Starting phenix.real_space_refine
on Wed Mar  4 20:15:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7njw_12425/03_2026/7njw_12425.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7njw_12425/03_2026/7njw_12425.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7njw_12425/03_2026/7njw_12425.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7njw_12425/03_2026/7njw_12425.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7njw_12425/03_2026/7njw_12425.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7njw_12425/03_2026/7njw_12425.map"
  }
  resolution = 3.67
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      28      5.16       5
     C    5346      2.51       5
     N    1316      2.21       5
     O    1399      1.98       5
     H    8337      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16426
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "L"
      Number of atoms: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1192
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 4, 'TRANS': 79}
    Chain: "M"
      Number of atoms: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1192
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 4, 'TRANS': 79}
    Chain: "N"
      Number of atoms: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1192
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 4, 'TRANS': 79}
    Chain: "O"
      Number of atoms: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1192
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 4, 'TRANS': 79}
    Chain: "P"
      Number of atoms: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1192
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 4, 'TRANS': 79}
    Chain: "Q"
      Number of atoms: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1192
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 4, 'TRANS': 79}
    Chain: "R"
      Number of atoms: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1192
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 4, 'TRANS': 79}
    Chain: "S"
      Number of atoms: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1192
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 4, 'TRANS': 79}
    Chain: "T"
      Number of atoms: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1192
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 4, 'TRANS': 79}
    Chain: "a"
      Number of atoms: 3767
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 3767
          Classifications: {'peptide': 238}
          Link IDs: {'PTRANS': 10, 'TRANS': 227}
    Chain: "d"
      Number of atoms: 952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 952
          Classifications: {'peptide': 61}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 58}
    Chain: "b"
      Number of atoms: 979
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 979
          Classifications: {'peptide': 63}
          Link IDs: {'PTRANS': 3, 'TRANS': 59}
  Time building chain proxies: 2.82, per 1000 atoms: 0.17
  Number of scatterers: 16426
  At special positions: 0
  Unit cell: (92.96, 78.02, 116.2, 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      28     16.00
     O    1399      8.00
     N    1316      7.00
     C    5346      6.00
     H    8337      1.00
    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: 1.20
  Conformation dependent library (CDL) restraints added in 435.5 milliseconds
  

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1904

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 2 sheets defined
      87.3% alpha, 0.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'L' and resid 4 through 46
      removed outlier: 3.662A  pdb=" N   ILE L   8 " --> pdb=" O   ASP L   4 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 49 through 80
      removed outlier: 3.976A  pdb=" N   THR L  55 " --> pdb=" O   GLY L  51 " (cutoff:3.500A)
      Proline residue:  L  56  - end of helix
      removed outlier: 3.812A  pdb=" N   ALA L  67 " --> pdb=" O   LEU L  63 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   TYR L  68 " --> pdb=" O   VAL L  64 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 4 through 46
      removed outlier: 3.722A  pdb=" N   ILE M   8 " --> pdb=" O   ASP M   4 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 49 through 81
      removed outlier: 4.898A  pdb=" N   THR M  55 " --> pdb=" O   GLY M  51 " (cutoff:3.500A)
      Proline residue:  M  56  - end of helix
    Processing helix  chain 'N' and resid 4 through 46
      removed outlier: 4.025A  pdb=" N   ILE N   8 " --> pdb=" O   ASP N   4 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 49 through 81
      removed outlier: 3.702A  pdb=" N   PHE N  54 " --> pdb=" O   GLN N  50 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   THR N  55 " --> pdb=" O   GLY N  51 " (cutoff:3.500A)
      Proline residue:  N  56  - end of helix
