Starting phenix.real_space_refine
on Sun Apr  5 17:21:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/10xz_75521/04_2026/10xz_75521.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/10xz_75521/04_2026/10xz_75521.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/10xz_75521/04_2026/10xz_75521.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/10xz_75521/04_2026/10xz_75521.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/10xz_75521/04_2026/10xz_75521.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/10xz_75521/04_2026/10xz_75521.map"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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     294      5.49       5
     S      10      5.16       5
     C    6654      2.51       5
     N    2263      2.21       5
     O    2822      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12043
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 789
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 789
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 657
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 823
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "D"
      Number of atoms: 743
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
      Conformer: "B"
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
          bond proxies already assigned to first conformer: 738
    Chain: "E"
      Number of atoms: 808
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 97, 800
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
      Conformer: "B"
        Number of residues, atoms: 97, 800
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
          bond proxies already assigned to first conformer: 803
    Chain: "F"
      Number of atoms: 641
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 641
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 823
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "H"
      Number of atoms: 732
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 725
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 93, 725
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          bond proxies already assigned to first conformer: 727
    Chain: "I"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
  Time building chain proxies: 3.10, per 1000 atoms: 0.26
  Number of scatterers: 12043
  At special positions: 0
  Unit cell: (74.328, 123.228, 116.056, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     P     294     15.00
     O    2822      8.00
     N    2263      7.00
     C    6654      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: 0.92
  Conformation dependent library (CDL) restraints added in 441.4 milliseconds
  

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1418

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 9 sheets defined
      73.4% alpha, 2.6% beta
      147 base pairs and 265 stacking pairs defined.
    Time for finding SS restraints: 1.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 49
    Processing helix  chain 'A' and resid 50 through 57
      removed outlier: 3.581A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.525A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.690A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.360A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 123
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 4.159A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.701A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.543A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.370A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 124
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.070A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.716A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.219A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.983A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.271A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78

    406 hydrogen bonds defined for protein.
    1191 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      376 hydrogen bonds
      752 hydrogen bond angles
      0 basepair planarities
      147 basepair parallelities
      265 stacking parallelities
  Total time for adding SS restraints: 2.28

  Time building geometry restraints manager: 1.27 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: 2140
        1.33 -     1.45: 4252
        1.45 -     1.57: 5863
        1.57 -     1.69: 586
        1.69 -     1.80: 20
  Bond restraints: 12861
  Sorted by residual:
  bond pdb=" N   MET A 120 "
       pdb=" CA  MET A 120 "
    ideal  model  delta    sigma   weight residual
    1.453  1.483 -0.030 8.30e-03 1.45e+04 1.27e+01
  bond pdb=" CG  GLU A  97 "
       pdb=" CD  GLU A  97 "
    ideal  model  delta    sigma   weight residual
    1.516  1.468  0.048 2.50e-02 1.60e+03 3.73e+00
  bond pdb=" N   GLN E  68 "
       pdb=" CA  GLN E  68 "
    ideal  model  delta    sigma   weight residual
