Starting phenix.real_space_refine
on Wed Sep 17 22:44:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ox0_17251/09_2025/8ox0_17251.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ox0_17251/09_2025/8ox0_17251.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ox0_17251/09_2025/8ox0_17251.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ox0_17251/09_2025/8ox0_17251.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ox0_17251/09_2025/8ox0_17251.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ox0_17251/09_2025/8ox0_17251.cif"
  }
  resolution = 2.52
  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=   0.001
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     290      5.49       5
     S      14      5.16       5
     C    6773      2.51       5
     N    2308      2.21       5
     O    2886      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12271
  Number of models: 1
  Model: ""
    Number of chains: 20
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 708
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 708
          Classifications: {'peptide': 88}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 86}
    Chain: "C"
      Number of atoms: 847
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 847
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 5, 'TRANS': 104}
    Chain: "D"
      Number of atoms: 774
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 774
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 2, 'TRANS': 95}
    Chain: "E"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 810
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 694
          Classifications: {'peptide': 86}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 84}
    Chain: "G"
      Number of atoms: 847
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 847
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 5, 'TRANS': 104}
    Chain: "H"
      Number of atoms: 774
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 774
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 2, 'TRANS': 95}
    Chain: "J"
      Number of atoms: 3064
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 3064
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "I"
      Number of atoms: 2881
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2881
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}
    Chain: "D"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 10
          Classifications: {'water': 10}
          Link IDs: {None: 9}
    Chain: "E"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Classifications: {'water': 6}
          Link IDs: {None: 5}
    Chain: "F"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Classifications: {'water': 5}
          Link IDs: {None: 4}
    Chain: "G"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}
    Chain: "H"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Classifications: {'water': 6}
          Link IDs: {None: 5}
    Chain: "J"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}
    Chain: "I"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 2.70, per 1000 atoms: 0.22
  Number of scatterers: 12271
  At special positions: 0
  Unit cell: (92.71, 118.99, 125.56, 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      14     16.00
     P     290     15.00
     O    2886      8.00
     N    2308      7.00
     C    6773      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: 0.81
  Conformation dependent library (CDL) restraints added in 350.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1470

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      70.8% alpha, 3.0% beta
      143 base pairs and 278 stacking pairs defined.
    Time for finding SS restraints: 2.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    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 131
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.712A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 92
      removed outlier: 3.519A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    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: 4.490A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.530A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 100 through 121
      removed outlier: 3.524A  pdb=" N   SER D 121 " --> pdb=" O   LYS D 117 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 3.624A  pdb=" N   SER E  57 " --> pdb=" O   ARG E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 4.009A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.218A  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 131
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.852A  pdb=" N   GLN F  27 " --> pdb=" O   ASP F  24 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.802A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.512A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (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 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 121
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.899A  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: 6.567A  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: 7.089A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (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 'C' and resid 100 through 102
      removed outlier: 6.657A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.836A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.113A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78

    409 hydrogen bonds defined for protein.
    1203 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      355 hydrogen bonds
      706 hydrogen bond angles
      0 basepair planarities
      143 basepair parallelities
      278 stacking parallelities
  Total time for adding SS restraints: 2.48

