Starting phenix.real_space_refine
on Sat Aug 23 13:59:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g6g_29767/08_2025/8g6g_29767.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g6g_29767/08_2025/8g6g_29767.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g6g_29767/08_2025/8g6g_29767.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g6g_29767/08_2025/8g6g_29767.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g6g_29767/08_2025/8g6g_29767.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g6g_29767/08_2025/8g6g_29767.map"
  }
  resolution = 2.93
  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=   0.002 sd=   0.022
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     314      5.49       5
     S      13      5.16       5
     C    7177      2.51       5
     N    2427      2.21       5
     O    3054      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12985
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 803
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'MLY:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 795
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "D"
      Number of atoms: 742
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 742
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'MLY:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "F"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 619
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "G"
      Number of atoms: 809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 809
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 723
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 723
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "I"
      Number of atoms: 3196
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 3196
          Classifications: {'DNA': 157}
          Link IDs: {'rna3p': 156}
    Chain: "J"
      Number of atoms: 3241
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 3241
          Classifications: {'DNA': 157}
          Link IDs: {'rna3p': 156}
    Chain: "K"
      Number of atoms: 593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 593
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N   LEU K  73 " occ=0.63
      ... (6 atoms not shown)
      pdb=" CD2 LEU K  73 " occ=0.63
    residue:
      pdb=" N   ARG K  74 " occ=0.73
      ... (9 atoms not shown)
      pdb=" NH2 ARG K  74 " occ=0.73
  Time building chain proxies: 2.75, per 1000 atoms: 0.21
  Number of scatterers: 12985
  At special positions: 0
  Unit cell: (124.696, 93.304, 133.416, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      13     16.00
     P     314     15.00
     O    3054      8.00
     N    2427      7.00
     C    7177      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: 1.01
  Conformation dependent library (CDL) restraints added in 324.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1546

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 11 sheets defined
      69.9% alpha, 4.6% beta
      157 base pairs and 292 stacking pairs defined.
    Time for finding SS restraints: 1.57
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.625A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.512A  pdb=" N   ALA A 114 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.512A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.524A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.224A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 17 through 22
    Processing helix  chain 'C' and resid 26 through 36
      removed outlier: 3.628A  pdb=" N   VAL C  30 " --> pdb=" O   PRO C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 73
    Processing helix  chain 'C' and resid 79 through 89
    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 101 through 121
      removed outlier: 3.523A  pdb=" N   LYS D 105 " --> pdb=" O   GLY D 101 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.675A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.129A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.503A  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
      removed outlier: 3.636A  pdb=" N   VAL G  30 " --> pdb=" O   PRO G  26 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.510A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
      removed outlier: 3.661A  pdb=" N   MET H  56 " --> pdb=" O   SER H  52 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 121
      removed outlier: 3.946A  pdb=" N   LYS H 105 " --> pdb=" O   GLY H 101 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   HIS H 106 " --> pdb=" O   GLU H 102 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 22 through 35
    Processing helix  chain 'K' and resid 37 through 41
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.786A  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
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.055A  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: 6.732A  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: 6.730A  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: 7.002A  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
    Processing sheet with id=AB2, first strand: chain 'K' and resid 12 through 16

    427 hydrogen bonds defined for protein.
