21), residues: 520
  sheet:  None (None), residues: 0
  loop : -1.06 (0.40), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F  36 
 TYR   0.009   0.001   TYR E 102 
 PHE   0.011   0.001   PHE E  68 
 HIS   0.006   0.001   HIS G  79 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.14 (11542)
  covalent geometry    : angle       0.63581 /  0.36 (16637)
  hydrogen bonds       : bond        0.04175 /  2.85 (  707)
  hydrogen bonds       : angle       3.23952 /  2.28 ( 1794)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 ARG cc_start: 0.7814 (mtp85) cc_final: 0.7550 (mtp85)
REVERT: B   35 ARG cc_start: 0.8423 (ttm170) cc_final: 0.8088 (tpp-160)
REVERT: D   43 ILE cc_start: 0.6679 (mm) cc_final: 0.6395 (mt)
REVERT: D   82 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8610 (mp)
REVERT: D  119 LYS cc_start: 0.8618 (ttmt) cc_final: 0.8033 (tmmt)
REVERT: F   87 LYS cc_start: 0.8827 (ttpt) cc_final: 0.8463 (ttmt)
REVERT: H   84 LYS cc_start: 0.8027 (mmtt) cc_final: 0.7560 (mmtt)
REVERT: C   62 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7444 (mm-30)
  outliers start: 13
  outliers final: 10
  residues processed: 99
  average time/residue: 0.1341
  time to fit residues: 17.7849
Evaluate side-chains
  101 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain D residue   82 ILE
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue  116 HIS
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain G residue   82 THR
Chi-restraints excluded: chain G residue   89 GLU
Chi-restraints excluded: chain G residue   98 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 71 optimal weight:   30.0000
   chunk 27 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 88 optimal weight:   30.0000
   chunk 67 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 49 optimal weight:    5.9990
   chunk 56 optimal weight:    0.6980
   overall best weight:    0.8984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  48 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.183088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.124875 restraints weight = 14993.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.126799 restraints weight = 10536.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.126621 restraints weight = 9578.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.127372 restraints weight = 8638.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.127486 restraints weight = 8336.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.3000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  11542  Z= 0.139
  Angle     :  0.622  11.654  16637  Z= 0.354
  Chirality :  0.043   0.284   1902
  Planarity :  0.004   0.044   1240
  Dihedral  : 31.565 179.834   3513
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 13.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 22.49 %
    Favored  : 75.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.65 (0.30), residues: 711
  helix:  1.84 (0.21), residues: 518
  sheet:  None (None), residues: 0
  loop : -0.98 (0.40), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F  36 
 TYR   0.009   0.001   TYR E 102 
 PHE   0.011   0.001   PHE E  68 
 HIS   0.007   0.001   HIS B  71 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.14 (11542)
  covalent geometry    : angle       0.62165 /  0.35 (16637)
  hydrogen bonds       : bond        0.04130 /  2.84 (  707)
  hydrogen bonds       : angle       3.20322 /  2.25 ( 1794)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
REVERT: B   31 ARG cc_start: 0.7831 (mtp85) cc_final: 0.7563 (mtp85)
REVERT: B   35 ARG cc_start: 0.8454 (ttm170) cc_final: 0.8130 (tpp-160)
REVERT: D   43 ILE cc_start: 0.6639 (mm) cc_final: 0.6382 (mt)
REVERT: D   82 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8585 (mp)
REVERT: D  119 LYS cc_start: 0.8604 (ttmt) cc_final: 0.8012 (tmmt)
REVERT: F   87 LYS cc_start: 0.8823 (ttpt) cc_final: 0.8468 (ttmt)
REVERT: H   84 LYS cc_start: 0.8026 (mmtt) cc_final: 0.7533 (mmtt)
REVERT: C   62 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7431 (mm-30)
  outliers start: 13
  outliers final: 11
  residues processed: 98
  average time/residue: 0.1285
  time to fit residues: 17.1067
Evaluate side-chains
  98 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain D residue   82 ILE
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue  116 HIS
Chi-restraints excluded: chain F residue   44 SER
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain G residue   82 THR
Chi-restraints excluded: chain G residue   89 GLU
Chi-restraints excluded: chain G residue   98 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 73 optimal weight:   30.0000
   chunk 72 optimal weight:   20.0000
   chunk 2 optimal weight:    0.9980
   chunk 91 optimal weight:   50.0000
   chunk 49 optimal weight:    5.9990
   chunk 29 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   chunk 18 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    2.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 116 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 = 0.4180 r_free = 0.4180 target = 0.179754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.122863 restraints weight = 15122.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.123965 restraints weight = 10479.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.124664 restraints weight = 9560.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.125230 restraints weight = 8521.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.125357 restraints weight = 8145.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.2898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  11542  Z= 0.225
  Angle     :  0.688  12.082  16637  Z= 0.380
  Chirality :  0.045   0.283   1902
  Planarity :  0.005   0.044   1240
  Dihedral  : 31.707 179.172   3513
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 14.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 22.65 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.29), residues: 711
  helix:  1.38 (0.21), residues: 519
  sheet:  None (None), residues: 0
  loop : -1.05 (0.40), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F  36 
 TYR   0.016   0.002   TYR E 102 
 PHE   0.012   0.002   PHE A  87 
 HIS   0.007   0.002   HIS B  71 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00500 /  0.23 (11542)
  covalent geometry    : angle       0.68819 /  0.38 (16637)
  hydrogen bonds       : bond        0.04553 /  3.11 (  707)
  hydrogen bonds       : angle       3.35690 /  2.38 ( 1794)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1463.70 seconds
wall clock time: 26 minutes 11.77 seconds (1571.77 seconds total)