  Time building geometry restraints manager: 1.16 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1694
        1.33 -     1.45: 4763
        1.45 -     1.57: 5960
        1.57 -     1.69: 578
        1.69 -     1.81: 24
  Bond restraints: 13019
  Sorted by residual:
  bond pdb=" C   ARG F  95 "
       pdb=" O   ARG F  95 "
    ideal  model  delta    sigma   weight residual
    1.233  1.203  0.030 1.15e-02 7.56e+03 7.02e+00
  bond pdb=" CA  GLU E 105 "
       pdb=" C   GLU E 105 "
    ideal  model  delta    sigma   weight residual
    1.524  1.557 -0.033 1.27e-02 6.20e+03 6.83e+00
  bond pdb=" CA  LYS F  31 "
       pdb=" C   LYS F  31 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.029 1.23e-02 6.61e+03 5.75e+00
  bond pdb=" C   PRO G  26 "
       pdb=" O   PRO G  26 "
    ideal  model  delta    sigma   weight residual
    1.235  1.217  0.018 7.90e-03 1.60e+04 4.96e+00
  bond pdb=" CA  GLU A 105 "
       pdb=" C   GLU A 105 "
    ideal  model  delta    sigma   weight residual
    1.524  1.551 -0.028 1.27e-02 6.20e+03 4.74e+00
  ... (remaining 13014 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.30: 16684
        1.30 -     2.60: 1752
        2.60 -     3.89: 341
        3.89 -     5.19: 20
        5.19 -     6.49: 7
  Bond angle restraints: 18804
  Sorted by residual:
  angle pdb=" O3'  DA I  14 "
        pdb=" C3'  DA I  14 "
        pdb=" C2'  DA I  14 "
      ideal   model   delta    sigma   weight residual
     111.50  106.11    5.39 1.50e+00 4.44e-01 1.29e+01
  angle pdb=" O3'  DT J -26 "
        pdb=" C3'  DT J -26 "
        pdb=" C2'  DT J -26 "
      ideal   model   delta    sigma   weight residual
     111.50  106.16    5.34 1.50e+00 4.44e-01 1.27e+01
  angle pdb=" C4'  DT I -18 "
        pdb=" C3'  DT I -18 "
        pdb=" O3'  DT I -18 "
      ideal   model   delta    sigma   weight residual
     110.00  114.63   -4.63 1.50e+00 4.44e-01 9.51e+00
  angle pdb=" O3'  DA I  44 "
        pdb=" C3'  DA I  44 "
        pdb=" C2'  DA I  44 "
      ideal   model   delta    sigma   weight residual
     111.50  107.05    4.45 1.50e+00 4.44e-01 8.78e+00
  angle pdb=" C2'  DT J -26 "
        pdb=" C1'  DT J -26 "
        pdb=" N1   DT J -26 "
      ideal   model   delta    sigma   weight residual
     113.50  117.90   -4.40 1.50e+00 4.44e-01 8.61e+00
  ... (remaining 18799 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.46: 5747
       35.46 -    70.92: 1401
       70.92 -   106.38: 4
      106.38 -   141.83: 0
      141.83 -   177.29: 3
  Dihedral angle restraints: 7155
    sinusoidal: 4876
      harmonic: 2279
  Sorted by residual:
  dihedral pdb=" C4'  DT I -18 "
           pdb=" C3'  DT I -18 "
           pdb=" O3'  DT I -18 "
           pdb=" P    DA I -17 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   42.71  177.29     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DA J -71 "
           pdb=" C3'  DA J -71 "
           pdb=" O3'  DA J -71 "
           pdb=" P    DT J -70 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   43.55  176.45     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DC I  22 "
           pdb=" C3'  DC I  22 "
           pdb=" O3'  DC I  22 "
           pdb=" P    DC I  23 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   64.11  155.89     1      3.50e+01 8.16e-04 1.50e+01
  ... (remaining 7152 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1307
       0.048 -    0.096: 634
       0.096 -    0.144: 144
       0.144 -    0.193: 36
       0.193 -    0.241: 8
  Chirality restraints: 2129
  Sorted by residual:
  chirality pdb=" C3'  DC I  22 "
            pdb=" C4'  DC I  22 "
            pdb=" O3'  DC I  22 "
            pdb=" C2'  DC I  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.42   -0.24 2.00e-01 2.50e+01 1.45e+00
  chirality pdb=" C3'  DA J -71 "
            pdb=" C4'  DA J -71 "
            pdb=" O3'  DA J -71 "
            pdb=" C2'  DA J -71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.43   -0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CA  ARG C  88 "
            pdb=" N   ARG C  88 "
            pdb=" C   ARG C  88 "
            pdb=" CB  ARG C  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 2126 not shown)