    1.459  1.482 -0.023 1.19e-02 7.06e+03 3.58e+00
  bond pdb=" CB  ASP B  24 "
       pdb=" CG  ASP B  24 "
    ideal  model  delta    sigma   weight residual
    1.516  1.558 -0.042 2.50e-02 1.60e+03 2.86e+00
  bond pdb=" CA  SER H  32 "
       pdb=" CB  SER H  32 "
    ideal  model  delta    sigma   weight residual
    1.530  1.497  0.033 2.00e-02 2.50e+03 2.77e+00
  ... (remaining 12856 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 18369
        2.20 -     4.39: 237
        4.39 -     6.59: 23
        6.59 -     8.78: 3
        8.78 -    10.98: 1
  Bond angle restraints: 18633
  Sorted by residual:
  angle pdb=" N   VAL B  21 "
        pdb=" CA  VAL B  21 "
        pdb=" C   VAL B  21 "
      ideal   model   delta    sigma   weight residual
     112.12  109.16    2.96 8.40e-01 1.42e+00 1.24e+01
  angle pdb=" CA  ASP B  24 "
        pdb=" CB  ASP B  24 "
        pdb=" CG  ASP B  24 "
      ideal   model   delta    sigma   weight residual
     112.60  115.84   -3.24 1.00e+00 1.00e+00 1.05e+01
  angle pdb=" CA  LEU D 101 "
        pdb=" CB  LEU D 101 "
        pdb=" CG  LEU D 101 "
      ideal   model   delta    sigma   weight residual
     116.30  127.28  -10.98 3.50e+00 8.16e-02 9.84e+00
  angle pdb=" CA  ARG D  31 "
        pdb=" CB  ARG D  31 "
        pdb=" CG  ARG D  31 "
      ideal   model   delta    sigma   weight residual
     114.10  120.35   -6.25 2.00e+00 2.50e-01 9.76e+00
  angle pdb=" CB  GLU E  59 "
        pdb=" CG  GLU E  59 "
        pdb=" CD  GLU E  59 "
      ideal   model   delta    sigma   weight residual
     112.60  117.76   -5.16 1.70e+00 3.46e-01 9.21e+00
  ... (remaining 18628 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.91: 5092
       28.91 -    57.82: 1769
       57.82 -    86.72: 119
       86.72 -   115.63: 1
      115.63 -   144.54: 3
  Dihedral angle restraints: 6984
    sinusoidal: 4782
      harmonic: 2202
  Sorted by residual:
  dihedral pdb=" CA  LEU A  48 "
           pdb=" C   LEU A  48 "
           pdb=" N   ARG A  49 "
           pdb=" CA  ARG A  49 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.17   24.83     0      5.00e+00 4.00e-02 2.47e+01
  dihedral pdb=" C4'  DG J  82 "
           pdb=" C3'  DG J  82 "
           pdb=" O3'  DG J  82 "
           pdb=" P    DT J  83 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   75.46  144.54     1      3.50e+01 8.16e-04 1.42e+01
  dihedral pdb=" C4'  DT J  15 "
           pdb=" C3'  DT J  15 "
           pdb=" O3'  DT J  15 "
           pdb=" P    DC J  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   77.53  142.47     1      3.50e+01 8.16e-04 1.41e+01
  ... (remaining 6981 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1885
       0.056 -    0.113: 211
       0.113 -    0.169: 21
       0.169 -    0.225: 2
       0.225 -    0.282: 1
  Chirality restraints: 2120
  Sorted by residual:
  chirality pdb=" CG  LEU D 101 "
            pdb=" CB  LEU D 101 "
            pdb=" CD1 LEU D 101 "
            pdb=" CD2 LEU D 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.31   -0.28 2.00e-01 2.50e+01 1.98e+00
  chirality pdb=" CA  MET A 120 "
            pdb=" N   MET A 120 "
            pdb=" C   MET A 120 "
            pdb=" CB  MET A 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  ASP B  24 "
            pdb=" N   ASP B  24 "
            pdb=" C   ASP B  24 "
            pdb=" CB  ASP B  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.42e-01
  ... (remaining 2117 not shown)

  Planarity restraints: 1338
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG E  42 "   -0.035 5.00e-02 4.00e+02   5.25e-02 4.41e+00
        pdb=" N   PRO E  43 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO E  43 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO E  43 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C  79 "   -0.029 5.00e-02 4.00e+02   4.41e-02 3.11e+00
        pdb=" N   PRO C  80 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO C  80 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO C  80 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I 100 "   -0.024 2.00e-02 2.50e+03   1.02e-02 3.10e+00
        pdb=" N9   DG I 100 "    0.023 2.00e-02 2.50e+03
        pdb=" C8   DG I 100 "    0.004 2.00e-02 2.50e+03
        pdb=" N7   DG I 100 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DG I 100 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I 100 "   -0.004 2.00e-02 2.50e+03
        pdb=" O6   DG I 100 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1   DG I 100 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2   DG I 100 "    0.004 2.00e-02 2.50e+03
        pdb=" N2   DG I 100 "    0.002 2.00e-02 2.50e+03
        pdb=" N3   DG I 100 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DG I 100 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1335 not shown)

  Histogram of nonbonded interaction distances:
        2.50 -     2.98: 5221
        2.98 -     3.46: 11113
        3.46 -     3.94: 25205