    1248 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      405 hydrogen bonds
      810 hydrogen bond angles
      0 basepair planarities
      157 basepair parallelities
      292 stacking parallelities
  Total time for adding SS restraints: 2.35

  Time building geometry restraints manager: 1.27 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2444
        1.33 -     1.45: 4527
        1.45 -     1.57: 6232
        1.57 -     1.69: 626
        1.69 -     1.81: 24
  Bond restraints: 13853
  Sorted by residual:
  bond pdb=" P    DA J  26 "
       pdb=" OP2  DA J  26 "
    ideal  model  delta    sigma   weight residual
    1.480  1.518 -0.038 2.00e-02 2.50e+03 3.56e+00
  bond pdb=" P    DA J  16 "
       pdb=" OP2  DA J  16 "
    ideal  model  delta    sigma   weight residual
    1.480  1.518 -0.038 2.00e-02 2.50e+03 3.54e+00
  bond pdb=" P    DC J -25 "
       pdb=" OP2  DC J -25 "
    ideal  model  delta    sigma   weight residual
    1.480  1.517 -0.037 2.00e-02 2.50e+03 3.51e+00
  bond pdb=" P    DG J  27 "
       pdb=" OP2  DG J  27 "
    ideal  model  delta    sigma   weight residual
    1.480  1.516 -0.036 2.00e-02 2.50e+03 3.28e+00
  bond pdb=" P    DG J  27 "
       pdb=" OP1  DG J  27 "
    ideal  model  delta    sigma   weight residual
    1.480  1.514 -0.034 2.00e-02 2.50e+03 2.86e+00
  ... (remaining 13848 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 19740
        2.00 -     4.00: 292
        4.00 -     6.01: 27
        6.01 -     8.01: 3
        8.01 -    10.01: 2
  Bond angle restraints: 20064
  Sorted by residual:
  angle pdb=" C3'  DC J -26 "
        pdb=" O3'  DC J -26 "
        pdb=" P    DC J -25 "
      ideal   model   delta    sigma   weight residual
     120.20  112.73    7.47 1.50e+00 4.44e-01 2.48e+01
  angle pdb=" C3'  DT J  15 "
        pdb=" O3'  DT J  15 "
        pdb=" P    DA J  16 "
      ideal   model   delta    sigma   weight residual
     120.20  114.24    5.96 1.50e+00 4.44e-01 1.58e+01
  angle pdb=" C3'  DT J  25 "
        pdb=" O3'  DT J  25 "
        pdb=" P    DA J  26 "
      ideal   model   delta    sigma   weight residual
     120.20  114.49    5.71 1.50e+00 4.44e-01 1.45e+01
  angle pdb=" O3'  DG J  27 "
        pdb=" P    DA J  28 "
        pdb=" O5'  DA J  28 "
      ideal   model   delta    sigma   weight residual
     104.00   98.43    5.57 1.50e+00 4.44e-01 1.38e+01
  angle pdb=" N   MET K   1 "
        pdb=" CA  MET K   1 "
        pdb=" C   MET K   1 "
      ideal   model   delta    sigma   weight residual
     111.00  100.99   10.01 2.80e+00 1.28e-01 1.28e+01
  ... (remaining 20059 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.90: 5934
       35.90 -    71.80: 1566
       71.80 -   107.70: 10
      107.70 -   143.60: 3
      143.60 -   179.50: 1
  Dihedral angle restraints: 7514
    sinusoidal: 5121
      harmonic: 2393
  Sorted by residual:
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   40.50  179.50     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DC I   4 "
           pdb=" C3'  DC I   4 "
           pdb=" O3'  DC I   4 "
           pdb=" P    DC I   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   88.90  131.10     1      3.50e+01 8.16e-04 1.30e+01
  dihedral pdb=" C4'  DC J  34 "
           pdb=" C3'  DC J  34 "
           pdb=" O3'  DC J  34 "
           pdb=" P    DT J  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   90.72  129.28     1      3.50e+01 8.16e-04 1.28e+01
  ... (remaining 7511 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.095: 2242
       0.095 -    0.191: 45
       0.191 -    0.286: 0
       0.286 -    0.381: 0
       0.381 -    0.476: 5
  Chirality restraints: 2292
  Sorted by residual:
  chirality pdb=" P    DC J -27 "
            pdb=" OP1  DC J -27 "
            pdb=" OP2  DC J -27 "
            pdb=" O5'  DC J -27 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.82   -0.48 2.00e-01 2.50e+01 5.67e+00
  chirality pdb=" P    DA J  16 "
            pdb=" OP1  DA J  16 "
            pdb=" OP2  DA J  16 "
            pdb=" O5'  DA J  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.80   -0.45 2.00e-01 2.50e+01 5.11e+00
  chirality pdb=" P    DC J -25 "
            pdb=" OP1  DC J -25 "
            pdb=" OP2  DC J -25 "
            pdb=" O5'  DC J -25 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.80   -0.45 2.00e-01 2.50e+01 5.10e+00
  ... (remaining 2289 not shown)

  Planarity restraints: 1452
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET K   1 "    0.011 2.00e-02 2.50e+03   2.17e-02 4.73e+00
        pdb=" C   MET K   1 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   MET K   1 "    0.014 2.00e-02 2.50e+03
        pdb=" N   GLN K   2 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  57 "    0.023 2.00e-02 2.50e+03   1.02e-02 2.85e+00
        pdb=" N9   DA I  57 "   -0.022 2.00e-02 2.50e+03
        pdb=" C8   DA I  57 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7   DA I  57 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5   DA I  57 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DA I  57 "    0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I  57 "    0.007 2.00e-02 2.50e+03
        pdb=" N1   DA I  57 "    0.002 2.00e-02 2.50e+03
        pdb=" C2   DA I  57 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3   DA I  57 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DA I  57 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  26 "   -0.023 2.00e-02 2.50e+03   9.73e-03 2.84e+00
        pdb=" N9   DG I  26 "    0.023 2.00e-02 2.50e+03
