Starting phenix.real_space_refine
on Sat Sep 12 02:22:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ohb_12899/09_2026/7ohb_12899.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ohb_12899/09_2026/7ohb_12899.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ohb_12899/09_2026/7ohb_12899.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ohb_12899/09_2026/7ohb_12899.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ohb_12899/09_2026/7ohb_12899.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ohb_12899/09_2026/7ohb_12899.map"
  }
  resolution = 3.4
  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=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     290      5.49       5
     S      18      5.16       5
     C    7560      2.51       5
     N    2501      2.21       5
     O    3055      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 13424
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    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: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 834
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 756
          Classifications: {'peptide': 96}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
    Chain: "E"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 627
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "G"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 834
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 746
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 2955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2955
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2990
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2990
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "K"
      Number of atoms: 1416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 180, 1416
          Classifications: {'peptide': 180}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 171}
  Time building chain proxies: 2.77, per 1000 atoms: 0.21
  Number of scatterers: 13424
  At special positions: 0
  Unit cell: (92.4, 116.55, 133.35, 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      18     16.00
     P     290     15.00
     O    3055      8.00
     N    2501      7.00
     C    7560      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.88
  Conformation dependent library (CDL) restraints added in 405.1 milliseconds
  

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1768

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 10 sheets defined
      64.8% alpha, 7.2% beta
      144 base pairs and 266 stacking pairs defined.
    Time for finding SS restraints: 1.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.991A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.807A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 92
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.318A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 100 through 121
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 4.144A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.853A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.563A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 21
      removed outlier: 3.590A  pdb=" N   ARG G  20 " --> pdb=" O   THR G  16 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.377A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 121
    Processing helix  chain 'K' and resid 81 through 88
      removed outlier: 3.649A  pdb=" N   VAL K  85 " --> pdb=" O   ASP K  81 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 128 through 147
    Processing helix  chain 'K' and resid 171 through 179
      removed outlier: 3.599A  pdb=" N   LEU K 175 " --> pdb=" O   ARG K 171 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 219 through 236
      removed outlier: 4.087A  pdb=" N   ILE K 223 " --> pdb=" O   GLN K 219 " (cutoff:3.500A)
      Proline residue:  K 232  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.004A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.471A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.132A  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
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.998A  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: 7.512A  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 'K' and resid 92 through 93
      removed outlier: 3.602A  pdb=" N   VAL K 102 " --> pdb=" O   ILE K 115 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   THR K 124 " --> pdb=" O   THR K 112 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   LYS K 120 " --> pdb=" O   PHE K 116 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   GLY K 125 " --> pdb=" O   ILE K  70 " (cutoff:3.500A)
      removed outlier: 5.381A  pdb=" N   ILE K  70 " --> pdb=" O   GLY K 125 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   VAL K 161 " --> pdb=" O   GLN K  68 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   ILE K  70 " --> pdb=" O   ASN K 159 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   ASN K 159 " --> pdb=" O   ILE K  70 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   ALA K  72 " --> pdb=" O   ILE K 157 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   ILE K 157 " --> pdb=" O   ALA K  72 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   VAL K  74 " --> pdb=" O   PHE K 155 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   PHE K 155 " --> pdb=" O   VAL K  74 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ILE K 212 " --> pdb=" O   CYS K 164 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   VAL K 213 " --> pdb=" O   LEU K 205 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LEU K 205 " --> pdb=" O   VAL K 213 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   THR K 215 " --> pdb=" O   VAL K 203 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   VAL K 203 " --> pdb=" O   THR K 215 " (cutoff:3.500A)

    472 hydrogen bonds defined for protein.
    1389 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      368 hydrogen bonds
      736 hydrogen bond angles
      0 basepair planarities
      144 basepair parallelities
      266 stacking parallelities
  Total time for adding SS restraints: 2.56

