Starting phenix.real_space_refine
on Wed May 14 15:22:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ox0_17251/05_2025/8ox0_17251.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ox0_17251/05_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_17251/05_2025/8ox0_17251.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ox0_17251/05_2025/8ox0_17251.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ox0_17251/05_2025/8ox0_17251.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ox0_17251/05_2025/8ox0_17251.cif"
  }
  resolution = 2.52
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.76, per 1000 atoms: 0.71
  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: 2.99
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 6.20
  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: 5.11

  Time building geometry restraints manager: 3.56 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:             4.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.580
  Check model and map are aligned:         0.000
  Set scattering table:                    0.060
  Process input model:                     36.470
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.050
  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:13.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   55.260
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 HIS   0.006   0.002   HIS F  75 
 PHE   0.019   0.004   PHE H  67 
 TYR   0.018   0.004   TYR B  51 
 ARG   0.011   0.001   ARG C  42 

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

*********************** 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  : 0.935 
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: 1.9600
  time to fit residues: 305.6245
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  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    7.9990
   chunk 77 optimal weight:    8.9990
   chunk 42 optimal weight:    0.9990
   chunk 26 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 79 optimal weight:    7.9990
   chunk 30 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   chunk 92 optimal weight:    8.9990
   overall best weight:    1.5584

-------------------------------------------------------------------------------
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 = 0.090469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.071667 restraints weight = 21993.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 1.25
r_work: 0.3025 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2891 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8687
moved from start:          0.0741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13019  Z= 0.177
  Angle     :  0.596   6.802  18804  Z= 0.363
  Chirality :  0.035   0.143   2129
  Planarity :  0.004   0.039   1375
  Dihedral  : 30.900 179.789   4095
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  9.31 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.39 (0.29), residues: 771
  helix:  2.38 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.47 (0.33), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.007   0.001   PHE F  61 
 TYR   0.010   0.001   TYR H  37 
 ARG   0.003   0.000   ARG C  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06089 (  764)
  hydrogen bonds       : angle       3.15994 ( 1909)
  covalent geometry    : bond        0.00377 (13019)
  covalent geometry    : angle       0.59589 (18804)

*********************** 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
  139 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 131
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 ARG cc_start: 0.8671 (ttt180) cc_final: 0.8461 (ttp-110)
REVERT: A   64 LYS cc_start: 0.9018 (mttt) cc_final: 0.8715 (mttm)
REVERT: B   91 LYS cc_start: 0.8753 (tttp) cc_final: 0.8274 (ttpt)
REVERT: E   59 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8602 (pm20)
REVERT: E   64 LYS cc_start: 0.8596 (mtmm) cc_final: 0.8317 (mtmm)
REVERT: E   68 GLN cc_start: 0.8686 (tt0) cc_final: 0.8230 (tt0)
REVERT: E  133 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7972 (mt-10)
REVERT: G   15 LYS cc_start: 0.8726 (mtmm) cc_final: 0.8149 (mtpt)
REVERT: G   73 ASN cc_start: 0.8505 (m110) cc_final: 0.8231 (m110)
REVERT: G   90 ASP cc_start: 0.8531 (t0) cc_final: 0.8323 (t0)
REVERT: G   95 LYS cc_start: 0.9026 (tttt) cc_final: 0.8689 (tppt)
REVERT: H   31 LYS cc_start: 0.8570 (mtpp) cc_final: 0.8298 (mttp)
REVERT: H  105 LYS cc_start: 0.8485 (ttpt) cc_final: 0.8120 (mmtm)
REVERT: H  113 LYS cc_start: 0.8762 (ttmm) cc_final: 0.8470 (ttmt)
  outliers start: 8
  outliers final: 4
  residues processed: 133
  average time/residue: 1.9026
  time to fit residues: 267.2248
Evaluate side-chains
  131 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 125
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   24 ASP
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 24 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 64 optimal weight:    0.5980
   chunk 67 optimal weight:    4.9990
   chunk 99 optimal weight:    8.9990
   chunk 92 optimal weight:   10.0000
   chunk 57 optimal weight:    2.9990
   chunk 82 optimal weight:    7.9990
   chunk 54 optimal weight:    0.0870
   chunk 65 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    1.5162