        pdb=" C8   DG I  26 "    0.003 2.00e-02 2.50e+03
        pdb=" N7   DG I  26 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DG I  26 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I  26 "   -0.003 2.00e-02 2.50e+03
        pdb=" O6   DG I  26 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1   DG I  26 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DG I  26 "    0.001 2.00e-02 2.50e+03
        pdb=" N2   DG I  26 "    0.003 2.00e-02 2.50e+03
        pdb=" N3   DG I  26 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DG I  26 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1449 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1888
        2.77 -     3.30: 10455
        3.30 -     3.84: 24438
        3.84 -     4.37: 29891
        4.37 -     4.90: 42828
  Nonbonded interactions: 109500
  Sorted by model distance:
  nonbonded pdb=" O   ASN C  73 "
            pdb=" ND2 ASN C  73 "
     model   vdw
     2.238 3.120
  nonbonded pdb=" OG1 THR B  73 "
            pdb=" OD2 ASP B  85 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" OG  SER C  18 "
            pdb=" O   PHE C  25 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OG1 THR H  87 "
            pdb=" OE1 GLU H  90 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" NH1 ARG G  32 "
            pdb=" OP1  DG J -44 "
     model   vdw
     2.303 3.120
  ... (remaining 109495 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 39 through 134)
  selection = (chain 'E' and resid 39 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 25 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 16 through 118)
}
ncs_group {
  reference = (chain 'D' and resid 29 through 121)
  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=0.63 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:             1.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     12.560
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:5.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
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      :  0.003   0.045  13853  Z= 0.164
  Angle     :  0.567  10.009  20064  Z= 0.341
  Chirality :  0.039   0.476   2292
  Planarity :  0.004   0.039   1452
  Dihedral  : 28.343 179.500   5968
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 22.79 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.83 (0.29), residues: 801
  helix:  2.78 (0.22), residues: 543
  sheet:  1.47 (1.60), residues: 12
  loop : -0.25 (0.36), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F  39 
 TYR   0.009   0.001   TYR F  51 
 PHE   0.009   0.001   PHE F  61 
 HIS   0.002   0.000   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (13853)
  covalent geometry    : angle       0.56656 (20064)
  hydrogen bonds       : bond        0.12007 (  832)
  hydrogen bonds       : angle       3.68167 ( 2058)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 126
  time to evaluate  : 0.381 
Fit side-chains
  outliers start: 8
  outliers final: 5
  residues processed: 133
  average time/residue: 0.9951
  time to fit residues: 139.3393
Evaluate side-chains
  132 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 127
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain G residue  116 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    0.1980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    7.9990
   chunk 106 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  25 ASN
C  73 ASN
H  60 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.162604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.135384 restraints weight = 13563.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.3796 rms_B_bonded: 0.86
r_work: 0.3481 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3310 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3116
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3116 r_free = 0.3116    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3116 r_free = 0.3116    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3116
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8679
moved from start:          0.0537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13853  Z= 0.192
  Angle     :  0.529   5.529  20064  Z= 0.326
  Chirality :  0.033   0.127   2292
  Planarity :  0.004   0.038   1452
  Dihedral  : 30.104 179.704   4352
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 21.63 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.12 (0.29), residues: 801
  helix:  2.98 (0.22), residues: 548
  sheet:  0.49 (1.20), residues: 17
  loop : -0.08 (0.37), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 131 
 TYR   0.009   0.001   TYR F  51 
 PHE   0.009   0.001   PHE F  61 
 HIS   0.002   0.000   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (13853)
  covalent geometry    : angle       0.52936 (20064)
  hydrogen bonds       : bond        0.05851 (  832)
  hydrogen bonds       : angle       2.95767 ( 2058)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
REVERT: B   92 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7754 (ttp80)
REVERT: B   95 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8176 (mtt-85)
REVERT: H   60 ASN cc_start: 0.8939 (OUTLIER) cc_final: 0.8552 (m-40)
REVERT: K    1 MET cc_start: 0.5051 (pp-130) cc_final: 0.4501 (tmm)
  outliers start: 16
  outliers final: 5
  residues processed: 141
  average time/residue: 0.9655
  time to fit residues: 143.3404
Evaluate side-chains
  140 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 132