  Planarity restraints: 1375
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG J -35 "   -0.034 2.00e-02 2.50e+03   1.43e-02 6.12e+00
        pdb=" N9   DG J -35 "    0.032 2.00e-02 2.50e+03
        pdb=" C8   DG J -35 "    0.003 2.00e-02 2.50e+03
        pdb=" N7   DG J -35 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DG J -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DG J -35 "   -0.005 2.00e-02 2.50e+03
        pdb=" O6   DG J -35 "   -0.011 2.00e-02 2.50e+03
        pdb=" N1   DG J -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DG J -35 "    0.003 2.00e-02 2.50e+03
        pdb=" N2   DG J -35 "    0.002 2.00e-02 2.50e+03
        pdb=" N3   DG J -35 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DG J -35 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG J  15 "   -0.033 2.00e-02 2.50e+03   1.38e-02 5.74e+00
        pdb=" N9   DG J  15 "    0.028 2.00e-02 2.50e+03
        pdb=" C8   DG J  15 "    0.001 2.00e-02 2.50e+03
        pdb=" N7   DG J  15 "    0.007 2.00e-02 2.50e+03
        pdb=" C5   DG J  15 "    0.005 2.00e-02 2.50e+03
        pdb=" C6   DG J  15 "   -0.006 2.00e-02 2.50e+03
        pdb=" O6   DG J  15 "   -0.015 2.00e-02 2.50e+03
        pdb=" N1   DG J  15 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DG J  15 "    0.007 2.00e-02 2.50e+03
        pdb=" N2   DG J  15 "    0.001 2.00e-02 2.50e+03
        pdb=" N3   DG J  15 "    0.003 2.00e-02 2.50e+03
        pdb=" C4   DG J  15 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B  64 "   -0.011 2.00e-02 2.50e+03   2.27e-02 5.17e+00
        pdb=" C   ASN B  64 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ASN B  64 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   VAL B  65 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1372 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.70: 424
        2.70 -     3.25: 10392
        3.25 -     3.80: 22837
        3.80 -     4.35: 29973
        4.35 -     4.90: 41615
  Nonbonded interactions: 105241
  Sorted by model distance:
  nonbonded pdb=" O   ARG F  23 "
            pdb=" OD1 ASP F  24 "
     model   vdw
     2.156 3.040
  nonbonded pdb=" OG1 THR H  87 "
            pdb=" OE1 GLU H  90 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" OG1 THR F  73 "
            pdb=" OD2 ASP F  85 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" NH2 ARG B  35 "
            pdb=" OP2  DG J   8 "
     model   vdw
     2.336 3.120
  nonbonded pdb=" N2   DG J  21 "
            pdb=" O2   DC I -21 "
     model   vdw
     2.340 2.496
  ... (remaining 105236 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 37 through 134)
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 17 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.790
  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:                     13.460
  Find NCS groups from input model:        0.120
  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:6.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.035  13019  Z= 0.416
  Angle     :  0.876   6.490  18804  Z= 0.568
  Chirality :  0.058   0.241   2129
  Planarity :  0.005   0.042   1375
  Dihedral  : 27.178 177.293   5685
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 2.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  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 aren not related in a simple way.
  whole:  1.78 (0.28), residues: 771
  helix:  1.92 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.55 (0.32), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C  42 
 TYR   0.018   0.004   TYR B  51 
 PHE   0.019   0.004   PHE H  67 
 HIS   0.006   0.002   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00695 (13019)
  covalent geometry    : angle       0.87630 (18804)
  hydrogen bonds       : bond        0.12714 (  764)
  hydrogen bonds       : angle       3.90005 ( 1909)

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 ARG cc_start: 0.8164 (ttt180) cc_final: 0.7737 (ttp-110)
REVERT: A   64 LYS cc_start: 0.7812 (mttt) cc_final: 0.7605 (mttp)
REVERT: B   91 LYS cc_start: 0.7694 (tttp) cc_final: 0.7174 (ttpt)
REVERT: C   90 ASP cc_start: 0.7168 (t0) cc_final: 0.6927 (t70)
REVERT: C   91 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7506 (mp0)
REVERT: D   48 ASP cc_start: 0.8654 (m-30) cc_final: 0.8277 (OUTLIER)
REVERT: D   96 ARG cc_start: 0.7629 (mtm180) cc_final: 0.7230 (mtt90)
REVERT: E   68 GLN cc_start: 0.7502 (tt0) cc_final: 0.7122 (tt0)
REVERT: F   93 GLN cc_start: 0.7487 (mm-40) cc_final: 0.7141 (mp10)
REVERT: G   15 LYS cc_start: 0.7822 (mtmm) cc_final: 0.7282 (mtpt)
REVERT: G   73 ASN cc_start: 0.7834 (m110) cc_final: 0.7588 (m110)
REVERT: G   75 LYS cc_start: 0.8046 (mttt) cc_final: 0.7783 (mtpp)
REVERT: G   90 ASP cc_start: 0.7528 (t0) cc_final: 0.7269 (t0)
REVERT: G   95 LYS cc_start: 0.8030 (tttt) cc_final: 0.7660 (tppt)
REVERT: G   99 ARG cc_start: 0.7726 (mmm160) cc_final: 0.7242 (mpt180)
REVERT: H   31 LYS cc_start: 0.8126 (mtpp) cc_final: 0.7752 (mttp)
REVERT: H  105 LYS cc_start: 0.7467 (ttpt) cc_final: 0.7063 (mmtm)
  outliers start: 0
  outliers final: 1
  residues processed: 148
  average time/residue: 1.0371
  time to fit residues: 161.1136
Evaluate side-chains
  129 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    8.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.5188