-------------------------------------------------------------------------------
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 = 0.3548 r_free = 0.3548 target = 0.090619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.071727 restraints weight = 22241.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 1.28
r_work: 0.3023 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2890 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8687
moved from start:          0.0836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  13019  Z= 0.176
  Angle     :  0.589   6.864  18804  Z= 0.360
  Chirality :  0.035   0.142   2129
  Planarity :  0.004   0.038   1375
  Dihedral  : 30.852 179.355   4095
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 10.38 %
    Favored  : 88.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.50 (0.29), residues: 771
  helix:  2.48 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.50 (0.33), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.010   0.001   PHE A  67 
 TYR   0.010   0.001   TYR H  37 
 ARG   0.006   0.000   ARG D  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05846 (  764)
  hydrogen bonds       : angle       3.09706 ( 1909)
  covalent geometry    : bond        0.00374 (13019)
  covalent geometry    : angle       0.58885 (18804)

*********************** 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: 9
    poor density    : 128
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 ARG cc_start: 0.8684 (ttt180) cc_final: 0.8446 (ttp-110)
REVERT: A   64 LYS cc_start: 0.9015 (mttt) cc_final: 0.8716 (mttp)
REVERT: B   91 LYS cc_start: 0.8785 (tttp) cc_final: 0.8314 (ttpt)
REVERT: E   59 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8598 (pm20)
REVERT: E   64 LYS cc_start: 0.8579 (mtmm) cc_final: 0.8327 (mtmm)
REVERT: E   68 GLN cc_start: 0.8684 (tt0) cc_final: 0.8224 (tt0)
REVERT: E  133 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8004 (mt-10)
REVERT: F   93 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7027 (mp10)
REVERT: G   15 LYS cc_start: 0.8720 (mtmm) cc_final: 0.8148 (mtpt)
REVERT: G   73 ASN cc_start: 0.8492 (m110) cc_final: 0.8212 (m110)
REVERT: G   90 ASP cc_start: 0.8540 (t0) cc_final: 0.8340 (t0)
REVERT: G   95 LYS cc_start: 0.9025 (tttt) cc_final: 0.8681 (tppt)
REVERT: H   31 LYS cc_start: 0.8563 (mtpp) cc_final: 0.8289 (mttp)
REVERT: H  105 LYS cc_start: 0.8483 (ttpt) cc_final: 0.8111 (mmtm)
REVERT: H  113 LYS cc_start: 0.8764 (ttmm) cc_final: 0.8498 (ttmt)
  outliers start: 9
  outliers final: 4
  residues processed: 130
  average time/residue: 1.8707
  time to fit residues: 256.9359
Evaluate side-chains
  135 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 128
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
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 34 optimal weight:    7.9990
   chunk 8 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   chunk 95 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 101 optimal weight:   10.0000
   chunk 26 optimal weight:    0.9990
   chunk 94 optimal weight:    5.9990
   chunk 72 optimal weight:   20.0000
   chunk 64 optimal weight:    4.9990
   overall best weight:    3.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.089369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.070542 restraints weight = 22215.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.3169 rms_B_bonded: 1.27
r_work: 0.2997 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8705
moved from start:          0.1066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059  13019  Z= 0.273
  Angle     :  0.621   7.779  18804  Z= 0.375
  Chirality :  0.038   0.155   2129
  Planarity :  0.005   0.035   1375
  Dihedral  : 30.919 178.736   4095
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 10.23 %
    Favored  : 87.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.55 (0.29), residues: 771
  helix:  2.54 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.55 (0.33), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D  46 
 PHE   0.013   0.002   PHE A 104 
 TYR   0.012   0.002   TYR E  54 
 ARG   0.005   0.000   ARG D  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06122 (  764)
  hydrogen bonds       : angle       2.98091 ( 1909)
  covalent geometry    : bond        0.00624 (13019)
  covalent geometry    : angle       0.62078 (18804)