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain H residue   60 ASN
Chi-restraints excluded: chain H residue  117 CYS
Chi-restraints excluded: chain K residue    3 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 68 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 84 optimal weight:    8.9990
   chunk 2 optimal weight:    0.9990
   chunk 85 optimal weight:    8.9990
   chunk 61 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
H  60 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.162486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.134648 restraints weight = 13713.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3782 rms_B_bonded: 0.88
r_work: 0.3412 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3237 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3026
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3026 r_free = 0.3026    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3026 r_free = 0.3026    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3026
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8736
moved from start:          0.0698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13853  Z= 0.194
  Angle     :  0.525   5.171  20064  Z= 0.323
  Chirality :  0.033   0.127   2292
  Planarity :  0.004   0.036   1452
  Dihedral  : 30.068 179.867   4344
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 21.63 %
    Favored  : 75.91 %
  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:  3.22 (0.29), residues: 801
  helix:  3.05 (0.22), residues: 542
  sheet:  0.49 (1.16), residues: 17
  loop :  0.05 (0.37), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  72 
 TYR   0.009   0.001   TYR F  51 
 PHE   0.008   0.001   PHE F  61 
 HIS   0.002   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 (13853)
  covalent geometry    : angle       0.52458 (20064)
  hydrogen bonds       : bond        0.05772 (  832)
  hydrogen bonds       : angle       2.87054 ( 2058)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 133
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
REVERT: B   92 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7737 (ttp80)
REVERT: B   93 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7560 (mp10)
REVERT: D   32 GLU cc_start: 0.8202 (pt0) cc_final: 0.7982 (pt0)
  outliers start: 17
  outliers final: 6
  residues processed: 143
  average time/residue: 0.8638
  time to fit residues: 130.0211
Evaluate side-chains
  138 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 130
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   15 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 86 optimal weight:   20.0000
   chunk 29 optimal weight:    7.9990
   chunk 60 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 88 optimal weight:    5.9990
   chunk 73 optimal weight:    6.9990
   chunk 87 optimal weight:    8.9990
   chunk 91 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0270
   chunk 0 optimal weight:    4.9990
   overall best weight:    3.0046

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
H  60 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.158773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.131720 restraints weight = 13563.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3737 rms_B_bonded: 0.78
r_work: 0.3398 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3225 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3024
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3024
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8754
moved from start:          0.1005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.053  13853  Z= 0.330
  Angle     :  0.612   6.293  20064  Z= 0.370
  Chirality :  0.039   0.167   2292
  Planarity :  0.005   0.040   1452
  Dihedral  : 30.315 178.235   4344
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 22.21 %
    Favored  : 75.04 %
  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: 801
  helix:  2.63 (0.22), residues: 548
  sheet:  0.25 (1.22), residues: 17
  loop : -0.36 (0.35), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  40 
 TYR   0.014   0.002   TYR E  54 
 PHE   0.011   0.002   PHE D  67 
 HIS   0.003   0.001   HIS D 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00741 (13853)
  covalent geometry    : angle       0.61202 (20064)
  hydrogen bonds       : bond        0.08576 (  832)
  hydrogen bonds       : angle       3.06367 ( 2058)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 132
  time to evaluate  : 0.346 
Fit side-chains
REVERT: D   32 GLU cc_start: 0.8213 (pt0) cc_final: 0.8010 (pt0)
REVERT: K    1 MET cc_start: 0.5454 (pp-130) cc_final: 0.5163 (pp-130)
  outliers start: 19
  outliers final: 8
  residues processed: 140
  average time/residue: 0.9425
  time to fit residues: 138.7356
Evaluate side-chains
  138 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 130
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue  117 CYS
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   15 LYS
Chi-restraints excluded: chain H residue  117 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 72 optimal weight:    8.9990
   chunk 93 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 92 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 89 optimal weight:    3.9990
   chunk 86 optimal weight:   20.0000
   chunk 94 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
H  60 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.160499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.133259 restraints weight = 13608.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3762 rms_B_bonded: 0.80