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

Flipped N/Q/H residues before XYZ refinement:
G  24 GLN
H  44 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.090463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.071622 restraints weight = 22009.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 1.26
r_work: 0.3024 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2890 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8684
moved from start:          0.0751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13019  Z= 0.180
  Angle     :  0.610   6.928  18804  Z= 0.368
  Chirality :  0.036   0.139   2129
  Planarity :  0.004   0.042   1375
  Dihedral  : 30.918 179.966   4095
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  :  9.01 %
    Favored  : 89.47 %
  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 aren not related in a simple way.
  whole:  2.40 (0.29), residues: 771
  helix:  2.39 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.47 (0.33), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  30 
 TYR   0.011   0.001   TYR H  37 
 PHE   0.010   0.002   PHE A  67 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (13019)
  covalent geometry    : angle       0.60959 (18804)
  hydrogen bonds       : bond        0.05913 (  764)
  hydrogen bonds       : angle       3.21360 ( 1909)

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 132
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9009 (mttt) cc_final: 0.8708 (mttp)
REVERT: B   91 LYS cc_start: 0.8748 (tttp) cc_final: 0.8266 (ttpt)
REVERT: E   59 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8572 (pm20)
REVERT: E   64 LYS cc_start: 0.8572 (mtmm) cc_final: 0.8292 (mtmm)
REVERT: E   68 GLN cc_start: 0.8677 (tt0) cc_final: 0.8214 (tt0)
REVERT: E  133 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7991 (mt-10)
REVERT: G   15 LYS cc_start: 0.8729 (mtmm) cc_final: 0.8156 (mtpt)
REVERT: G   73 ASN cc_start: 0.8489 (m110) cc_final: 0.8207 (m110)
REVERT: G   95 LYS cc_start: 0.9017 (tttt) cc_final: 0.8676 (tppt)
REVERT: G   99 ARG cc_start: 0.8084 (mmm160) cc_final: 0.7877 (mpt180)
REVERT: H   31 LYS cc_start: 0.8566 (mtpp) cc_final: 0.8295 (mttp)
REVERT: H  105 LYS cc_start: 0.8477 (ttpt) cc_final: 0.8114 (mmmm)
REVERT: H  113 LYS cc_start: 0.8770 (ttmm) cc_final: 0.8499 (ttmt)
  outliers start: 10
  outliers final: 4
  residues processed: 135
  average time/residue: 1.0426
  time to fit residues: 147.8650
Evaluate side-chains
  134 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 128
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain H residue   36 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 74 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   chunk 84 optimal weight:   10.0000
   chunk 87 optimal weight:   10.0000
   chunk 75 optimal weight:   10.0000
   chunk 41 optimal weight:    7.9990
   chunk 61 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 64 optimal weight:    3.9990
   overall best weight:    2.7588

-------------------------------------------------------------------------------
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 = 0.3540 r_free = 0.3540 target = 0.090188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.071325 restraints weight = 22267.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 1.26
r_work: 0.3015 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2883 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8688
moved from start:          0.0873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  13019  Z= 0.224
  Angle     :  0.600   7.067  18804  Z= 0.365
  Chirality :  0.036   0.157   2129
  Planarity :  0.004   0.036   1375
  Dihedral  : 30.822 178.899   4095
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 10.99 %
    Favored  : 87.48 %
  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 aren not related in a simple way.
  whole:  2.51 (0.29), residues: 771
  helix:  2.49 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.50 (0.33), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D  30 
 TYR   0.010   0.001   TYR H  37 
 PHE   0.009   0.001   PHE A  67 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 (13019)
  covalent geometry    : angle       0.59985 (18804)
  hydrogen bonds       : bond        0.05990 (  764)
  hydrogen bonds       : angle       3.04012 ( 1909)

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 127
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9023 (mttt) cc_final: 0.8716 (mttp)
REVERT: B   91 LYS cc_start: 0.8784 (tttp) cc_final: 0.8302 (ttpt)
REVERT: E   64 LYS cc_start: 0.8608 (mtmm) cc_final: 0.8333 (mtmm)
REVERT: E   68 GLN cc_start: 0.8718 (tt0) cc_final: 0.8306 (tt0)
REVERT: E  133 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7986 (mt-10)
REVERT: F   93 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7092 (mp10)
REVERT: G   15 LYS cc_start: 0.8704 (mtmm) cc_final: 0.8140 (mtpt)
REVERT: G   73 ASN cc_start: 0.8477 (m110) cc_final: 0.8190 (m110)
REVERT: G   95 LYS cc_start: 0.9015 (tttt) cc_final: 0.8674 (tppt)
REVERT: H   31 LYS cc_start: 0.8576 (mtpp) cc_final: 0.8304 (mttp)
REVERT: H  105 LYS cc_start: 0.8511 (ttpt) cc_final: 0.8136 (mmtp)
  outliers start: 10
  outliers final: 6
  residues processed: 129
  average time/residue: 1.0332
  time to fit residues: 140.0815
Evaluate side-chains
  132 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 124
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain H residue   36 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 62 optimal weight:    4.9990
   chunk 89 optimal weight:   10.0000
   chunk 76 optimal weight:    8.9990
   chunk 21 optimal weight:    2.9990
   chunk 85 optimal weight:    7.9990
   chunk 92 optimal weight:   10.0000
   chunk 97 optimal weight:    8.9990
   overall best weight:    2.0986