      removed outlier: 3.726A  pdb=" N   ILE N  59 " --> pdb=" O   THR N  55 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ASN N  71 " --> pdb=" O   ALA N  67 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 4 through 46
    Processing helix  chain 'O' and resid 49 through 80
      removed outlier: 4.496A  pdb=" N   THR O  55 " --> pdb=" O   GLY O  51 " (cutoff:3.500A)
      Proline residue:  O  56  - end of helix
      removed outlier: 4.076A  pdb=" N   ALA O  67 " --> pdb=" O   LEU O  63 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ASN O  71 " --> pdb=" O   ALA O  67 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 4 through 46
      removed outlier: 3.569A  pdb=" N   ILE P   8 " --> pdb=" O   ASP P   4 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 49 through 80
      removed outlier: 4.008A  pdb=" N   THR P  55 " --> pdb=" O   GLY P  51 " (cutoff:3.500A)
      Proline residue:  P  56  - end of helix
      removed outlier: 3.588A  pdb=" N   ALA P  66 " --> pdb=" O   GLY P  62 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 4 through 46
      removed outlier: 3.654A  pdb=" N   ILE Q   8 " --> pdb=" O   ASP Q   4 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 49 through 81
      removed outlier: 4.143A  pdb=" N   THR Q  55 " --> pdb=" O   GLY Q  51 " (cutoff:3.500A)
      Proline residue:  Q  56  - end of helix
    Processing helix  chain 'R' and resid 4 through 46
      removed outlier: 3.968A  pdb=" N   ILE R   8 " --> pdb=" O   ASP R   4 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 49 through 80
      removed outlier: 4.912A  pdb=" N   THR R  55 " --> pdb=" O   GLY R  51 " (cutoff:3.500A)
      Proline residue:  R  56  - end of helix
    Processing helix  chain 'S' and resid 4 through 46
      removed outlier: 3.766A  pdb=" N   ILE S   8 " --> pdb=" O   ASP S   4 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 49 through 81
      removed outlier: 4.642A  pdb=" N   THR S  55 " --> pdb=" O   GLY S  51 " (cutoff:3.500A)
      Proline residue:  S  56  - end of helix
      removed outlier: 3.890A  pdb=" N   ILE S  59 " --> pdb=" O   THR S  55 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ALA S  66 " --> pdb=" O   GLY S  62 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   ALA S  67 " --> pdb=" O   LEU S  63 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ASN S  71 " --> pdb=" O   ALA S  67 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   PHE S  80 " --> pdb=" O   ALA S  76 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 4 through 46
      removed outlier: 3.739A  pdb=" N   ILE T   8 " --> pdb=" O   ASP T   4 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 49 through 81
      removed outlier: 4.041A  pdb=" N   PHE T  54 " --> pdb=" O   GLN T  50 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   THR T  55 " --> pdb=" O   GLY T  51 " (cutoff:3.500A)
      Proline residue:  T  56  - end of helix
      removed outlier: 3.542A  pdb=" N   ILE T  59 " --> pdb=" O   THR T  55 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   ALA T  67 " --> pdb=" O   LEU T  63 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 28 through 51
    Processing helix  chain 'a' and resid 60 through 81
    Processing helix  chain 'a' and resid 88 through 107
    Processing helix  chain 'a' and resid 126 through 129
    Processing helix  chain 'a' and resid 130 through 154
      removed outlier: 3.709A  pdb=" N   VAL a 134 " --> pdb=" O   ASP a 130 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 156 through 165
      removed outlier: 3.600A  pdb=" N   ILE a 160 " --> pdb=" O   VAL a 156 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 170 through 204
      removed outlier: 3.610A  pdb=" N   ILE a 175 " --> pdb=" O   ALA a 171 " (cutoff:3.500A)
      Proline residue:  a 182  - end of helix
      removed outlier: 3.618A  pdb=" N   ARG a 188 " --> pdb=" O   SER a 184 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   LEU a 189 " --> pdb=" O   LEU a 185 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   GLY a 196 " --> pdb=" O   ASN a 192 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ALA a 201 " --> pdb=" O   GLY a 197 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 207 through 245
      removed outlier: 3.943A  pdb=" N   TRP a 212 " --> pdb=" O   TRP a 208 " (cutoff:3.500A)
      removed outlier: 6.115A  pdb=" N   PHE a 213 " --> pdb=" O   TYR a 209 " (cutoff:3.500A)
      Proline residue:  a 214  - end of helix
      removed outlier: 3.916A  pdb=" N   PHE a 224 " --> pdb=" O   THR a 220 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 2 through 22
    Processing helix  chain 'd' and resid 22 through 61
    Processing helix  chain 'b' and resid 29 through 48
      removed outlier: 3.573A  pdb=" N   ALA b  33 " --> pdb=" O   GLY b  29 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 49 through 84
    Processing sheet with id=AA1, first strand: chain 'a' and resid 20 through 22
    Processing sheet with id=AA2, first strand: chain 'a' and resid 112 through 114

    786 hydrogen bonds defined for protein.