r_work: 0.3418 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3099
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3099 r_free = 0.3099    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3099 r_free = 0.3099    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3099
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8742
moved from start:          0.0925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  13853  Z= 0.214
  Angle     :  0.568   6.382  20064  Z= 0.348
  Chirality :  0.035   0.127   2292
  Planarity :  0.004   0.039   1452
  Dihedral  : 30.324 178.144   4344
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 22.79 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.81 (0.29), residues: 801
  helix:  2.77 (0.22), residues: 548
  sheet:  0.24 (1.24), residues: 17
  loop : -0.28 (0.36), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  72 
 TYR   0.011   0.001   TYR E  54 
 PHE   0.009   0.001   PHE F  61 
 HIS   0.002   0.001   HIS K  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 (13853)
  covalent geometry    : angle       0.56778 (20064)
  hydrogen bonds       : bond        0.07236 (  832)
  hydrogen bonds       : angle       3.08377 ( 2058)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 0.343 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7556 (ttp80)
REVERT: B   93 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7673 (mp10)
REVERT: D   32 GLU cc_start: 0.8230 (pt0) cc_final: 0.8027 (pt0)
REVERT: F   93 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7148 (mp10)
REVERT: K    1 MET cc_start: 0.5741 (pp-130) cc_final: 0.5400 (pp-130)
  outliers start: 17
  outliers final: 8
  residues processed: 140
  average time/residue: 1.0674
  time to fit residues: 157.0618
Evaluate side-chains
  143 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 132
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   15 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 73 optimal weight:    6.9990
   chunk 52 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 22 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
C  73 ASN
H  60 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.160711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.133535 restraints weight = 13521.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.3759 rms_B_bonded: 0.82
r_work: 0.3426 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3256 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3087
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3087 r_free = 0.3087    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3087 r_free = 0.3087    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.93   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3087
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8721
moved from start:          0.0899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  13853  Z= 0.209
  Angle     :  0.559   5.218  20064  Z= 0.343
  Chirality :  0.035   0.131   2292
  Planarity :  0.004   0.038   1452
  Dihedral  : 30.314 179.128   4344
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 22.50 %
    Favored  : 75.04 %
  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:  2.88 (0.29), residues: 801
  helix:  2.82 (0.22), residues: 548
  sheet:  0.31 (1.24), residues: 17
  loop : -0.23 (0.36), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 134 
 TYR   0.010   0.001   TYR F  51 
 PHE   0.009   0.001   PHE F  61 
 HIS   0.002   0.000   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 (13853)
  covalent geometry    : angle       0.55880 (20064)
  hydrogen bonds       : bond        0.06863 (  832)
  hydrogen bonds       : angle       2.97770 ( 2058)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 0.217 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7529 (ttp80)
REVERT: B   93 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7656 (mp10)
REVERT: E  131 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7498 (mtp85)
REVERT: F   93 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7160 (mp10)
REVERT: H   60 ASN cc_start: 0.9013 (OUTLIER) cc_final: 0.8597 (m-40)
REVERT: K    1 MET cc_start: 0.5701 (pp-130) cc_final: 0.5323 (pp-130)
  outliers start: 17
  outliers final: 7
  residues processed: 141
  average time/residue: 0.9185
  time to fit residues: 136.1057
Evaluate side-chains
  144 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 132
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   15 LYS
Chi-restraints excluded: chain H residue   60 ASN
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 102 optimal weight:    0.7980
   chunk 101 optimal weight:    6.9990
   chunk 100 optimal weight:    7.9990
   chunk 9 optimal weight:    5.9990
   chunk 90 optimal weight:    3.9990
   chunk 73 optimal weight:    6.9990
   chunk 87 optimal weight:    8.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
H  60 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.160195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.132701 restraints weight = 13524.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3764 rms_B_bonded: 0.80
r_work: 0.3445 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3277 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3093
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3093 r_free = 0.3093    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.93   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3093 r_free = 0.3093    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3093