-------------------------------------------------------------------------------
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 = 0.3544 r_free = 0.3544 target = 0.090385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.071459 restraints weight = 22204.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 1.27
r_work: 0.3023 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2890 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8690
moved from start:          0.0926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  13019  Z= 0.191
  Angle     :  0.586   7.299  18804  Z= 0.357
  Chirality :  0.035   0.150   2129
  Planarity :  0.004   0.036   1375
  Dihedral  : 30.830 179.008   4095
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 11.60 %
    Favored  : 87.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.61 (0.29), residues: 771
  helix:  2.58 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.51 (0.33), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG D  30 
 TYR   0.010   0.001   TYR H  37 
 PHE   0.009   0.001   PHE A  67 
 HIS   0.002   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 (13019)
  covalent geometry    : angle       0.58636 (18804)
  hydrogen bonds       : bond        0.05720 (  764)
  hydrogen bonds       : angle       3.02505 ( 1909)

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 125
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9019 (mttt) cc_final: 0.8714 (mttp)
REVERT: B   91 LYS cc_start: 0.8789 (tttp) cc_final: 0.8325 (ttpt)
REVERT: E   64 LYS cc_start: 0.8591 (mtmm) cc_final: 0.8322 (mtmm)
REVERT: E   68 GLN cc_start: 0.8694 (tt0) cc_final: 0.8236 (tt0)
REVERT: E  133 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7989 (mt-10)
REVERT: F   93 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7019 (mp10)
REVERT: G   15 LYS cc_start: 0.8705 (mtmm) cc_final: 0.8149 (mtpt)
REVERT: G   73 ASN cc_start: 0.8453 (m110) cc_final: 0.8175 (m110)
REVERT: G   95 LYS cc_start: 0.9014 (tttt) cc_final: 0.8676 (tppt)
REVERT: H   31 LYS cc_start: 0.8601 (mtpp) cc_final: 0.8317 (mttp)
REVERT: H  105 LYS cc_start: 0.8503 (ttpt) cc_final: 0.8119 (mmtm)
  outliers start: 9
  outliers final: 6
  residues processed: 126
  average time/residue: 1.0115
  time to fit residues: 134.0294
Evaluate side-chains
  131 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 123
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain H residue   36 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 28 optimal weight:    0.0770
   chunk 90 optimal weight:    6.9990
   chunk 85 optimal weight:    7.9990
   chunk 81 optimal weight:    7.9990
   chunk 86 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:    7.9990
   chunk 99 optimal weight:    8.9990
   chunk 22 optimal weight:    3.9990
   chunk 88 optimal weight:   10.0000
   chunk 51 optimal weight:    8.9990
   overall best weight:    5.2146

-------------------------------------------------------------------------------
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 = 0.3516 r_free = 0.3516 target = 0.088766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.069851 restraints weight = 22413.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 1.30
r_work: 0.2983 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2850 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8718
moved from start:          0.1138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.069  13019  Z= 0.330
  Angle     :  0.647   7.842  18804  Z= 0.388
  Chirality :  0.041   0.157   2129
  Planarity :  0.005   0.041   1375
  Dihedral  : 31.060 178.947   4095
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 2.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 11.76 %
    Favored  : 86.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.41 (0.29), residues: 771
  helix:  2.44 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.63 (0.33), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  30 
 TYR   0.015   0.002   TYR E  54 
 PHE   0.014   0.002   PHE A 104 
 HIS   0.004   0.001   HIS D  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00754 (13019)
  covalent geometry    : angle       0.64750 (18804)
  hydrogen bonds       : bond        0.06623 (  764)
  hydrogen bonds       : angle       3.01444 ( 1909)