    2349 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.57

  Time building geometry restraints manager: 1.77 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 8336
        1.03 -     1.23: 13
        1.23 -     1.42: 3347
        1.42 -     1.62: 4843
        1.62 -     1.81: 55
  Bond restraints: 16594
  Sorted by residual:
  bond pdb=" CB  ILE L  40 "
       pdb=" CG2 ILE L  40 "
    ideal  model  delta    sigma   weight residual
    1.521  1.490  0.031 3.30e-02 9.18e+02 9.11e-01
  bond pdb=" CG1 ILE L  20 "
       pdb=" CD1 ILE L  20 "
    ideal  model  delta    sigma   weight residual
    1.513  1.477  0.036 3.90e-02 6.57e+02 8.74e-01
  bond pdb=" CA  VAL b  50 "
       pdb=" CB  VAL b  50 "
    ideal  model  delta    sigma   weight residual
    1.539  1.534  0.005 5.40e-03 3.43e+04 7.73e-01
  bond pdb=" C   GLN Q  50 "
       pdb=" O   GLN Q  50 "
    ideal  model  delta    sigma   weight residual
    1.236  1.246 -0.009 1.15e-02 7.56e+03 6.63e-01
  bond pdb=" C   THR O  55 "
       pdb=" O   THR O  55 "
    ideal  model  delta    sigma   weight residual
    1.244  1.237  0.007 9.10e-03 1.21e+04 6.52e-01
  ... (remaining 16589 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.22: 28946
        1.22 -     2.44: 1073
        2.44 -     3.66: 60
        3.66 -     4.88: 33
        4.88 -     6.10: 4
  Bond angle restraints: 30116
  Sorted by residual:
  angle pdb=" CA  GLN Q  50 "
        pdb=" CB  GLN Q  50 "
        pdb=" CG  GLN Q  50 "
      ideal   model   delta    sigma   weight residual
     114.10  120.20   -6.10 2.00e+00 2.50e-01 9.30e+00
  angle pdb=" C   CYS a 144 "
        pdb=" N   TYR a 145 "
        pdb=" CA  TYR a 145 "
      ideal   model   delta    sigma   weight residual
     120.68  116.35    4.33 1.70e+00 3.46e-01 6.48e+00
  angle pdb=" C   VAL b  50 "
        pdb=" CA  VAL b  50 "
        pdb=" CB  VAL b  50 "
      ideal   model   delta    sigma   weight residual
     114.00  110.69    3.31 1.31e+00 5.83e-01 6.38e+00
  angle pdb=" CA  TYR a 145 "
        pdb=" CB  TYR a 145 "
        pdb=" CG  TYR a 145 "
      ideal   model   delta    sigma   weight residual
     113.90  118.33   -4.43 1.80e+00 3.09e-01 6.05e+00
  angle pdb=" N   GLN Q  50 "
        pdb=" CA  GLN Q  50 "
        pdb=" CB  GLN Q  50 "
      ideal   model   delta    sigma   weight residual
     109.94  106.83    3.11 1.49e+00 4.50e-01 4.36e+00
  ... (remaining 30111 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 6742
       17.69 -    35.38: 601
       35.38 -    53.07: 286
       53.07 -    70.76: 124
       70.76 -    88.45: 6
  Dihedral angle restraints: 7759
    sinusoidal: 4150
      harmonic: 3609
  Sorted by residual:
  dihedral pdb=" CA  ASP a 130 "
           pdb=" CB  ASP a 130 "
           pdb=" CG  ASP a 130 "
           pdb=" OD1 ASP a 130 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.53   56.53     1      2.00e+01 2.50e-03 1.08e+01
  dihedral pdb=" CB  GLU R  65 "
           pdb=" CG  GLU R  65 "
           pdb=" CD  GLU R  65 "
           pdb=" OE1 GLU R  65 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   85.99  -85.99     1      3.00e+01 1.11e-03 9.92e+00
  dihedral pdb=" CB  GLU R  48 "
           pdb=" CG  GLU R  48 "
           pdb=" CD  GLU R  48 "
           pdb=" OE1 GLU R  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -85.38   85.38     1      3.00e+01 1.11e-03 9.81e+00
  ... (remaining 7756 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 826
       0.027 -    0.055: 273
       0.055 -    0.082: 154
       0.082 -    0.110: 60
       0.110 -    0.137: 9
  Chirality restraints: 1322
  Sorted by residual:
  chirality pdb=" CA  VAL a  58 "
            pdb=" N   VAL a  58 "
            pdb=" C   VAL a  58 "
            pdb=" CB  VAL a  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.69e-01
  chirality pdb=" CA  ILE b  26 "
            pdb=" N   ILE b  26 "
            pdb=" C   ILE b  26 "
            pdb=" CB  ILE b  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.32e-01
  chirality pdb=" CA  PHE M  58 "
            pdb=" N   PHE M  58 "
            pdb=" C   PHE M  58 "
            pdb=" CB  PHE M  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 3.93e-01
  ... (remaining 1319 not shown)

  Planarity restraints: 2495
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN Q  50 "    0.010 2.00e-02 2.50e+03   1.58e-02 3.73e+00
        pdb=" CD  GLN Q  50 "   -0.034 2.00e-02 2.50e+03
        pdb=" OE1 GLN Q  50 "    0.013 2.00e-02 2.50e+03
        pdb=" NE2 GLN Q  50 "    0.009 2.00e-02 2.50e+03
        pdb="HE21 GLN Q  50 "    0.000 2.00e-02 2.50e+03
        pdb="HE22 GLN Q  50 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY a 191 "   -0.007 2.00e-02 2.50e+03   1.43e-02 2.04e+00
        pdb=" C   GLY a 191 "    0.025 2.00e-02 2.50e+03
        pdb=" O   GLY a 191 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ASN a 192 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE L  70 "   -0.007 2.00e-02 2.50e+03   1.35e-02 1.81e+00
        pdb=" C   ILE L  70 "    0.023 2.00e-02 2.50e+03
        pdb=" O   ILE L  70 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ASN L  71 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 2492 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 749
        2.18 -     2.78: 33249
        2.78 -     3.39: 50596
        3.39 -     3.99: 62536
        3.99 -     4.60: 99394