*********************** 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
  142 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 0.856 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 ARG cc_start: 0.8697 (ttt180) cc_final: 0.8445 (ttp-110)
REVERT: A   64 LYS cc_start: 0.9034 (mttt) cc_final: 0.8763 (mttp)
REVERT: B   91 LYS cc_start: 0.8798 (tttp) cc_final: 0.8324 (ttpt)
REVERT: E   68 GLN cc_start: 0.8709 (tt0) cc_final: 0.8305 (tt0)
REVERT: E  133 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7970 (mt-10)
REVERT: F   93 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7030 (mp10)
REVERT: G   15 LYS cc_start: 0.8694 (mtmm) cc_final: 0.8135 (mtpt)
REVERT: G   90 ASP cc_start: 0.8535 (t0) cc_final: 0.8259 (t0)
REVERT: G   95 LYS cc_start: 0.9007 (tttt) cc_final: 0.8669 (tppt)
REVERT: H   31 LYS cc_start: 0.8611 (mtpp) cc_final: 0.8335 (mttp)
REVERT: H  105 LYS cc_start: 0.8517 (ttpt) cc_final: 0.8091 (mmtm)
  outliers start: 13
  outliers final: 5
  residues processed: 130
  average time/residue: 1.8981
  time to fit residues: 260.5398
Evaluate side-chains
  132 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 125
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 75 optimal weight:   10.0000
   chunk 5 optimal weight:    4.9990
   chunk 27 optimal weight:    5.9990
   chunk 93 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9990
   chunk 55 optimal weight:    0.4980
   chunk 44 optimal weight:    3.9990
   chunk 88 optimal weight:   10.0000
   chunk 37 optimal weight:    7.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    1.6986

-------------------------------------------------------------------------------
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 = 0.3539 r_free = 0.3539 target = 0.090107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.071287 restraints weight = 22083.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 1.26
r_work: 0.3015 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2882 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8693
moved from start:          0.1074

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= 0.186
  Angle     :  0.599   7.339  18804  Z= 0.364
  Chirality :  0.035   0.148   2129
  Planarity :  0.004   0.037   1375
  Dihedral  : 30.956 179.207   4095
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 11.15 %
    Favored  : 87.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.70 (0.29), residues: 771
  helix:  2.65 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.49 (0.33), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.010   0.002   PHE A  67 
 TYR   0.012   0.001   TYR H  37 
 ARG   0.003   0.000   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05682 (  764)
  hydrogen bonds       : angle       2.95871 ( 1909)
  covalent geometry    : bond        0.00407 (13019)
  covalent geometry    : angle       0.59939 (18804)

*********************** 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
  138 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 127
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 ARG cc_start: 0.8688 (ttt180) cc_final: 0.8445 (ttp-110)
REVERT: A   64 LYS cc_start: 0.9008 (mttt) cc_final: 0.8711 (mttp)
REVERT: B   91 LYS cc_start: 0.8771 (tttp) cc_final: 0.8311 (ttpt)
REVERT: E   68 GLN cc_start: 0.8700 (tt0) cc_final: 0.8226 (tt0)
REVERT: E  133 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7948 (mt-10)
REVERT: F   93 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7083 (mp10)
REVERT: G   15 LYS cc_start: 0.8689 (mtmm) cc_final: 0.8157 (mtpt)
REVERT: G   90 ASP cc_start: 0.8520 (t0) cc_final: 0.8245 (t0)
REVERT: G   95 LYS cc_start: 0.9012 (tttt) cc_final: 0.8653 (tppt)
REVERT: H   31 LYS cc_start: 0.8620 (mtpp) cc_final: 0.8336 (mttp)
REVERT: H  105 LYS cc_start: 0.8495 (ttpt) cc_final: 0.8086 (mmtm)
REVERT: H  113 LYS cc_start: 0.8774 (ttmm) cc_final: 0.8498 (ttmt)
  outliers start: 11
  outliers final: 7
  residues processed: 130
  average time/residue: 1.8774
  time to fit residues: 258.0769
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  : 0.874 
-------------------------------------------------------------------------------
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  118 THR
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 G residue   92 GLU
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 101 optimal weight:   10.0000
   chunk 73 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 56 optimal weight:    7.9990
   chunk 48 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 83 optimal weight:    8.9990
   chunk 97 optimal weight:    8.9990
   overall best weight:    2.3990

-------------------------------------------------------------------------------
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 = 0.3538 r_free = 0.3538 target = 0.090043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.071175 restraints weight = 22407.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 1.27
r_work: 0.3015 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2883 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8695
moved from start:          0.1104

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= 0.213
  Angle     :  0.592   6.930  18804  Z= 0.360
  Chirality :  0.036   0.154   2129
  Planarity :  0.004   0.037   1375
  Dihedral  : 30.937 178.676   4095
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 10.99 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.71 (0.29), residues: 771
  helix:  2.66 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.48 (0.34), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F  75 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.010   0.001   TYR E  54 
 ARG   0.005   0.000   ARG D  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05574 (  764)
  hydrogen bonds       : angle       2.91716 ( 1909)
  covalent geometry    : bond        0.00478 (13019)
  covalent geometry    : angle       0.59224 (18804)