        3.94 -     4.42: 27880
        4.42 -     4.90: 36781
  Nonbonded interactions: 106200
  Sorted by model distance:
  nonbonded pdb=" O5'  DA I 124 "
            pdb=" O4'  DA I 124 "
     model   vdw
     2.505 2.432
  nonbonded pdb=" CB  GLU A  97 "
            pdb=" OE1 GLU A  97 "
     model   vdw
     2.539 2.752
  nonbonded pdb=" O5'  DG J  23 "
            pdb=" O4'  DG J  23 "
     model   vdw
     2.551 2.432
  nonbonded pdb=" O   LEU A  60 "
            pdb=" OE1 GLU A  97 "
     model   vdw
     2.557 3.040
  nonbonded pdb=" N   ARG D  31 "
            pdb=" N   SER D  32 "
     model   vdw
     2.573 2.560
  ... (remaining 106195 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' and (resid 38 through 128 or resid 130 through 133))
  selection = (chain 'E' and (resid 38 through 128 or resid 130 through 133))
}
ncs_group {
  reference = (chain 'B' and resid 22 through 101)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and (resid 32 through 81 or resid 83 through 124))
  selection = (chain 'H' and (resid 32 through 81 or resid 83 through 124))
}

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=0.45 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.120
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     14.090
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
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      :  0.005   0.048  12861  Z= 0.213
  Angle     :  0.631  10.977  18633  Z= 0.374
  Chirality :  0.038   0.282   2120
  Planarity :  0.005   0.059   1338
  Dihedral  : 28.595 144.540   5566
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 21.39 %
    Favored  : 78.29 %
  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:  1.88 (0.30), residues: 743
  helix:  1.96 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -0.79 (0.39), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG H  86 
 TYR   0.014   0.002   TYR B  88 
 PHE   0.008   0.002   PHE E  67 
 HIS   0.005   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 (12861)
  covalent geometry    : angle       0.63142 (18633)
  hydrogen bonds       : bond        0.10033 (  782)
  hydrogen bonds       : angle       3.68555 ( 1943)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 155
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.8468 (mmm-85) cc_final: 0.7987 (mtp-110)
REVERT: A   73 GLU cc_start: 0.8758 (tt0) cc_final: 0.8537 (tt0)
REVERT: B   93 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7473 (mp10)
REVERT: C   36 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8683 (mmtp)
REVERT: C   73 ASN cc_start: 0.8773 (t0) cc_final: 0.8500 (t0)
REVERT: D  108 LYS cc_start: 0.8734 (mtpp) cc_final: 0.8376 (mtmm)
REVERT: E   73 GLU cc_start: 0.8649 (tt0) cc_final: 0.8428 (tt0)
REVERT: G   73 ASN cc_start: 0.8709 (t0) cc_final: 0.8107 (t0)
REVERT: H   68 ASP cc_start: 0.8952 (t0) cc_final: 0.8697 (t0)
REVERT: H   99 ARG cc_start: 0.8721 (mtm-85) cc_final: 0.8391 (mtt90)
REVERT: H  108 LYS cc_start: 0.8615 (mtpp) cc_final: 0.8177 (mttt)
  outliers start: 2
  outliers final: 0
  residues processed: 155
  average time/residue: 0.9488
  time to fit residues: 154.5968
Evaluate side-chains
  154 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 153
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
E  68 GLN
E  85 GLN
G  73 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.102073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.070109 restraints weight = 36522.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 1.91
r_work: 0.2780 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2773
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2773 r_free = 0.2773    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2773 r_free = 0.2773    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2773
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.0312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12861  Z= 0.172
  Angle     :  0.573   9.242  18633  Z= 0.347
  Chirality :  0.034   0.265   2120
  Planarity :  0.004   0.047   1338
  Dihedral  : 30.816 144.639   4066
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 20.29 %
    Favored  : 78.29 %
  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:  2.40 (0.30), residues: 743
  helix:  2.31 (0.22), residues: 553
  sheet:  None (None), residues: 0
  loop : -0.64 (0.40), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  86 
 TYR   0.012   0.001   TYR D  40 
 PHE   0.014   0.002   PHE E  67 
 HIS   0.003   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (12861)
  covalent geometry    : angle       0.57265 (18633)
  hydrogen bonds       : bond        0.04208 (  782)
  hydrogen bonds       : angle       3.20010 ( 1943)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 154
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.8482 (mmm-85) cc_final: 0.7984 (mtp-110)
REVERT: B   92 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8622 (mtp85)