  Nonbonded interactions: 246524
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN a  72 "
            pdb="HE21 GLN a  76 "
     model   vdw
     1.575 2.450
  nonbonded pdb="HE22 GLN S  46 "
            pdb=" O   ALA T  44 "
     model   vdw
     1.620 2.450
  nonbonded pdb=" O   PHE S  78 "
            pdb=" HG1 THR S  82 "
     model   vdw
     1.668 2.450
  nonbonded pdb=" OE1 GLU P  48 "
            pdb=" H   GLU P  48 "
     model   vdw
     1.674 2.450
  nonbonded pdb=" O   ASP b  70 "
            pdb=" HG  SER b  74 "
     model   vdw
     1.690 2.450
  ... (remaining 246519 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 'L'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'O'
  selection = chain 'P'
  selection = chain 'Q'
  selection = chain 'R'
  selection = chain 'S'
  selection = chain 'T'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             11.810
  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:             0.100
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     15.600
  Find NCS groups from input model:        0.130
  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:             0.010
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
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   0.036   8257  Z= 0.149
  Angle     :  0.504   6.098  11218  Z= 0.280
  Chirality :  0.038   0.137   1322
  Planarity :  0.004   0.032   1440
  Dihedral  : 14.130  88.454   2789
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.21 (0.27), residues: 1094
  helix:  1.49 (0.18), residues: 942
  sheet: -1.27 (1.82), residues: 10
  loop :  2.11 (0.63), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG M  45 
 TYR   0.008   0.001   TYR a 145 
 PHE   0.019   0.001   PHE M  58 
 TRP   0.012   0.001   TRP a 218 
 HIS   0.003   0.001   HIS a 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8257)
  covalent geometry    : angle       0.50431 (11218)
  hydrogen bonds       : bond        0.13265 (  786)
  hydrogen bonds       : angle       6.65291 ( 2349)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   75 MET cc_start: 0.8269 (tmm) cc_final: 0.7822 (tmm)
REVERT: a   84 LYS cc_start: 0.7107 (pttt) cc_final: 0.6859 (pttm)
REVERT: d   46 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7631 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1840
  time to fit residues: 27.1739
Evaluate side-chains
  81 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.0060
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
P  46 GLN
R  50 GLN
** S  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
T  46 GLN
** a 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.089023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.082362 restraints weight = 62662.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.084674 restraints weight = 23662.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.086083 restraints weight = 11247.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.086870 restraints weight = 6330.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.087324 restraints weight = 4031.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.0890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8257  Z= 0.169
  Angle     :  0.518   5.303  11218  Z= 0.284
  Chirality :  0.039   0.137   1322
  Planarity :  0.004   0.036   1440
  Dihedral  :  3.601  15.490   1149
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  5.05 %
    Favored  : 94.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.25 (0.26), residues: 1094
  helix:  2.15 (0.17), residues: 951
  sheet: -1.22 (1.87), residues: 10
  loop :  2.84 (0.65), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG M  45 
 TYR   0.027   0.001   TYR a 145 
 PHE   0.017   0.001   PHE M  58 
 TRP   0.011   0.001   TRP a 218 
 HIS   0.003   0.001   HIS a 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 8257)
  covalent geometry    : angle       0.51788 (11218)
  hydrogen bonds       : bond        0.05226 (  786)
  hydrogen bonds       : angle       4.49741 ( 2349)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 83
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   75 MET cc_start: 0.8435 (tmm) cc_final: 0.7746 (tmm)
REVERT: d   46 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7614 (tm-30)
  outliers start: 6
  outliers final: 6
  residues processed: 88
  average time/residue: 0.1805
  time to fit residues: 23.0905
Evaluate side-chains
  85 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   41 SER
Chi-restraints excluded: chain O residue   72 LEU
Chi-restraints excluded: chain R residue   55 THR
Chi-restraints excluded: chain T residue   20 ILE
Chi-restraints excluded: chain a residue  192 ASN
Chi-restraints excluded: chain a residue  242 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 47 optimal weight:    0.4980
   chunk 80 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
M  71 ASN
** S  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.086950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.080235 restraints weight = 64190.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.082534 restraints weight = 24204.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.083934 restraints weight = 11443.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.084706 restraints weight = 6443.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.085078 restraints weight = 4189.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.1297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8257  Z= 0.229
  Angle     :  0.544   7.414  11218  Z= 0.299