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 123
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8509 (pm20) cc_final: 0.8286 (pm20)
REVERT: A   64 LYS cc_start: 0.9029 (mttt) cc_final: 0.8717 (mttp)
REVERT: B   91 LYS cc_start: 0.8790 (tttp) cc_final: 0.8303 (ttpt)
REVERT: E  133 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7962 (mt-10)
REVERT: F   93 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7141 (mp10)
REVERT: G   15 LYS cc_start: 0.8716 (mtmm) cc_final: 0.8159 (mtpt)
REVERT: G   95 LYS cc_start: 0.9012 (tttt) cc_final: 0.8674 (tppt)
REVERT: H   31 LYS cc_start: 0.8645 (mtpp) cc_final: 0.8368 (mttp)
REVERT: H  105 LYS cc_start: 0.8558 (ttpt) cc_final: 0.8117 (mmtm)
  outliers start: 11
  outliers final: 6
  residues processed: 126
  average time/residue: 1.0057
  time to fit residues: 133.4697
Evaluate side-chains
  130 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 122
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain D residue   36 VAL
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain H residue   36 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   chunk 92 optimal weight:    8.9990
   chunk 93 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 57 optimal weight:    0.5980
   chunk 89 optimal weight:    8.9990
   chunk 74 optimal weight:   10.0000
   chunk 77 optimal weight:    7.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    2.2586

-------------------------------------------------------------------------------
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 = 0.3530 r_free = 0.3530 target = 0.089566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.070676 restraints weight = 22269.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 1.27
r_work: 0.3001 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2869 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8706
moved from start:          0.1132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  13019  Z= 0.212
  Angle     :  0.618   7.282  18804  Z= 0.374
  Chirality :  0.037   0.151   2129
  Planarity :  0.004   0.037   1375
  Dihedral  : 31.094 179.430   4095
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 11.30 %
    Favored  : 86.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.51 (0.29), residues: 771
  helix:  2.52 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.60 (0.33), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  30 
 TYR   0.013   0.002   TYR H  37 
 PHE   0.011   0.002   PHE A 104 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 (13019)
  covalent geometry    : angle       0.61789 (18804)
  hydrogen bonds       : bond        0.06155 (  764)
  hydrogen bonds       : angle       2.99085 ( 1909)

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 124
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8517 (pm20) cc_final: 0.8262 (pm20)
REVERT: A   64 LYS cc_start: 0.9016 (mttt) cc_final: 0.8709 (mttm)
REVERT: B   91 LYS cc_start: 0.8770 (tttp) cc_final: 0.8308 (ttpt)
REVERT: E   68 GLN cc_start: 0.8705 (tt0) cc_final: 0.8235 (tt0)
REVERT: E  133 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7940 (mt-10)
REVERT: F   93 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7147 (mp10)
REVERT: G   15 LYS cc_start: 0.8691 (mtmm) cc_final: 0.8166 (mtpt)
REVERT: G   90 ASP cc_start: 0.8310 (t70) cc_final: 0.7950 (t0)
REVERT: G   95 LYS cc_start: 0.9004 (tttt) cc_final: 0.8675 (tppt)
REVERT: H   31 LYS cc_start: 0.8616 (mtpp) cc_final: 0.8341 (mttp)
REVERT: H  105 LYS cc_start: 0.8537 (ttpt) cc_final: 0.8102 (mmtm)
  outliers start: 14
  outliers final: 7
  residues processed: 128
  average time/residue: 0.9931
  time to fit residues: 133.9304
Evaluate side-chains
  132 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 123
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain H residue   36 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 26 optimal weight:    8.9990
   chunk 80 optimal weight:    6.9990
   chunk 95 optimal weight:    6.9990
   chunk 28 optimal weight:    8.9990
   chunk 39 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 91 optimal weight:    7.9990
   chunk 81 optimal weight:    5.9990
   chunk 37 optimal weight:    8.9990
   overall best weight:    2.5986

-------------------------------------------------------------------------------
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 = 0.3530 r_free = 0.3530 target = 0.089618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.070757 restraints weight = 22091.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 1.26
r_work: 0.3004 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2873 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8700
moved from start:          0.1154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  13019  Z= 0.226
  Angle     :  0.610   7.485  18804  Z= 0.371
  Chirality :  0.037   0.152   2129
  Planarity :  0.004   0.038   1375
  Dihedral  : 31.080 178.986   4095
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 11.45 %
    Favored  : 86.41 %
  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 aren not related in a simple way.
  whole:  2.53 (0.29), residues: 771
  helix:  2.55 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.61 (0.33), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  30 
 TYR   0.011   0.002   TYR E  54 
 PHE   0.009   0.002   PHE A 104 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 (13019)
  covalent geometry    : angle       0.61011 (18804)
  hydrogen bonds       : bond        0.05971 (  764)
  hydrogen bonds       : angle       2.95783 ( 1909)