REVERT: C   36 LYS cc_start: 0.8993 (mmmm) cc_final: 0.8649 (mmtp)
REVERT: C   73 ASN cc_start: 0.8752 (t0) cc_final: 0.8474 (t0)
REVERT: D  108 LYS cc_start: 0.8676 (mtpp) cc_final: 0.8326 (mtmm)
REVERT: F   92 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8491 (ttp80)
REVERT: G   73 ASN cc_start: 0.8666 (t0) cc_final: 0.8051 (t0)
REVERT: H   34 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7791 (tptp)
REVERT: H   68 ASP cc_start: 0.8952 (t0) cc_final: 0.8689 (t0)
REVERT: H   99 ARG cc_start: 0.8695 (mtm-85) cc_final: 0.8386 (mtt90)
  outliers start: 9
  outliers final: 1
  residues processed: 158
  average time/residue: 0.9219
  time to fit residues: 153.1652
Evaluate side-chains
  157 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 153
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain H residue   34 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   overall best weight:    2.5388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.100896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.068684 restraints weight = 37006.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.2987 rms_B_bonded: 1.95
r_work: 0.2746 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2732
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2732 r_free = 0.2732    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2732 r_free = 0.2732    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2732
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8593
moved from start:          0.0546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.045  12861  Z= 0.298
  Angle     :  0.594   7.336  18633  Z= 0.356
  Chirality :  0.038   0.252   2120
  Planarity :  0.004   0.049   1338
  Dihedral  : 30.766 144.966   4063
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 19.65 %
    Favored  : 78.61 %
  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:  2.49 (0.30), residues: 743
  helix:  2.40 (0.22), residues: 553
  sheet:  None (None), residues: 0
  loop : -0.67 (0.39), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F  35 
 TYR   0.012   0.002   TYR F  51 
 PHE   0.010   0.002   PHE A  67 
 HIS   0.005   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00683 (12861)
  covalent geometry    : angle       0.59437 (18633)
  hydrogen bonds       : bond        0.04531 (  782)
  hydrogen bonds       : angle       3.00513 ( 1943)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 154
  time to evaluate  : 0.315 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8617 (mtp85)
REVERT: B   93 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7565 (mp10)
REVERT: C   73 ASN cc_start: 0.8774 (t0) cc_final: 0.8511 (t160)
REVERT: G   64 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8511 (tm-30)
REVERT: G   73 ASN cc_start: 0.8684 (t0) cc_final: 0.8073 (t0)
REVERT: H   34 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7808 (tptp)
REVERT: H   99 ARG cc_start: 0.8733 (mtm-85) cc_final: 0.8424 (mtt90)
  outliers start: 11
  outliers final: 3
  residues processed: 159
  average time/residue: 0.9484
  time to fit residues: 158.6116
Evaluate side-chains
  160 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 153
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   34 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 85 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 89 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.101894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.069524 restraints weight = 41205.908|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 2.01
r_work: 0.2760 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2748
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2748 r_free = 0.2748    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2748 r_free = 0.2748    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2748
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.0578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12861  Z= 0.174
  Angle     :  0.576   9.245  18633  Z= 0.346
  Chirality :  0.034   0.262   2120
  Planarity :  0.004   0.046   1338
  Dihedral  : 30.833 146.011   4063
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 19.18 %
    Favored  : 78.45 %
  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:  2.66 (0.31), residues: 743
  helix:  2.51 (0.22), residues: 553
  sheet:  None (None), residues: 0
  loop : -0.58 (0.39), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  86 
 TYR   0.011   0.001   TYR D  40 
 PHE   0.010   0.001   PHE A  67 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (12861)
  covalent geometry    : angle       0.57606 (18633)
  hydrogen bonds       : bond        0.04171 (  782)
  hydrogen bonds       : angle       2.97183 ( 1943)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 151
  time to evaluate  : 0.336 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8583 (mtp85)
REVERT: B   93 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7546 (mp10)