  Chirality :  0.039   0.134   1322
  Planarity :  0.004   0.045   1440
  Dihedral  :  3.686  15.449   1149
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  7.38 %
    Favored  : 91.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.33 (0.26), residues: 1094
  helix:  2.22 (0.16), residues: 951
  sheet: -1.17 (1.95), residues: 10
  loop :  2.74 (0.65), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG M  45 
 TYR   0.024   0.002   TYR a 145 
 PHE   0.020   0.002   PHE M  58 
 TRP   0.011   0.001   TRP a 218 
 HIS   0.002   0.001   HIS a 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 ( 8257)
  covalent geometry    : angle       0.54412 (11218)
  hydrogen bonds       : bond        0.04947 (  786)
  hydrogen bonds       : angle       4.27983 ( 2349)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   75 MET cc_start: 0.8522 (tmm) cc_final: 0.8228 (tmm)
  outliers start: 9
  outliers final: 9
  residues processed: 85
  average time/residue: 0.1773
  time to fit residues: 21.7373
Evaluate side-chains
  80 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   41 SER
Chi-restraints excluded: chain M residue   71 ASN
Chi-restraints excluded: chain N residue   61 VAL
Chi-restraints excluded: chain O residue   72 LEU
Chi-restraints excluded: chain R residue   55 THR
Chi-restraints excluded: chain a residue  192 ASN
Chi-restraints excluded: chain a residue  198 ILE
Chi-restraints excluded: chain a residue  242 SER
Chi-restraints excluded: chain b residue   76 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 99 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** S  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.088762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.081990 restraints weight = 62279.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.084277 restraints weight = 23223.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.085679 restraints weight = 10937.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.086507 restraints weight = 6250.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.086988 restraints weight = 4036.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.1396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8257  Z= 0.179
  Angle     :  0.518   6.929  11218  Z= 0.281
  Chirality :  0.039   0.140   1322
  Planarity :  0.004   0.046   1440
  Dihedral  :  3.686  14.923   1149
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  8.16 %
    Favored  : 90.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.53 (0.26), residues: 1094
  helix:  2.35 (0.17), residues: 951
  sheet: -1.03 (1.99), residues: 10
  loop :  2.81 (0.65), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG M  45 
 TYR   0.020   0.001   TYR a 145 
 PHE   0.018   0.001   PHE M  58 
 TRP   0.013   0.001   TRP a 218 
 HIS   0.002   0.001   HIS d  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 8257)
  covalent geometry    : angle       0.51814 (11218)
  hydrogen bonds       : bond        0.04755 (  786)
  hydrogen bonds       : angle       4.11202 ( 2349)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   75 MET cc_start: 0.8540 (tmm) cc_final: 0.8242 (tmm)
REVERT: Q   75 MET cc_start: 0.8678 (tmm) cc_final: 0.8252 (tmm)
  outliers start: 10
  outliers final: 8
  residues processed: 84
  average time/residue: 0.1850
  time to fit residues: 22.2249
Evaluate side-chains
  80 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   41 SER
Chi-restraints excluded: chain N residue   61 VAL
Chi-restraints excluded: chain O residue   72 LEU
Chi-restraints excluded: chain R residue   55 THR
Chi-restraints excluded: chain a residue  192 ASN
Chi-restraints excluded: chain a residue  198 ILE
Chi-restraints excluded: chain a residue  242 SER
Chi-restraints excluded: chain b residue   76 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 52 optimal weight:    0.2980
   chunk 105 optimal weight:    1.9990
   chunk 53 optimal weight:    0.2980
   chunk 40 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** a 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.089314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.082542 restraints weight = 62466.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.084860 restraints weight = 23197.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.086114 restraints weight = 10858.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.086999 restraints weight = 6517.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.087474 restraints weight = 4172.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.1535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8257  Z= 0.158
  Angle     :  0.495   5.778  11218  Z= 0.265
  Chirality :  0.038   0.136   1322
  Planarity :  0.004   0.045   1440
  Dihedral  :  3.608  14.630   1149
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  9.20 %
    Favored  : 89.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.83 (0.26), residues: 1094
  helix:  2.55 (0.17), residues: 951
  sheet: -1.06 (1.97), residues: 10
  loop :  2.88 (0.65), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG M  45 
 TYR   0.022   0.001   TYR a 145 
 PHE   0.017   0.001   PHE M  58 
 TRP   0.013   0.001   TRP a 218 