*********************** 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
  136 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 ARG cc_start: 0.8701 (ttt180) cc_final: 0.8454 (ttp-110)
REVERT: A   64 LYS cc_start: 0.9012 (mttt) cc_final: 0.8713 (mttp)
REVERT: B   91 LYS cc_start: 0.8793 (tttp) cc_final: 0.8334 (ttpt)
REVERT: E   68 GLN cc_start: 0.8705 (tt0) cc_final: 0.8230 (tt0)
REVERT: E  133 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7957 (mt-10)
REVERT: F   93 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7055 (mp10)
REVERT: G   15 LYS cc_start: 0.8687 (mtmm) cc_final: 0.8161 (mtpt)
REVERT: G   90 ASP cc_start: 0.8522 (t0) cc_final: 0.8217 (t0)
REVERT: G   95 LYS cc_start: 0.9015 (tttt) cc_final: 0.8662 (tppt)
REVERT: H   31 LYS cc_start: 0.8620 (mtpp) cc_final: 0.8333 (mttp)
REVERT: H  105 LYS cc_start: 0.8516 (ttpt) cc_final: 0.8110 (mmtp)
  outliers start: 13
  outliers final: 9
  residues processed: 126
  average time/residue: 1.8975
  time to fit residues: 252.1219
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  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   87 SER
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   87 ILE
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain H residue   68 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:    6.9990
   chunk 46 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 56 optimal weight:    8.9990
   chunk 98 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 79 optimal weight:    7.9990
   chunk 92 optimal weight:   10.0000
   chunk 82 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   chunk 100 optimal weight:    8.9990
   overall best weight:    3.9988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.089365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.070523 restraints weight = 22253.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 1.27
r_work: 0.2999 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2867 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8709
moved from start:          0.1233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059  13019  Z= 0.274
  Angle     :  0.616   6.946  18804  Z= 0.371
  Chirality :  0.038   0.157   2129
  Planarity :  0.005   0.035   1375
  Dihedral  : 31.043 178.758   4095
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.56 (0.29), residues: 771
  helix:  2.57 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.61 (0.34), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.011   0.002   PHE A 104 
 TYR   0.012   0.002   TYR E  54 
 ARG   0.007   0.000   ARG D  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06002 (  764)
  hydrogen bonds       : angle       2.91811 ( 1909)
  covalent geometry    : bond        0.00624 (13019)
  covalent geometry    : angle       0.61567 (18804)

*********************** 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
  137 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 123
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 ARG cc_start: 0.8713 (ttt180) cc_final: 0.8470 (ttp-110)
REVERT: A   64 LYS cc_start: 0.9024 (mttt) cc_final: 0.8718 (mttp)
REVERT: B   91 LYS cc_start: 0.8784 (tttp) cc_final: 0.8316 (ttpt)
REVERT: C   73 ASN cc_start: 0.7803 (m-40) cc_final: 0.7308 (t0)
REVERT: E   68 GLN cc_start: 0.8725 (tt0) cc_final: 0.8332 (tt0)
REVERT: E  133 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7911 (mt-10)
REVERT: F   93 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7417 (mp10)
REVERT: G   15 LYS cc_start: 0.8710 (mtmm) cc_final: 0.8162 (mtpt)
REVERT: G   90 ASP cc_start: 0.8508 (t0) cc_final: 0.8239 (t0)
REVERT: G   95 LYS cc_start: 0.9008 (tttt) cc_final: 0.8670 (tppt)
REVERT: H   31 LYS cc_start: 0.8660 (mtpp) cc_final: 0.8372 (mttp)
REVERT: H  105 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8098 (mmtm)
  outliers start: 14
  outliers final: 7
  residues processed: 126
  average time/residue: 1.8564
  time to fit residues: 247.0552
Evaluate side-chains
  130 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
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 G residue   87 ILE
Chi-restraints excluded: chain H residue   36 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 28 optimal weight:   10.0000
   chunk 81 optimal weight:    6.9990
   chunk 75 optimal weight:   10.0000
   chunk 76 optimal weight:    7.9990
   chunk 78 optimal weight:    8.9990
   chunk 94 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 88 optimal weight:   10.0000
   chunk 77 optimal weight:    6.9990
   overall best weight:    4.1588