REVERT: C   73 ASN cc_start: 0.8764 (t0) cc_final: 0.8509 (t0)
REVERT: D  108 LYS cc_start: 0.8640 (mtpp) cc_final: 0.8288 (mtmm)
REVERT: E   73 GLU cc_start: 0.8753 (tt0) cc_final: 0.8522 (tt0)
REVERT: F   92 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8480 (ttp80)
REVERT: G   64 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8488 (tm-30)
REVERT: G   73 ASN cc_start: 0.8676 (t0) cc_final: 0.8134 (t0)
REVERT: G   75 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8799 (mttm)
REVERT: H   34 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7801 (tptp)
REVERT: H   99 ARG cc_start: 0.8699 (mtm-85) cc_final: 0.8357 (mtt90)
  outliers start: 15
  outliers final: 6
  residues processed: 156
  average time/residue: 0.9199
  time to fit residues: 150.8673
Evaluate side-chains
  162 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 150
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain G residue   75 LYS
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   34 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 92 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   chunk 96 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.101706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.069563 restraints weight = 36990.089|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 1.91
r_work: 0.2768 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2756
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2756 r_free = 0.2756    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2756 r_free = 0.2756    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2756
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8575
moved from start:          0.0599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12861  Z= 0.216
  Angle     :  0.570   7.012  18633  Z= 0.344
  Chirality :  0.035   0.225   2120
  Planarity :  0.004   0.045   1338
  Dihedral  : 30.788 145.452   4063
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 19.18 %
    Favored  : 78.45 %
  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:  2.70 (0.30), residues: 743
  helix:  2.54 (0.22), residues: 553
  sheet:  None (None), residues: 0
  loop : -0.57 (0.40), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  42 
 TYR   0.010   0.001   TYR D  40 
 PHE   0.011   0.002   PHE A  67 
 HIS   0.003   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 (12861)
  covalent geometry    : angle       0.56988 (18633)
  hydrogen bonds       : bond        0.03909 (  782)
  hydrogen bonds       : angle       2.92119 ( 1943)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 152
  time to evaluate  : 0.325 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8588 (mtp85)
REVERT: B   93 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7583 (mp10)
REVERT: C   73 ASN cc_start: 0.8777 (t0) cc_final: 0.8495 (t160)
REVERT: D  108 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8308 (mtmm)
REVERT: E   73 GLU cc_start: 0.8730 (tt0) cc_final: 0.8480 (tt0)
REVERT: F   92 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8472 (ttp80)
REVERT: G   64 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8484 (tm-30)
REVERT: G   73 ASN cc_start: 0.8676 (t0) cc_final: 0.8109 (t0)
REVERT: G   75 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8807 (mttm)
REVERT: H   34 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7805 (tptp)
REVERT: H   99 ARG cc_start: 0.8702 (mtm-85) cc_final: 0.8383 (mtt90)
  outliers start: 15
  outliers final: 5
  residues processed: 158
  average time/residue: 0.9564
  time to fit residues: 158.8431
Evaluate side-chains
  163 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 152
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain G residue   75 LYS
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   34 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 94 optimal weight:    3.9990
   chunk 82 optimal weight:    4.9990
   chunk 90 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 14 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 97 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
C 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.101746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.069096 restraints weight = 43936.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.3001 rms_B_bonded: 2.08
r_work: 0.2752 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2742
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2742 r_free = 0.2742    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2742 r_free = 0.2742    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2742
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.0632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  12861  Z= 0.204
  Angle     :  0.566   7.545  18633  Z= 0.342
  Chirality :  0.035   0.255   2120
  Planarity :  0.004   0.045   1338
  Dihedral  : 30.794 145.541   4063
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 19.18 %
