Starting phenix.real_space_refine
on Wed Jul 30 15:44:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g6g_29767/07_2025/8g6g_29767.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g6g_29767/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g6g_29767/07_2025/8g6g_29767.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g6g_29767/07_2025/8g6g_29767.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g6g_29767/07_2025/8g6g_29767.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g6g_29767/07_2025/8g6g_29767.cif"
  }
  resolution = 2.93
  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=   0.002 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.49, per 1000 atoms: 0.65
  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: 3.38
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 6.63
  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: 5.54

  Time building geometry restraints manager: 4.09 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:             2.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.090
  Set scattering table:                    0.100
  Process input model:                     38.270
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.060
  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:             0.010
  Load rotamer database and sin/cos tables:13.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   54.830
-------------------------------------------------------------------------------
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 (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:  2.83 (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
 HIS   0.002   0.000   HIS F  75 
 PHE   0.009   0.001   PHE F  61 
 TYR   0.009   0.001   TYR F  51 
 ARG   0.001   0.000   ARG F  39 

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

*********************** 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  : 0.913 
Fit side-chains
  outliers start: 8
  outliers final: 5
  residues processed: 133
  average time/residue: 1.9723
  time to fit residues: 277.1753
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  : 0.988 
-------------------------------------------------------------------------------
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 91 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0020
   chunk 27 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 84 optimal weight:    8.9990
   chunk 32 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 63 optimal weight:    4.9990
   chunk 98 optimal weight:    3.9990
   overall best weight:    1.1390

-------------------------------------------------------------------------------
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 = 0.4167 r_free = 0.4167 target = 0.163340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.136342 restraints weight = 13562.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3795 rms_B_bonded: 0.86
r_work: 0.3465 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3282 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3097
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3097
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8693
moved from start:          0.0575

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= 0.181
  Angle     :  0.523   5.367  20064  Z= 0.322
  Chirality :  0.033   0.128   2292
  Planarity :  0.004   0.037   1452
  Dihedral  : 30.071 179.819   4352
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 21.77 %
    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 (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:  3.20 (0.29), residues: 801
  helix:  3.03 (0.22), residues: 548
  sheet:  0.48 (1.20), residues: 17
  loop : -0.03 (0.37), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F  75 
 PHE   0.008   0.001   PHE F  61 
 TYR   0.008   0.001   TYR F  51 
 ARG   0.003   0.000   ARG A 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05455 (  832)
  hydrogen bonds       : angle       2.93854 ( 2058)
  covalent geometry    : bond        0.00386 (13853)
  covalent geometry    : angle       0.52253 (20064)

*********************** 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
  147 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
REVERT: B   92 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7752 (ttp80)
REVERT: B   93 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.7582 (mp10)
REVERT: B   95 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8203 (mtt-85)
REVERT: H   60 ASN cc_start: 0.8904 (OUTLIER) cc_final: 0.8521 (m-40)
REVERT: K    1 MET cc_start: 0.4887 (pp-130) cc_final: 0.4383 (tmm)
  outliers start: 16
  outliers final: 5
  residues processed: 139
  average time/residue: 1.9975
  time to fit residues: 292.9985
Evaluate side-chains
  140 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 131
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   93 GLN
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 26 optimal weight:    1.9990
   chunk 71 optimal weight:   20.0000
   chunk 75 optimal weight:    4.9990
   chunk 65 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 64 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   chunk 96 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 94 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.4160 r_free = 0.4160 target = 0.162776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.134968 restraints weight = 13650.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3786 rms_B_bonded: 0.89
r_work: 0.3424 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3248 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3069
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3069
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8728
moved from start:          0.0674

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= 0.189
  Angle     :  0.522   5.146  20064  Z= 0.322
  Chirality :  0.033   0.127   2292
  Planarity :  0.004   0.036   1452
  Dihedral  : 30.076 179.936   4344
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 22.21 %
    Favored  : 75.62 %
  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:  3.22 (0.29), residues: 801
  helix:  3.06 (0.22), residues: 548
  sheet:  0.51 (1.18), residues: 17
  loop : -0.03 (0.37), residues: 236

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05656 (  832)
  hydrogen bonds       : angle       2.88194 ( 2058)
  covalent geometry    : bond        0.00407 (13853)
  covalent geometry    : angle       0.52164 (20064)