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8715
moved from start:          0.0974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039  13853  Z= 0.257
  Angle     :  0.571   7.973  20064  Z= 0.347
  Chirality :  0.036   0.146   2292
  Planarity :  0.004   0.038   1452
  Dihedral  : 30.216 177.935   4344
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 21.63 %
    Favored  : 75.33 %
  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:  2.74 (0.29), residues: 801
  helix:  2.72 (0.22), residues: 548
  sheet:  0.44 (1.26), residues: 17
  loop : -0.31 (0.36), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  40 
 TYR   0.011   0.002   TYR E  54 
 PHE   0.009   0.002   PHE B  61 
 HIS   0.002   0.001   HIS D 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00572 (13853)
  covalent geometry    : angle       0.57115 (20064)
  hydrogen bonds       : bond        0.07206 (  832)
  hydrogen bonds       : angle       2.96069 ( 2058)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 0.259 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7532 (ttp80)
REVERT: B   93 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7645 (mp10)
REVERT: E  131 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.7473 (mtp85)
REVERT: K    1 MET cc_start: 0.5717 (pp-130) cc_final: 0.5445 (pp-130)
  outliers start: 21
  outliers final: 11
  residues processed: 140
  average time/residue: 1.0200
  time to fit residues: 149.9904
Evaluate side-chains
  145 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 131
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain D residue  117 CYS
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   15 LYS
Chi-restraints excluded: chain H residue  117 CYS
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 99 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9990
   chunk 88 optimal weight:    5.9990
   chunk 23 optimal weight:    0.5980
   chunk 73 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9990
   chunk 102 optimal weight:    7.9990
   chunk 8 optimal weight:    0.7980
   chunk 104 optimal weight:    0.0570
   overall best weight:    0.6902

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.161825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.135957 restraints weight = 13522.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 0.74
r_work: 0.3438 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3273 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3123
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3123
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.0931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  13853  Z= 0.173
  Angle     :  0.551   7.281  20064  Z= 0.338
  Chirality :  0.033   0.128   2292
  Planarity :  0.004   0.038   1452
  Dihedral  : 30.225 177.797   4344
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 23.22 %
    Favored  : 74.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.99 (0.29), residues: 801
  helix:  2.90 (0.22), residues: 548
  sheet:  0.42 (1.25), residues: 17
  loop : -0.18 (0.37), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  72 
 TYR   0.011   0.001   TYR F  51 
 PHE   0.009   0.001   PHE F  61 
 HIS   0.002   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (13853)
  covalent geometry    : angle       0.55071 (20064)
  hydrogen bonds       : bond        0.06173 (  832)
  hydrogen bonds       : angle       2.99490 ( 2058)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 130
  time to evaluate  : 0.323 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7557 (ttp80)
REVERT: B   93 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7621 (mp10)
REVERT: E  131 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7480 (mtp85)
REVERT: K    1 MET cc_start: 0.5710 (pp-130) cc_final: 0.5430 (pp-130)
  outliers start: 13
  outliers final: 7
  residues processed: 139
  average time/residue: 1.0193
  time to fit residues: 148.9605
Evaluate side-chains
  139 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 129
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   15 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 83 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 71 optimal weight:   20.0000
   chunk 0 optimal weight:    5.9990
   chunk 7 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 47 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
C  73 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.161675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.134542 restraints weight = 13592.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3779 rms_B_bonded: 0.81
r_work: 0.3424 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3241 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3094
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3094 r_free = 0.3094    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3094 r_free = 0.3094    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3094
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8739
moved from start:          0.0911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13853  Z= 0.194
  Angle     :  0.545   7.249  20064  Z= 0.333
  Chirality :  0.034   0.127   2292
  Planarity :  0.004   0.038   1452
  Dihedral  : 30.205 179.036   4344
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 23.22 %
    Favored  : 74.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.04 (0.29), residues: 801
  helix:  2.93 (0.22), residues: 547
  sheet:  0.44 (1.24), residues: 17