    Favored  : 78.45 %
  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:  2.72 (0.30), residues: 743
  helix:  2.56 (0.22), residues: 553
  sheet:  None (None), residues: 0
  loop : -0.57 (0.40), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  86 
 TYR   0.010   0.001   TYR D  40 
 PHE   0.010   0.001   PHE A  67 
 HIS   0.003   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 (12861)
  covalent geometry    : angle       0.56605 (18633)
  hydrogen bonds       : bond        0.03875 (  782)
  hydrogen bonds       : angle       2.90894 ( 1943)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 151
  time to evaluate  : 0.336 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8589 (mtp85)
REVERT: B   93 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7578 (mp10)
REVERT: C   73 ASN cc_start: 0.8774 (t0) cc_final: 0.8495 (t160)
REVERT: D  108 LYS cc_start: 0.8668 (mtpp) cc_final: 0.8328 (mtmm)
REVERT: F   92 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8483 (ttp80)
REVERT: G   15 LYS cc_start: 0.7783 (ttmm) cc_final: 0.7568 (ttpp)
REVERT: G   64 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8492 (tm-30)
REVERT: G   73 ASN cc_start: 0.8675 (t0) cc_final: 0.8110 (t0)
REVERT: G   75 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8795 (mttm)
REVERT: H   34 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7781 (tptp)
REVERT: H   99 ARG cc_start: 0.8704 (mtm-85) cc_final: 0.8359 (mtt90)
  outliers start: 15
  outliers final: 6
  residues processed: 157
  average time/residue: 0.9640
  time to fit residues: 159.1663
Evaluate side-chains
  163 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 151
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain G residue   75 LYS
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   34 LYS
Chi-restraints excluded: chain H residue   39 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 87 optimal weight:    8.9990
   chunk 27 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   chunk 80 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.101250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.069268 restraints weight = 33201.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 1.82
r_work: 0.2775 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2775
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2753
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2753 r_free = 0.2753    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2753 r_free = 0.2753    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2753
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.0710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  12861  Z= 0.237
  Angle     :  0.572   6.899  18633  Z= 0.345
  Chirality :  0.036   0.222   2120
  Planarity :  0.004   0.044   1338
  Dihedral  : 30.803 145.882   4063
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 18.38 %
    Favored  : 79.08 %
  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:  2.72 (0.30), residues: 743
  helix:  2.57 (0.22), residues: 553
  sheet:  None (None), residues: 0
  loop : -0.58 (0.39), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  42 
 TYR   0.010   0.002   TYR D  40 
 PHE   0.011   0.002   PHE A  67 
 HIS   0.004   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00536 (12861)
  covalent geometry    : angle       0.57225 (18633)
  hydrogen bonds       : bond        0.04114 (  782)
  hydrogen bonds       : angle       2.86775 ( 1943)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 152
  time to evaluate  : 0.245 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8581 (mtp85)
REVERT: B   93 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7601 (mp10)
REVERT: C   73 ASN cc_start: 0.8781 (t0) cc_final: 0.8519 (t160)
REVERT: D  108 LYS cc_start: 0.8693 (mtpp) cc_final: 0.8360 (mtmm)
REVERT: F   92 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8467 (ttp80)
REVERT: G   73 ASN cc_start: 0.8693 (t0) cc_final: 0.8103 (t0)
REVERT: G   75 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8813 (mttm)
REVERT: H   34 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7800 (tptp)
REVERT: H   99 ARG cc_start: 0.8690 (mtm-85) cc_final: 0.8375 (mtt90)
  outliers start: 16
  outliers final: 6
  residues processed: 159
  average time/residue: 0.9576
  time to fit residues: 160.0281
Evaluate side-chains
  163 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 152
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   75 LYS
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   34 LYS
Chi-restraints excluded: chain H residue   39 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 91 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   chunk 96 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 90 optimal weight:    4.9990
   chunk 78 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   chunk 97 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   chunk 88 optimal weight:    6.9990