*********************** 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
  147 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 132
  time to evaluate  : 1.146 
Fit side-chains
   revert: symmetry clash
REVERT: B   92 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7769 (ttp80)
REVERT: K    1 MET cc_start: 0.5496 (pp-130) cc_final: 0.5100 (tmm)
  outliers start: 15
  outliers final: 6
  residues processed: 142
  average time/residue: 2.6839
  time to fit residues: 403.5942
Evaluate side-chains
  139 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 132
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   92 ARG
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 61 optimal weight:    4.9990
   chunk 68 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 96 optimal weight:    3.9990
   chunk 106 optimal weight:   30.0000
   chunk 56 optimal weight:    3.9990
   overall best weight:    2.1388

-------------------------------------------------------------------------------
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 = 0.160442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.133219 restraints weight = 13466.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3762 rms_B_bonded: 0.80
r_work: 0.3410 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3231 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3070
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3070 r_free = 0.3070    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3071 r_free = 0.3071    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.93   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3071
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8749
moved from start:          0.0744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040  13853  Z= 0.256
  Angle     :  0.559   5.468  20064  Z= 0.342
  Chirality :  0.036   0.147   2292
  Planarity :  0.004   0.038   1452
  Dihedral  : 30.135 178.131   4344
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 21.48 %
    Favored  : 75.47 %
  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:  2.98 (0.29), residues: 801
  helix:  2.90 (0.22), residues: 547
  sheet:  0.54 (1.20), residues: 17
  loop : -0.19 (0.36), residues: 237

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07262 (  832)
  hydrogen bonds       : angle       2.95614 ( 2058)
  covalent geometry    : bond        0.00564 (13853)
  covalent geometry    : angle       0.55901 (20064)

*********************** 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
  156 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
REVERT: B   92 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7778 (ttp80)
REVERT: D   32 GLU cc_start: 0.8162 (pt0) cc_final: 0.7945 (pt0)
  outliers start: 21
  outliers final: 10
  residues processed: 143
  average time/residue: 2.2173
  time to fit residues: 334.6775
Evaluate side-chains
  145 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 134
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   92 ARG
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   93 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
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 93 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   chunk 85 optimal weight:    8.9990
   chunk 56 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   overall best weight:    1.6586

-------------------------------------------------------------------------------
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 = 0.4141 r_free = 0.4141 target = 0.161075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.133609 restraints weight = 13567.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3761 rms_B_bonded: 0.83
r_work: 0.3448 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3281 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3111
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3111 r_free = 0.3111    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.93   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3111 r_free = 0.3111    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3111
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.0727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  13853  Z= 0.223
  Angle     :  0.550   5.692  20064  Z= 0.337
  Chirality :  0.035   0.133   2292
  Planarity :  0.004   0.038   1452
  Dihedral  : 30.149 178.501   4344
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 22.06 %
    Favored  : 75.47 %
  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:  2.97 (0.29), residues: 801
  helix:  2.89 (0.22), residues: 547
  sheet:  0.26 (1.21), residues: 17
  loop : -0.17 (0.36), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 113 
 PHE   0.009   0.001   PHE B  61 
 TYR   0.010   0.001   TYR E  54 
 ARG   0.002   0.000   ARG A  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06847 (  832)
  hydrogen bonds       : angle       2.96206 ( 2058)
  covalent geometry    : bond        0.00486 (13853)
  covalent geometry    : angle       0.54976 (20064)

*********************** 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
  147 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
REVERT: B   92 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7756 (ttp80)
REVERT: D   32 GLU cc_start: 0.8127 (pt0) cc_final: 0.7911 (pt0)
  outliers start: 17
  outliers final: 10
  residues processed: 138
  average time/residue: 2.1078
  time to fit residues: 306.5673
Evaluate side-chains
  142 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 131
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   56 MET
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   93 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 82 optimal weight:    4.9990
   overall best weight:    1.4784

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.161237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.134263 restraints weight = 13735.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.3775 rms_B_bonded: 0.78
r_work: 0.3439 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3261 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3048
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3048 r_free = 0.3048    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3048 r_free = 0.3048    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3048
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8719
moved from start:          0.0730

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= 0.212
  Angle     :  0.549   9.112  20064  Z= 0.336
  Chirality :  0.034   0.130   2292
  Planarity :  0.004   0.038   1452
  Dihedral  : 30.152 178.705   4344
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 22.35 %
    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 (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:  2.98 (0.29), residues: 801
  helix:  2.90 (0.22), residues: 547
  sheet:  0.17 (1.23), residues: 17
  loop : -0.16 (0.36), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F  75 
 PHE   0.009   0.001   PHE B  61 
 TYR   0.010   0.001   TYR F  51 
 ARG   0.003   0.000   ARG A  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06716 (  832)
  hydrogen bonds       : angle       2.95075 ( 2058)
  covalent geometry    : bond        0.00461 (13853)
  covalent geometry    : angle       0.54943 (20064)