  loop : -0.14 (0.37), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 131 
 TYR   0.009   0.001   TYR F  51 
 PHE   0.008   0.001   PHE F  61 
 HIS   0.002   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 (13853)
  covalent geometry    : angle       0.54503 (20064)
  hydrogen bonds       : bond        0.06134 (  832)
  hydrogen bonds       : angle       2.90285 ( 2058)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 0.350 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7576 (ttp80)
REVERT: B   93 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.7602 (mp10)
REVERT: E  131 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.7530 (mtp85)
REVERT: F   93 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7283 (mp10)
REVERT: K    1 MET cc_start: 0.5475 (pp-130) cc_final: 0.5190 (pp-130)
  outliers start: 13
  outliers final: 5
  residues processed: 136
  average time/residue: 1.0446
  time to fit residues: 148.9847
Evaluate side-chains
  138 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 129
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   15 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 89 optimal weight:    4.9990
   chunk 8 optimal weight:    0.6980
   chunk 76 optimal weight:    3.9990
   chunk 103 optimal weight:    1.9990
   chunk 100 optimal weight:    7.9990
   chunk 29 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9980
   chunk 73 optimal weight:    6.9990
   overall best weight:    1.5184

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.161473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.134162 restraints weight = 13607.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3787 rms_B_bonded: 0.81
r_work: 0.3458 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3283 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3117
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3117 r_free = 0.3117    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3117 r_free = 0.3117    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3117
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8705
moved from start:          0.0929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  13853  Z= 0.209
  Angle     :  0.547   7.035  20064  Z= 0.334
  Chirality :  0.034   0.128   2292
  Planarity :  0.004   0.037   1452
  Dihedral  : 30.118 178.550   4344
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 23.37 %
    Favored  : 74.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.98 (0.29), residues: 801
  helix:  2.89 (0.22), residues: 548
  sheet:  0.44 (1.23), residues: 17
  loop : -0.19 (0.36), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  72 
 TYR   0.009   0.001   TYR F  51 
 PHE   0.008   0.001   PHE F  61 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 (13853)
  covalent geometry    : angle       0.54711 (20064)
  hydrogen bonds       : bond        0.06151 (  832)
  hydrogen bonds       : angle       2.87394 ( 2058)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 128
  time to evaluate  : 0.312 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7518 (ttp80)
REVERT: B   93 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7593 (mp10)
REVERT: E  131 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7527 (mtp85)
REVERT: K    1 MET cc_start: 0.5600 (pp-130) cc_final: 0.5312 (pp-130)
  outliers start: 12
  outliers final: 5
  residues processed: 135
  average time/residue: 1.0526
  time to fit residues: 149.0325
Evaluate side-chains
  137 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 129
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   15 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 26 optimal weight:    7.9990
   chunk 103 optimal weight:    8.9990
   chunk 47 optimal weight:    0.9980
   chunk 105 optimal weight:    8.9990
   chunk 14 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   overall best weight:    1.0782

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.161809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.134532 restraints weight = 13604.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3775 rms_B_bonded: 0.79
r_work: 0.3450 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3277 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3106
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3106 r_free = 0.3106    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3106 r_free = 0.3106    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3106
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8701
moved from start:          0.0947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13853  Z= 0.184
  Angle     :  0.542   7.000  20064  Z= 0.332
  Chirality :  0.033   0.127   2292
  Planarity :  0.004   0.037   1452
  Dihedral  : 30.116 178.551   4344
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 23.66 %
    Favored  : 74.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.00 (0.29), residues: 801
  helix:  2.91 (0.22), residues: 548
  sheet:  0.46 (1.23), residues: 17
  loop : -0.18 (0.37), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  32 
 TYR   0.009   0.001   TYR F  51 
 PHE   0.009   0.001   PHE F  61 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (13853)
  covalent geometry    : angle       0.54205 (20064)
  hydrogen bonds       : bond        0.06083 (  832)
  hydrogen bonds       : angle       2.87748 ( 2058)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4601.25 seconds
wall clock time: 78 minutes 49.96 seconds (4729.96 seconds total)