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8517 (pm20) cc_final: 0.8316 (pm20)
REVERT: A   64 LYS cc_start: 0.9011 (mttt) cc_final: 0.8703 (mttm)
REVERT: B   91 LYS cc_start: 0.8768 (tttp) cc_final: 0.8307 (ttpt)
REVERT: E   68 GLN cc_start: 0.8700 (tt0) cc_final: 0.8233 (tt0)
REVERT: E  133 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7954 (mt-10)
REVERT: F   93 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7140 (mp10)
REVERT: G   15 LYS cc_start: 0.8690 (mtmm) cc_final: 0.8166 (mtpt)
REVERT: G   95 LYS cc_start: 0.9010 (tttt) cc_final: 0.8665 (tppt)
REVERT: H   31 LYS cc_start: 0.8612 (mtpp) cc_final: 0.8335 (mttp)
REVERT: H  105 LYS cc_start: 0.8537 (ttpt) cc_final: 0.8098 (mmtm)
  outliers start: 14
  outliers final: 11
  residues processed: 126
  average time/residue: 1.0220
  time to fit residues: 135.5797
Evaluate side-chains
  135 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain D residue   36 VAL
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain F residue   59 LYS
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain H residue   68 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 80 optimal weight:    6.9990
   chunk 76 optimal weight:    8.9990
   chunk 28 optimal weight:   10.0000
   chunk 45 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 93 optimal weight:    8.9990
   chunk 74 optimal weight:   10.0000
   chunk 96 optimal weight:    6.9990
   chunk 97 optimal weight:    8.9990
   overall best weight:    3.1788

-------------------------------------------------------------------------------
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 = 0.3530 r_free = 0.3530 target = 0.089601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.070720 restraints weight = 22185.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 1.27
r_work: 0.3004 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2873 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8702
moved from start:          0.1169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  13019  Z= 0.236
  Angle     :  0.606   7.153  18804  Z= 0.368
  Chirality :  0.037   0.154   2129
  Planarity :  0.004   0.037   1375
  Dihedral  : 31.069 178.919   4095
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 11.15 %
    Favored  : 86.72 %
  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 aren not related in a simple way.
  whole:  2.55 (0.29), residues: 771
  helix:  2.56 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.61 (0.33), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  30 
 TYR   0.011   0.002   TYR E  54 
 PHE   0.009   0.002   PHE A 104 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 (13019)
  covalent geometry    : angle       0.60588 (18804)
  hydrogen bonds       : bond        0.05882 (  764)
  hydrogen bonds       : angle       2.94172 ( 1909)

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8520 (pm20) cc_final: 0.8243 (pm20)
REVERT: A   64 LYS cc_start: 0.9018 (mttt) cc_final: 0.8712 (mttm)
REVERT: B   91 LYS cc_start: 0.8775 (tttp) cc_final: 0.8316 (ttpt)
REVERT: E   68 GLN cc_start: 0.8700 (tt0) cc_final: 0.8230 (tt0)
REVERT: E  133 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7952 (mt-10)
REVERT: F   93 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7157 (mp10)
REVERT: G   15 LYS cc_start: 0.8692 (mtmm) cc_final: 0.8168 (mtpt)
REVERT: G   95 LYS cc_start: 0.9015 (tttt) cc_final: 0.8673 (tppt)
REVERT: H   31 LYS cc_start: 0.8614 (mtpp) cc_final: 0.8337 (mttp)
REVERT: H  105 LYS cc_start: 0.8541 (ttpt) cc_final: 0.8105 (mmtm)
  outliers start: 14
  outliers final: 11
  residues processed: 126
  average time/residue: 1.0023
  time to fit residues: 133.0078
Evaluate side-chains
  134 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain D residue   36 VAL
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain F residue   59 LYS
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain H residue   68 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 75 optimal weight:   10.0000
   chunk 35 optimal weight:    0.7980
   chunk 49 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 82 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 15 optimal weight:    7.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
H  44 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.090059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.071181 restraints weight = 22244.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 1.28
r_work: 0.3012 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2880 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8703
moved from start:          0.1180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13019  Z= 0.184
  Angle     :  0.598   7.983  18804  Z= 0.364
  Chirality :  0.035   0.153   2129
  Planarity :  0.004   0.037   1375
  Dihedral  : 31.065 179.030   4095
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 10.99 %
    Favored  : 86.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.60 (0.29), residues: 771
  helix:  2.60 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.59 (0.33), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D  30 
 TYR   0.010   0.001   TYR H  37 
 PHE   0.010   0.001   PHE A  67 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (13019)
  covalent geometry    : angle       0.59774 (18804)
  hydrogen bonds       : bond        0.05714 (  764)
  hydrogen bonds       : angle       2.93874 ( 1909)