*********************** 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
  146 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 130
  time to evaluate  : 1.131 
Fit side-chains
   revert: symmetry clash
REVERT: B   92 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7688 (ttp80)
REVERT: D   32 GLU cc_start: 0.8163 (pt0) cc_final: 0.7944 (pt0)
  outliers start: 16
  outliers final: 7
  residues processed: 138
  average time/residue: 3.1717
  time to fit residues: 460.7188
Evaluate side-chains
  139 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 131
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue  117 CYS
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 98 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 86 optimal weight:   20.0000
   chunk 16 optimal weight:    0.9990
   chunk 83 optimal weight:    4.9990
   chunk 62 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.4151 r_free = 0.4151 target = 0.161891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.134673 restraints weight = 13593.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.3773 rms_B_bonded: 0.80
r_work: 0.3462 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3296 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3124
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3124 r_free = 0.3124    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 = 0.3124 r_free = 0.3124    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3124
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.0704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  13853  Z= 0.174
  Angle     :  0.537   7.418  20064  Z= 0.331
  Chirality :  0.033   0.126   2292
  Planarity :  0.004   0.038   1452
  Dihedral  : 30.151 178.779   4344
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 22.79 %
    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 (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:  3.06 (0.29), residues: 801
  helix:  2.96 (0.22), residues: 547
  sheet:  0.08 (1.25), residues: 17
  loop : -0.12 (0.37), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS F  75 
 PHE   0.009   0.001   PHE F  61 
 TYR   0.010   0.001   TYR F  51 
 ARG   0.002   0.000   ARG A  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06469 (  832)
  hydrogen bonds       : angle       2.95194 ( 2058)
  covalent geometry    : bond        0.00365 (13853)
  covalent geometry    : angle       0.53733 (20064)

*********************** 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
  145 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 132
  time to evaluate  : 1.085 
Fit side-chains
   revert: symmetry clash
REVERT: B   92 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7724 (ttp80)
REVERT: D   32 GLU cc_start: 0.8135 (pt0) cc_final: 0.7918 (pt0)
  outliers start: 13
  outliers final: 8
  residues processed: 140
  average time/residue: 2.0529
  time to fit residues: 303.0297
Evaluate side-chains
  141 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 132
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
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 C residue   76 THR
Chi-restraints excluded: chain D residue   56 MET
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 83 optimal weight:    4.9990
   chunk 53 optimal weight:    0.8980
   chunk 87 optimal weight:    8.9990
   chunk 39 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 105 optimal weight:    9.9990
   chunk 14 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.4153 r_free = 0.4153 target = 0.162071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.135037 restraints weight = 13616.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3786 rms_B_bonded: 0.78
r_work: 0.3428 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3264 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3102
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3102 r_free = 0.3102    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3102 r_free = 0.3102    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3102
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8720
moved from start:          0.0696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071  13853  Z= 0.188
  Angle     :  0.539   9.283  20064  Z= 0.331
  Chirality :  0.033   0.127   2292
  Planarity :  0.004   0.037   1452
  Dihedral  : 30.155 178.985   4344
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 22.93 %
    Favored  : 75.18 %
  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:  3.10 (0.29), residues: 801
  helix:  2.99 (0.22), residues: 547
  sheet:  0.11 (1.24), residues: 17
  loop : -0.11 (0.37), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS F  75 
 PHE   0.009   0.001   PHE F  61 
 TYR   0.010   0.001   TYR F  51 
 ARG   0.003   0.000   ARG A  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06177 (  832)
  hydrogen bonds       : angle       2.93684 ( 2058)
  covalent geometry    : bond        0.00401 (13853)
  covalent geometry    : angle       0.53906 (20064)

*********************** 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
  144 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 131
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8546 (mtt)
REVERT: B   92 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7683 (ttp80)
REVERT: D   32 GLU cc_start: 0.8162 (pt0) cc_final: 0.7943 (pt0)
  outliers start: 13
  outliers final: 6
  residues processed: 138
  average time/residue: 2.0621
  time to fit residues: 299.7993
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  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain B residue   92 ARG
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 85 optimal weight:    8.9990
   chunk 76 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 71 optimal weight:   20.0000
   chunk 66 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 87 optimal weight:    7.9990
   chunk 94 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   overall best weight:    2.5988