 HIS   0.002   0.001   HIS d  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 8257)
  covalent geometry    : angle       0.49494 (11218)
  hydrogen bonds       : bond        0.04494 (  786)
  hydrogen bonds       : angle       3.97104 ( 2349)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   75 MET cc_start: 0.8578 (tmm) cc_final: 0.8276 (tmm)
REVERT: M   75 MET cc_start: 0.8722 (tmm) cc_final: 0.8409 (tmm)
REVERT: P   75 MET cc_start: 0.8379 (ttp) cc_final: 0.8108 (ttp)
REVERT: Q   75 MET cc_start: 0.8697 (tmm) cc_final: 0.8285 (tmm)
REVERT: a   76 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7799 (mp10)
  outliers start: 7
  outliers final: 7
  residues processed: 86
  average time/residue: 0.1955
  time to fit residues: 23.7566
Evaluate side-chains
  83 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   41 SER
Chi-restraints excluded: chain N residue   61 VAL
Chi-restraints excluded: chain O residue   72 LEU
Chi-restraints excluded: chain R residue   55 THR
Chi-restraints excluded: chain a residue  192 ASN
Chi-restraints excluded: chain a residue  242 SER
Chi-restraints excluded: chain b residue   76 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 84 optimal weight:    0.6980
   chunk 96 optimal weight:    0.9980
   chunk 89 optimal weight:    0.5980
   chunk 53 optimal weight:    0.1980
   chunk 82 optimal weight:    0.0870
   chunk 52 optimal weight:    0.1980
   chunk 61 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.3358

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

Flipped N/Q/H residues before XYZ refinement:
** a 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.090482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.083720 restraints weight = 61143.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.086039 restraints weight = 22486.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.087379 restraints weight = 10465.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.088252 restraints weight = 6041.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.088734 restraints weight = 3866.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.1675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8257  Z= 0.126
  Angle     :  0.479   5.457  11218  Z= 0.251
  Chirality :  0.039   0.138   1322
  Planarity :  0.004   0.044   1440
  Dihedral  :  3.534  14.618   1149
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 10.49 %
    Favored  : 88.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.24 (0.25), residues: 1094
  helix:  2.97 (0.17), residues: 907
  sheet: -1.08 (1.92), residues: 10
  loop :  2.21 (0.55), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG M  52 
 TYR   0.022   0.001   TYR a 145 
 PHE   0.016   0.001   PHE M  58 
 TRP   0.013   0.001   TRP a 218 
 HIS   0.003   0.001   HIS a 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 8257)
  covalent geometry    : angle       0.47874 (11218)
  hydrogen bonds       : bond        0.04274 (  786)
  hydrogen bonds       : angle       3.82617 ( 2349)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   75 MET cc_start: 0.8596 (tmm) cc_final: 0.8287 (tmm)
REVERT: M   75 MET cc_start: 0.8649 (tmm) cc_final: 0.8291 (tmm)
REVERT: P   75 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8203 (ttp)
REVERT: Q   75 MET cc_start: 0.8702 (tmm) cc_final: 0.8295 (tmm)
REVERT: a   76 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7770 (mp10)
  outliers start: 4
  outliers final: 2
  residues processed: 83
  average time/residue: 0.1834
  time to fit residues: 21.8580
Evaluate side-chains
  79 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   75 MET
Chi-restraints excluded: chain a residue  192 ASN
Chi-restraints excluded: chain b residue   76 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 97 optimal weight:    0.2980
   chunk 91 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 70 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9990
   chunk 40 optimal weight:    0.5980
   chunk 60 optimal weight:    0.5980
   chunk 80 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 59 optimal weight:    0.2980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** a 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.090363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.083575 restraints weight = 61464.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.085927 restraints weight = 22703.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.087297 restraints weight = 10512.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.088125 restraints weight = 6006.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.088606 restraints weight = 3858.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.1771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8257  Z= 0.139
  Angle     :  0.484   5.251  11218  Z= 0.255
  Chirality :  0.038   0.135   1322
  Planarity :  0.004   0.041   1440
  Dihedral  :  3.482  14.407   1149
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 10.88 %
    Favored  : 88.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.33 (0.25), residues: 1094
  helix:  3.05 (0.16), residues: 907
  sheet: -1.19 (1.88), residues: 10
  loop :  2.15 (0.55), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG M  52 
 TYR   0.023   0.001   TYR a 145 
 PHE   0.016   0.001   PHE M  58 
 TRP   0.012   0.001   TRP a 218 