   overall best weight:    1.8784

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.101280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.068986 restraints weight = 41194.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 2.02
r_work: 0.2754 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2742
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2742 r_free = 0.2742    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2742 r_free = 0.2742    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2742
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.0712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  12861  Z= 0.237
  Angle     :  0.576   7.709  18633  Z= 0.346
  Chirality :  0.036   0.260   2120
  Planarity :  0.004   0.044   1338
  Dihedral  : 30.809 145.971   4063
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 19.18 %
    Favored  : 78.61 %
  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:  2.72 (0.30), residues: 743
  helix:  2.57 (0.22), residues: 553
  sheet:  None (None), residues: 0
  loop : -0.58 (0.40), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  42 
 TYR   0.013   0.002   TYR B  88 
 PHE   0.010   0.002   PHE A  67 
 HIS   0.004   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 (12861)
  covalent geometry    : angle       0.57643 (18633)
  hydrogen bonds       : bond        0.04081 (  782)
  hydrogen bonds       : angle       2.86941 ( 1943)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 151
  time to evaluate  : 0.351 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8589 (mtp85)
REVERT: B   93 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.7608 (mp10)
REVERT: C   73 ASN cc_start: 0.8780 (t0) cc_final: 0.8492 (t160)
REVERT: D  108 LYS cc_start: 0.8698 (mtpp) cc_final: 0.8373 (mtmm)
REVERT: F   92 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8483 (ttp80)
REVERT: G   73 ASN cc_start: 0.8694 (t0) cc_final: 0.8102 (t0)
REVERT: G   75 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8811 (mttm)
REVERT: H   99 ARG cc_start: 0.8698 (mtm-85) cc_final: 0.8384 (mtt90)
  outliers start: 14
  outliers final: 7
  residues processed: 157
  average time/residue: 0.9797
  time to fit residues: 161.5774
Evaluate side-chains
  162 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 151
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   75 LYS
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   39 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 85 optimal weight:   10.0000
   chunk 58 optimal weight:    4.9990
   chunk 49 optimal weight:    0.6980
   chunk 98 optimal weight:    4.9990
   chunk 97 optimal weight:    3.9990
   chunk 92 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0770
   chunk 43 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.7140

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.101966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.070315 restraints weight = 27593.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 1.68
r_work: 0.2802 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work: 0.2655 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2644
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2644 r_free = 0.2644    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2644 r_free = 0.2644    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2644
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.0700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12861  Z= 0.168
  Angle     :  0.566   7.518  18633  Z= 0.341
  Chirality :  0.033   0.250   2120
  Planarity :  0.004   0.043   1338
  Dihedral  : 30.834 146.329   4063
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 20.13 %
    Favored  : 78.29 %
  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:  2.84 (0.31), residues: 743
  helix:  2.65 (0.22), residues: 553
  sheet:  None (None), residues: 0
  loop : -0.53 (0.40), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  42 
 TYR   0.011   0.002   TYR D  40 
 PHE   0.012   0.002   PHE A  67 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (12861)
  covalent geometry    : angle       0.56641 (18633)
  hydrogen bonds       : bond        0.03910 (  782)
  hydrogen bonds       : angle       2.86250 ( 1943)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 154
  time to evaluate  : 0.311 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8625 (mtp85)
REVERT: B   93 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.7680 (mp10)
REVERT: C   73 ASN cc_start: 0.8778 (t0) cc_final: 0.8524 (t0)
REVERT: D  108 LYS cc_start: 0.8742 (mtpp) cc_final: 0.8404 (mtmm)
REVERT: F   92 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8535 (ttp80)
REVERT: G   73 ASN cc_start: 0.8705 (t0) cc_final: 0.8108 (t0)
REVERT: G   75 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8822 (mttm)
REVERT: H   99 ARG cc_start: 0.8767 (mtm-85) cc_final: 0.8459 (mtt90)
  outliers start: 10
  outliers final: 6