-------------------------------------------------------------------------------
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 = 0.4122 r_free = 0.4122 target = 0.159466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.132281 restraints weight = 13544.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3750 rms_B_bonded: 0.78
r_work: 0.3407 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3087
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3087 r_free = 0.3087    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3087 r_free = 0.3087    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3087
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8744
moved from start:          0.0927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.047  13853  Z= 0.293
  Angle     :  0.589   5.607  20064  Z= 0.358
  Chirality :  0.038   0.154   2292
  Planarity :  0.004   0.037   1452
  Dihedral  : 30.285 178.380   4344
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 22.06 %
    Favored  : 75.47 %
  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:  2.73 (0.29), residues: 801
  helix:  2.71 (0.22), residues: 548
  sheet:  0.18 (1.33), residues: 17
  loop : -0.29 (0.36), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 113 
 PHE   0.009   0.002   PHE B  61 
 TYR   0.013   0.002   TYR E  54 
 ARG   0.003   0.000   ARG B  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07859 (  832)
  hydrogen bonds       : angle       3.01229 ( 2058)
  covalent geometry    : bond        0.00655 (13853)
  covalent geometry    : angle       0.58854 (20064)

*********************** 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
  148 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 0.882 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7698 (ttp80)
REVERT: E  131 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.7448 (mtp85)
REVERT: H   60 ASN cc_start: 0.9015 (OUTLIER) cc_final: 0.8572 (m-40)
REVERT: K    1 MET cc_start: 0.5595 (pp-130) cc_final: 0.5188 (tmm)
  outliers start: 17
  outliers final: 8
  residues processed: 140
  average time/residue: 2.0527
  time to fit residues: 302.4767
Evaluate side-chains
  141 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 130
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
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 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 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   60 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 85 optimal weight:    8.9990
   chunk 88 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   chunk 86 optimal weight:   20.0000
   chunk 19 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 71 optimal weight:   20.0000
   chunk 30 optimal weight:    0.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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 = 0.4140 r_free = 0.4140 target = 0.160999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.133674 restraints weight = 13534.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 0.84
r_work: 0.3421 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3248 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3090
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3090 r_free = 0.3090    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3090 r_free = 0.3090    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3090
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8733
moved from start:          0.0868

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= 0.205
  Angle     :  0.556   5.350  20064  Z= 0.342
  Chirality :  0.035   0.129   2292
  Planarity :  0.004   0.038   1452
  Dihedral  : 30.281 178.799   4344
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 22.93 %
    Favored  : 75.47 %
  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:  2.86 (0.29), residues: 801
  helix:  2.80 (0.22), residues: 548
  sheet:  0.21 (1.32), residues: 17
  loop : -0.20 (0.36), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F  75 
 PHE   0.009   0.001   PHE F  61 
 TYR   0.010   0.001   TYR F  51 
 ARG   0.002   0.000   ARG A  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06737 (  832)
  hydrogen bonds       : angle       2.97944 ( 2058)
  covalent geometry    : bond        0.00442 (13853)
  covalent geometry    : angle       0.55628 (20064)

********************** 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: 11
    poor density    : 129
  time to evaluate  : 0.887 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7677 (ttp80)
REVERT: K    1 MET cc_start: 0.5243 (pp-130) cc_final: 0.4811 (tmm)
  outliers start: 11
  outliers final: 8
  residues processed: 137
  average time/residue: 2.0883
  time to fit residues: 301.3684
Evaluate side-chains
  139 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 130
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
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 C residue   76 THR
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue  117 CYS
Chi-restraints excluded: chain E residue   68 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 16 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 76 optimal weight:    3.9990
   chunk 10 optimal weight:    0.5980
   chunk 48 optimal weight:    0.6980
   chunk 9 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 107 optimal weight:    0.6980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4147 r_free = 0.4147 target = 0.161607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.134438 restraints weight = 13535.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.3770 rms_B_bonded: 0.86
r_work: 0.3432 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3267 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3113
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3113 r_free = 0.3113    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3113 r_free = 0.3113    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.94   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3113
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8713
moved from start:          0.0845

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= 0.171
  Angle     :  0.549   5.097  20064  Z= 0.339
  Chirality :  0.033   0.127   2292
  Planarity :  0.004   0.038   1452
  Dihedral  : 30.271 178.802   4344
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 23.37 %
    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 (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:  2.94 (0.29), residues: 801
  helix:  2.85 (0.22), residues: 548
  sheet:  0.19 (1.32), residues: 17
  loop : -0.16 (0.36), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F  75 
 PHE   0.009   0.001   PHE F  61 
 TYR   0.010   0.001   TYR F  51 
 ARG   0.003   0.000   ARG G  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06494 (  832)
  hydrogen bonds       : angle       2.98197 ( 2058)
  covalent geometry    : bond        0.00355 (13853)
  covalent geometry    : angle       0.54924 (20064)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10525.53 seconds
wall clock time: 185 minutes 59.78 seconds (11159.78 seconds total)