 HIS   0.003   0.001   HIS a 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8257)
  covalent geometry    : angle       0.48361 (11218)
  hydrogen bonds       : bond        0.04227 (  786)
  hydrogen bonds       : angle       3.79015 ( 2349)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   75 MET cc_start: 0.8590 (tmm) cc_final: 0.8290 (tmm)
REVERT: M   75 MET cc_start: 0.8633 (tmm) cc_final: 0.8261 (tmm)
REVERT: P   75 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8188 (ttp)
REVERT: Q   75 MET cc_start: 0.8758 (tmm) cc_final: 0.8360 (tmm)
REVERT: a   76 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7790 (mp10)
  outliers start: 6
  outliers final: 4
  residues processed: 83
  average time/residue: 0.1719
  time to fit residues: 20.4979
Evaluate side-chains
  85 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   75 MET
Chi-restraints excluded: chain Q residue   63 LEU
Chi-restraints excluded: chain a residue  192 ASN
Chi-restraints excluded: chain a residue  242 SER
Chi-restraints excluded: chain b residue   76 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 96 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 105 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** a 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.089274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.082476 restraints weight = 62470.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.084771 restraints weight = 23220.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.086124 restraints weight = 10902.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.086986 restraints weight = 6317.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.087488 restraints weight = 4071.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8257  Z= 0.186
  Angle     :  0.507   5.395  11218  Z= 0.272
  Chirality :  0.038   0.133   1322
  Planarity :  0.004   0.043   1440
  Dihedral  :  3.517  14.787   1149
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 10.62 %
    Favored  : 88.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.19 (0.25), residues: 1094
  helix:  2.95 (0.16), residues: 907
  sheet: -1.21 (1.92), residues: 10
  loop :  2.12 (0.55), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG a 153 
 TYR   0.023   0.001   TYR a 145 
 PHE   0.017   0.001   PHE M  58 
 TRP   0.010   0.001   TRP a 218 
 HIS   0.002   0.001   HIS d  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 8257)
  covalent geometry    : angle       0.50700 (11218)
  hydrogen bonds       : bond        0.04368 (  786)
  hydrogen bonds       : angle       3.84859 ( 2349)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   75 MET cc_start: 0.8594 (tmm) cc_final: 0.8302 (tmm)
REVERT: M   75 MET cc_start: 0.8648 (tmm) cc_final: 0.8256 (tmm)
REVERT: P   75 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8176 (ttp)
REVERT: Q   75 MET cc_start: 0.8794 (tmm) cc_final: 0.8400 (tmm)
REVERT: a   76 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7815 (mp10)
  outliers start: 9
  outliers final: 8
  residues processed: 85
  average time/residue: 0.1886
  time to fit residues: 22.9585
Evaluate side-chains
  88 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   41 SER
Chi-restraints excluded: chain O residue   72 LEU
Chi-restraints excluded: chain P residue   75 MET
Chi-restraints excluded: chain Q residue   63 LEU
Chi-restraints excluded: chain R residue   55 THR
Chi-restraints excluded: chain a residue  179 LEU
Chi-restraints excluded: chain a residue  192 ASN
Chi-restraints excluded: chain a residue  242 SER
Chi-restraints excluded: chain b residue   76 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 45 optimal weight:    0.4980
   chunk 40 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 95 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 34 optimal weight:    0.4980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** a 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.090221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.083403 restraints weight = 62053.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.085714 restraints weight = 23053.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.087135 restraints weight = 10821.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.087974 restraints weight = 6169.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.088453 restraints weight = 3975.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.1844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8257  Z= 0.150
  Angle     :  0.491   5.595  11218  Z= 0.260
  Chirality :  0.038   0.136   1322
  Planarity :  0.004   0.043   1440
  Dihedral  :  3.501  14.965   1149
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 11.01 %
    Favored  : 87.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.28 (0.25), residues: 1094
  helix:  3.02 (0.16), residues: 907
  sheet: -1.12 (1.90), residues: 10
  loop :  2.06 (0.54), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG M  52 
 TYR   0.022   0.001   TYR a 145 
 PHE   0.017   0.001   PHE M  58 
 TRP   0.011   0.001   TRP a 218 
 HIS   0.002   0.001   HIS a 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8257)
  covalent geometry    : angle       0.49103 (11218)
  hydrogen bonds       : bond        0.04275 (  786)
  hydrogen bonds       : angle       3.78502 ( 2349)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   75 MET cc_start: 0.8595 (tmm) cc_final: 0.8310 (tmm)