  residues processed: 158
  average time/residue: 0.9448
  time to fit residues: 156.9507
Evaluate side-chains
  164 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 154
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   75 LYS
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   39 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 1 optimal weight:    0.5980
   chunk 89 optimal weight:    5.9990
   chunk 59 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 93 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 70 optimal weight:    0.3980
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.7182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.101884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.069989 restraints weight = 38234.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 1.92
r_work: 0.2776 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2766
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2766 r_free = 0.2766    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2766 r_free = 0.2766    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2766
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8561
moved from start:          0.0734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  12861  Z= 0.172
  Angle     :  0.567   7.615  18633  Z= 0.342
  Chirality :  0.034   0.246   2120
  Planarity :  0.004   0.043   1338
  Dihedral  : 30.826 146.105   4063
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 20.76 %
    Favored  : 77.81 %
  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:  2.83 (0.31), residues: 743
  helix:  2.64 (0.22), residues: 553
  sheet:  None (None), residues: 0
  loop : -0.52 (0.40), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  42 
 TYR   0.011   0.001   TYR D  40 
 PHE   0.011   0.001   PHE A  67 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (12861)
  covalent geometry    : angle       0.56711 (18633)
  hydrogen bonds       : bond        0.03803 (  782)
  hydrogen bonds       : angle       2.85283 ( 1943)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 153
  time to evaluate  : 0.304 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8589 (mtp85)
REVERT: B   93 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7626 (mp10)
REVERT: C   73 ASN cc_start: 0.8767 (t0) cc_final: 0.8503 (t160)
REVERT: D  108 LYS cc_start: 0.8679 (mtpp) cc_final: 0.8344 (mtmm)
REVERT: F   92 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8473 (ttp80)
REVERT: G   73 ASN cc_start: 0.8679 (t0) cc_final: 0.8084 (t0)
REVERT: G   75 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8786 (mttm)
REVERT: H   99 ARG cc_start: 0.8662 (mtm-85) cc_final: 0.8348 (mtt90)
  outliers start: 9
  outliers final: 4
  residues processed: 157
  average time/residue: 0.9581
  time to fit residues: 157.8833
Evaluate side-chains
  161 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 153
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   75 LYS
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   39 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 72 optimal weight:   10.0000
   chunk 80 optimal weight:    3.9990
   chunk 10 optimal weight:    0.5980
   chunk 91 optimal weight:    4.9990
   chunk 76 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   chunk 20 optimal weight:    0.6980
   chunk 27 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    1.6384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.101491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.069336 restraints weight = 35046.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 1.87
r_work: 0.2766 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2757
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2757 r_free = 0.2757    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2757 r_free = 0.2757    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2757
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8560
moved from start:          0.0780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  12861  Z= 0.216
  Angle     :  0.572   7.418  18633  Z= 0.344
  Chirality :  0.035   0.244   2120
  Planarity :  0.004   0.044   1338
  Dihedral  : 30.788 145.628   4063
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 20.92 %
    Favored  : 77.65 %
  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:  2.80 (0.31), residues: 743
  helix:  2.62 (0.22), residues: 553
  sheet:  None (None), residues: 0
  loop : -0.53 (0.40), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  42 
 TYR   0.012   0.001   TYR B  88 
 PHE   0.011   0.002   PHE A  67 
 HIS   0.003   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 (12861)
  covalent geometry    : angle       0.57154 (18633)
  hydrogen bonds       : bond        0.03876 (  782)
  hydrogen bonds       : angle       2.82539 ( 1943)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5023.01 seconds
wall clock time: 85 minutes 49.83 seconds (5149.83 seconds total)