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8528 (pm20) cc_final: 0.8265 (pm20)
REVERT: A   64 LYS cc_start: 0.9020 (mttt) cc_final: 0.8717 (mttm)
REVERT: B   91 LYS cc_start: 0.8776 (tttp) cc_final: 0.8329 (ttpt)
REVERT: E   68 GLN cc_start: 0.8701 (tt0) cc_final: 0.8235 (tt0)
REVERT: E  133 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7919 (mt-10)
REVERT: F   93 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7168 (mp10)
REVERT: G   15 LYS cc_start: 0.8689 (mtmm) cc_final: 0.8170 (mtpt)
REVERT: G   95 LYS cc_start: 0.9020 (tttt) cc_final: 0.8680 (tppt)
REVERT: H   31 LYS cc_start: 0.8642 (mtpp) cc_final: 0.8343 (mttp)
REVERT: H  105 LYS cc_start: 0.8541 (ttpt) cc_final: 0.8109 (mmtm)
  outliers start: 16
  outliers final: 10
  residues processed: 127
  average time/residue: 1.0006
  time to fit residues: 133.8771
Evaluate side-chains
  134 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 122
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain F residue   59 LYS
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain H residue   68 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 46 optimal weight:   10.0000
   chunk 60 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 90 optimal weight:    6.9990
   chunk 7 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 28 optimal weight:    7.9990
   chunk 36 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0270
   overall best weight:    2.2046

-------------------------------------------------------------------------------
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 = 0.3537 r_free = 0.3537 target = 0.090007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.071135 restraints weight = 22367.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 1.27
r_work: 0.3013 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2881 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8698
moved from start:          0.1192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  13019  Z= 0.205
  Angle     :  0.594   7.095  18804  Z= 0.362
  Chirality :  0.036   0.152   2129
  Planarity :  0.004   0.037   1375
  Dihedral  : 31.057 178.976   4095
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 11.76 %
    Favored  : 86.41 %
  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 aren not related in a simple way.
  whole:  2.62 (0.29), residues: 771
  helix:  2.61 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.59 (0.33), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  30 
 TYR   0.011   0.001   TYR H  37 
 PHE   0.009   0.001   PHE A  67 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 (13019)
  covalent geometry    : angle       0.59448 (18804)
  hydrogen bonds       : bond        0.05623 (  764)
  hydrogen bonds       : angle       2.92059 ( 1909)

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 122
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8521 (pm20) cc_final: 0.8256 (pm20)
REVERT: A   64 LYS cc_start: 0.9011 (mttt) cc_final: 0.8707 (mttm)
REVERT: B   91 LYS cc_start: 0.8775 (tttp) cc_final: 0.8326 (ttpt)
REVERT: E   68 GLN cc_start: 0.8697 (tt0) cc_final: 0.8229 (tt0)
REVERT: E  133 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7943 (mt-10)
REVERT: F   93 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7161 (mp10)
REVERT: G   15 LYS cc_start: 0.8688 (mtmm) cc_final: 0.8166 (mtpt)
REVERT: G   95 LYS cc_start: 0.9018 (tttt) cc_final: 0.8669 (tppt)
REVERT: H   31 LYS cc_start: 0.8638 (mtpp) cc_final: 0.8339 (mttp)
REVERT: H  105 LYS cc_start: 0.8532 (ttpt) cc_final: 0.8094 (mmtm)
  outliers start: 12
  outliers final: 9
  residues processed: 125
  average time/residue: 1.0248
  time to fit residues: 134.9995
Evaluate side-chains
  132 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 121
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain F residue   59 LYS
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain H residue   68 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:    6.9990
   chunk 43 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 83 optimal weight:    8.9990
   chunk 39 optimal weight:    3.9990
   chunk 97 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   chunk 99 optimal weight:    7.9990
   chunk 16 optimal weight:    1.9990
   chunk 89 optimal weight:   10.0000
   chunk 21 optimal weight:    4.9990
   overall best weight:    3.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.089630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.070775 restraints weight = 22219.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 1.27
r_work: 0.3005 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8704
moved from start:          0.1290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057  13019  Z= 0.266
  Angle     :  0.610   6.806  18804  Z= 0.368
  Chirality :  0.038   0.155   2129
  Planarity :  0.004   0.035   1375
  Dihedral  : 31.035 178.712   4095
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 12.06 %
    Favored  : 86.26 %
  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 aren not related in a simple way.
  whole:  2.57 (0.29), residues: 771
  helix:  2.58 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.63 (0.34), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  30 
 TYR   0.011   0.002   TYR E  54 
 PHE   0.010   0.002   PHE A 104 
 HIS   0.003   0.001   HIS B  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00605 (13019)
  covalent geometry    : angle       0.60990 (18804)
  hydrogen bonds       : bond        0.05864 (  764)
  hydrogen bonds       : angle       2.89698 ( 1909)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5199.30 seconds
wall clock time: 89 minutes 4.65 seconds (5344.65 seconds total)