REVERT: M   75 MET cc_start: 0.8586 (tmm) cc_final: 0.8192 (tmm)
REVERT: P   75 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8207 (ttp)
REVERT: Q   75 MET cc_start: 0.8793 (tmm) cc_final: 0.8409 (tmm)
  outliers start: 8
  outliers final: 7
  residues processed: 89
  average time/residue: 0.1822
  time to fit residues: 23.3360
Evaluate side-chains
  86 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   41 SER
Chi-restraints excluded: chain O residue   72 LEU
Chi-restraints excluded: chain P residue   75 MET
Chi-restraints excluded: chain Q residue   63 LEU
Chi-restraints excluded: chain a residue  179 LEU
Chi-restraints excluded: chain a residue  192 ASN
Chi-restraints excluded: chain a residue  242 SER
Chi-restraints excluded: chain b residue   76 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 80 optimal weight:    0.0970
   chunk 81 optimal weight:    0.5980
   chunk 96 optimal weight:    0.2980
   chunk 51 optimal weight:    0.9980
   chunk 89 optimal weight:    0.0870
   chunk 41 optimal weight:    1.9990
   chunk 103 optimal weight:    0.5980
   chunk 84 optimal weight:    0.6980
   chunk 72 optimal weight:    0.7980
   overall best weight:    0.3356

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

Flipped N/Q/H residues before XYZ refinement:
a  72 GLN
** a 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
d  58 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.090978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.084247 restraints weight = 61036.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.086578 restraints weight = 22346.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.087960 restraints weight = 10341.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.088804 restraints weight = 5875.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.089195 restraints weight = 3762.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8257  Z= 0.125
  Angle     :  0.487   7.901  11218  Z= 0.254
  Chirality :  0.039   0.186   1322
  Planarity :  0.004   0.041   1440
  Dihedral  :  3.464  15.020   1149
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 11.40 %
    Favored  : 87.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.27 (0.26), residues: 1094
  helix:  2.87 (0.17), residues: 952
  sheet: -1.10 (1.87), residues: 10
  loop :  2.88 (0.65), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG M  52 
 TYR   0.021   0.001   TYR a 145 
 PHE   0.016   0.001   PHE M  58 
 TRP   0.012   0.001   TRP a 218 
 HIS   0.003   0.001   HIS a 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 8257)
  covalent geometry    : angle       0.48706 (11218)
  hydrogen bonds       : bond        0.04139 (  786)
  hydrogen bonds       : angle       3.72697 ( 2349)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   75 MET cc_start: 0.8616 (tmm) cc_final: 0.8326 (tmm)
REVERT: M   75 MET cc_start: 0.8584 (tmm) cc_final: 0.8200 (tmm)
REVERT: P   75 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8203 (ttp)
REVERT: Q   75 MET cc_start: 0.8819 (tmm) cc_final: 0.8426 (tmm)
  outliers start: 6
  outliers final: 5
  residues processed: 83
  average time/residue: 0.2017
  time to fit residues: 23.3718
Evaluate side-chains
  83 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   41 SER
Chi-restraints excluded: chain P residue   75 MET
Chi-restraints excluded: chain Q residue   63 LEU
Chi-restraints excluded: chain a residue  179 LEU
Chi-restraints excluded: chain a residue  192 ASN
Chi-restraints excluded: chain a residue  242 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0970
   chunk 31 optimal weight:    0.9990
   chunk 99 optimal weight:    1.9990
   chunk 101 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 80 optimal weight:    0.2980
   chunk 68 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** a 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.089996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.083235 restraints weight = 61698.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.085549 restraints weight = 22670.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.086904 restraints weight = 10500.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.087741 restraints weight = 6037.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.088235 restraints weight = 3911.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8257  Z= 0.169
  Angle     :  0.505   6.365  11218  Z= 0.269
  Chirality :  0.038   0.134   1322
  Planarity :  0.004   0.042   1440
  Dihedral  :  3.478  15.185   1149
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 11.92 %
    Favored  : 87.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.16 (0.26), residues: 1094
  helix:  2.79 (0.16), residues: 952
  sheet:  None (None), residues: 0
  loop :  2.54 (0.63), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG M  45 
 TYR   0.022   0.001   TYR a 145 
 PHE   0.016   0.001   PHE M  58 
 TRP   0.009   0.001   TRP a 218 
 HIS   0.002   0.001   HIS a 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 8257)
  covalent geometry    : angle       0.50495 (11218)
  hydrogen bonds       : bond        0.04267 (  786)
  hydrogen bonds       : angle       3.78049 ( 2349)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2336.98 seconds
wall clock time: 40 minutes 33.07 seconds (2433.07 seconds total)