-------------------------------------------------------------------------------
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 = 0.3526 r_free = 0.3526 target = 0.089361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.070503 restraints weight = 22423.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 1.28
r_work: 0.2998 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8710
moved from start:          0.1239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060  13019  Z= 0.282
  Angle     :  0.619   6.852  18804  Z= 0.372
  Chirality :  0.039   0.158   2129
  Planarity :  0.005   0.036   1375
  Dihedral  : 31.047 178.681   4095
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 12.21 %
    Favored  : 86.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.55 (0.29), residues: 771
  helix:  2.56 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.62 (0.34), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.011   0.002   PHE A 104 
 TYR   0.012   0.002   TYR E  54 
 ARG   0.008   0.000   ARG D  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05992 (  764)
  hydrogen bonds       : angle       2.91516 ( 1909)
  covalent geometry    : bond        0.00645 (13019)
  covalent geometry    : angle       0.61892 (18804)

*********************** 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
  131 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.855 
Fit side-chains
REVERT: A   53 ARG cc_start: 0.8719 (ttt180) cc_final: 0.8474 (ttp-110)
REVERT: A   64 LYS cc_start: 0.9027 (mttt) cc_final: 0.8725 (mttp)
REVERT: B   91 LYS cc_start: 0.8786 (tttp) cc_final: 0.8322 (ttpt)
REVERT: C   73 ASN cc_start: 0.7807 (m-40) cc_final: 0.7315 (t0)
REVERT: E   68 GLN cc_start: 0.8734 (tt0) cc_final: 0.8340 (tt0)
REVERT: E  133 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7902 (mt-10)
REVERT: F   93 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7476 (mp10)
REVERT: G   15 LYS cc_start: 0.8716 (mtmm) cc_final: 0.8169 (mtpt)
REVERT: G   90 ASP cc_start: 0.8523 (t0) cc_final: 0.8255 (t0)
REVERT: G   95 LYS cc_start: 0.9013 (tttt) cc_final: 0.8675 (tppt)
REVERT: H   31 LYS cc_start: 0.8658 (mtpp) cc_final: 0.8370 (mttp)
REVERT: H  105 LYS cc_start: 0.8565 (ttpt) cc_final: 0.8107 (mmtm)
  outliers start: 11
  outliers final: 7
  residues processed: 123
  average time/residue: 1.8733
  time to fit residues: 243.4056
Evaluate side-chains
  129 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 120
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
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 G residue   87 ILE
Chi-restraints excluded: chain H residue   36 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 84 optimal weight:    8.9990
   chunk 39 optimal weight:    0.3980
   chunk 13 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 98 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9990
   chunk 96 optimal weight:    6.9990
   chunk 81 optimal weight:    6.9990
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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 = 0.090149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.071313 restraints weight = 22220.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 1.27
r_work: 0.3015 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2884 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.1252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13019  Z= 0.177
  Angle     :  0.599   7.661  18804  Z= 0.363
  Chirality :  0.034   0.149   2129
  Planarity :  0.004   0.037   1375
  Dihedral  : 31.058 179.039   4095
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 12.52 %
    Favored  : 85.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.69 (0.29), residues: 771
  helix:  2.66 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.55 (0.34), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.010   0.002   PHE A  67 
 TYR   0.012   0.002   TYR H  37 
 ARG   0.009   0.000   ARG D  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05632 (  764)
  hydrogen bonds       : angle       2.91118 ( 1909)
  covalent geometry    : bond        0.00379 (13019)
  covalent geometry    : angle       0.59884 (18804)

*********************** 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
  131 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.890 
Fit side-chains
REVERT: A   53 ARG cc_start: 0.8697 (ttt180) cc_final: 0.8454 (ttp-110)
REVERT: A   64 LYS cc_start: 0.9008 (mttt) cc_final: 0.8704 (mttm)
REVERT: B   91 LYS cc_start: 0.8764 (tttp) cc_final: 0.8311 (ttpt)
REVERT: C   73 ASN cc_start: 0.7764 (m-40) cc_final: 0.7279 (t0)
REVERT: E   68 GLN cc_start: 0.8687 (tt0) cc_final: 0.8220 (tt0)
REVERT: E  133 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7878 (mt-10)
REVERT: F   93 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7394 (mp10)
REVERT: G   15 LYS cc_start: 0.8699 (mtmm) cc_final: 0.8178 (mtpt)
REVERT: G   90 ASP cc_start: 0.8485 (t0) cc_final: 0.8208 (t0)
REVERT: G   95 LYS cc_start: 0.8986 (tttt) cc_final: 0.8623 (tppt)
REVERT: H   31 LYS cc_start: 0.8644 (mtpp) cc_final: 0.8356 (mttp)
REVERT: H  105 LYS cc_start: 0.8542 (ttpt) cc_final: 0.8103 (mmtm)
  outliers start: 11
  outliers final: 6
  residues processed: 123
  average time/residue: 1.8014
  time to fit residues: 234.0066
Evaluate side-chains
  128 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 120
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
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  118 THR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 45 optimal weight:    2.9990
   chunk 99 optimal weight:    8.9990
   chunk 76 optimal weight:    8.9990
   chunk 9 optimal weight:   10.0000
   chunk 83 optimal weight:    8.9990
   chunk 88 optimal weight:   10.0000
   chunk 101 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9980
   chunk 89 optimal weight:   10.0000
   chunk 6 optimal weight:    2.9990
   overall best weight:    4.9988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.088768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.069932 restraints weight = 22232.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 1.29
r_work: 0.2986 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2856 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8721
moved from start:          0.1347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.070  13019  Z= 0.327
  Angle     :  0.647   6.943  18804  Z= 0.387
  Chirality :  0.040   0.154   2129
  Planarity :  0.005   0.037   1375
  Dihedral  : 31.150 178.700   4095
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 12.82 %
    Favored  : 85.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.44 (0.29), residues: 771
  helix:  2.49 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.69 (0.34), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  18 
 PHE   0.011   0.002   PHE A 104 
 TYR   0.013   0.002   TYR E  54 
 ARG   0.008   0.001   ARG D  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06469 (  764)
  hydrogen bonds       : angle       2.95824 ( 1909)
  covalent geometry    : bond        0.00750 (13019)
  covalent geometry    : angle       0.64652 (18804)

********************** 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
  131 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 121
  time to evaluate  : 0.937 
Fit side-chains
REVERT: A   53 ARG cc_start: 0.8719 (ttt180) cc_final: 0.8477 (ttp-110)
REVERT: A   64 LYS cc_start: 0.9033 (mttt) cc_final: 0.8729 (mttp)
REVERT: B   91 LYS cc_start: 0.8771 (tttp) cc_final: 0.8502 (ttmm)
REVERT: C   73 ASN cc_start: 0.7891 (m-40) cc_final: 0.7393 (t0)
REVERT: E  133 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7916 (mt-10)
REVERT: F   93 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7573 (mp10)
REVERT: G   15 LYS cc_start: 0.8735 (mtmm) cc_final: 0.8175 (mtpt)
REVERT: G   90 ASP cc_start: 0.8505 (t0) cc_final: 0.8227 (t0)
REVERT: G   95 LYS cc_start: 0.9001 (tttt) cc_final: 0.8663 (tppt)
REVERT: H   31 LYS cc_start: 0.8693 (mtpp) cc_final: 0.8424 (mttp)
REVERT: H  105 LYS cc_start: 0.8597 (ttpt) cc_final: 0.8125 (mmtm)
  outliers start: 10
  outliers final: 7
  residues processed: 125
  average time/residue: 1.8733
  time to fit residues: 247.3413
Evaluate side-chains
  129 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 120
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   21 VAL
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   87 ILE
Chi-restraints excluded: chain H residue   36 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 94 optimal weight:    5.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3546 r_free = 0.3546 target = 0.090480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.071704 restraints weight = 22146.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 1.27
r_work: 0.3022 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2891 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8689
moved from start:          0.1364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13019  Z= 0.164
  Angle     :  0.609   6.955  18804  Z= 0.368
  Chirality :  0.036   0.153   2129
  Planarity :  0.004   0.042   1375
  Dihedral  : 31.173 179.488   4095
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 13.44 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.61 (0.29), residues: 771
  helix:  2.61 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.58 (0.34), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F  75 
 PHE   0.010   0.001   PHE A  67 
 TYR   0.014   0.002   TYR H  37 
 ARG   0.008   0.001   ARG D  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05528 (  764)
  hydrogen bonds       : angle       2.94217 ( 1909)
  covalent geometry    : bond        0.00347 (13019)
  covalent geometry    : angle       0.60872 (18804)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9161.98 seconds
wall clock time: 158 minutes 1.35 seconds (9481.35 seconds total)