  Time building geometry restraints manager: 1.26 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2665
        1.33 -     1.45: 4528
        1.45 -     1.57: 6451
        1.57 -     1.69: 578
        1.69 -     1.82: 32
  Bond restraints: 14254
  Sorted by residual:
  bond pdb=" C3'  DT I  60 "
       pdb=" O3'  DT I  60 "
    ideal  model  delta    sigma   weight residual
    1.435  1.519 -0.084 1.30e-02 5.92e+03 4.21e+01
  bond pdb=" C5'  DA I  61 "
       pdb=" C4'  DA I  61 "
    ideal  model  delta    sigma   weight residual
    1.512  1.548 -0.036 7.00e-03 2.04e+04 2.62e+01
  bond pdb=" C3'  DG J -22 "
       pdb=" C2'  DG J -22 "
    ideal  model  delta    sigma   weight residual
    1.516  1.546 -0.030 8.00e-03 1.56e+04 1.43e+01
  bond pdb=" C3'  DC J  30 "
       pdb=" C2'  DC J  30 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.17e+01
  bond pdb=" C3'  DC I  21 "
       pdb=" C2'  DC I  21 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.11e+01
  ... (remaining 14249 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 19333
        2.06 -     4.11: 1071
        4.11 -     6.17: 62
        6.17 -     8.22: 17
        8.22 -    10.28: 3
  Bond angle restraints: 20486
  Sorted by residual:
  angle pdb=" O4'  DT I  60 "
        pdb=" C1'  DT I  60 "
        pdb=" N1   DT I  60 "
      ideal   model   delta    sigma   weight residual
     108.00  113.45   -5.45 7.00e-01 2.04e+00 6.06e+01
  angle pdb=" O5'  DA I  61 "
        pdb=" C5'  DA I  61 "
        pdb=" C4'  DA I  61 "
      ideal   model   delta    sigma   weight residual
     109.40  114.72   -5.32 8.00e-01 1.56e+00 4.42e+01
  angle pdb=" O4'  DA I  17 "
        pdb=" C1'  DA I  17 "
        pdb=" N9   DA I  17 "
      ideal   model   delta    sigma   weight residual
     108.00  103.35    4.65 7.00e-01 2.04e+00 4.41e+01
  angle pdb=" O5'  DA I -45 "
        pdb=" C5'  DA I -45 "
        pdb=" C4'  DA I -45 "
      ideal   model   delta    sigma   weight residual
     109.40  113.91   -4.51 8.00e-01 1.56e+00 3.17e+01
  angle pdb=" O4'  DG I  47 "
        pdb=" C1'  DG I  47 "
        pdb=" N9   DG I  47 "
      ideal   model   delta    sigma   weight residual
     108.00  104.29    3.71 7.00e-01 2.04e+00 2.81e+01
  ... (remaining 20481 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.96: 5269
       20.96 -    41.91: 1340
       41.91 -    62.87: 1178
       62.87 -    83.83: 66
       83.83 -   104.78: 6
  Dihedral angle restraints: 7859
    sinusoidal: 5121
      harmonic: 2738
  Sorted by residual:
  dihedral pdb=" CA  GLU K 108 "
           pdb=" C   GLU K 108 "
           pdb=" N   PRO K 109 "
           pdb=" CA  PRO K 109 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00  -39.57   39.57     0      5.00e+00 4.00e-02 6.26e+01
  dihedral pdb=" CA  PRO D 100 "
           pdb=" C   PRO D 100 "
           pdb=" N   GLY D 101 "
           pdb=" CA  GLY D 101 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.58  -21.42     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  LYS K 199 "
           pdb=" C   LYS K 199 "
           pdb=" N   PRO K 200 "
           pdb=" CA  PRO K 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.94   20.06     0      5.00e+00 4.00e-02 1.61e+01
  ... (remaining 7856 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 2001
       0.073 -    0.146: 306
       0.146 -    0.218: 23
       0.218 -    0.291: 4
       0.291 -    0.364: 2
  Chirality restraints: 2336
  Sorted by residual:
  chirality pdb=" C1'  DT I  60 "
            pdb=" O4'  DT I  60 "
            pdb=" C2'  DT I  60 "
            pdb=" N1   DT I  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.07    0.36 2.00e-01 2.50e+01 3.31e+00
  chirality pdb=" CB  ILE K 212 "
            pdb=" CA  ILE K 212 "
            pdb=" CG1 ILE K 212 "
            pdb=" CG2 ILE K 212 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.29 2.00e-01 2.50e+01 2.14e+00
  chirality pdb=" CB  THR K 111 "
            pdb=" CA  THR K 111 "
            pdb=" OG1 THR K 111 "
            pdb=" CG2 THR K 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.29    0.27 2.00e-01 2.50e+01 1.77e+00
  ... (remaining 2333 not shown)

  Planarity restraints: 1584
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL G  27 "   -0.017 2.00e-02 2.50e+03   3.33e-02 1.11e+01
        pdb=" C   VAL G  27 "    0.058 2.00e-02 2.50e+03
        pdb=" O   VAL G  27 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   GLY G  28 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I  60 "    0.006 2.00e-02 2.50e+03   1.84e-02 8.44e+00
        pdb=" N1   DT I  60 "   -0.037 2.00e-02 2.50e+03
        pdb=" C2   DT I  60 "    0.041 2.00e-02 2.50e+03
        pdb=" O2   DT I  60 "   -0.008 2.00e-02 2.50e+03
        pdb=" N3   DT I  60 "   -0.009 2.00e-02 2.50e+03
        pdb=" C4   DT I  60 "    0.004 2.00e-02 2.50e+03
        pdb=" O4   DT I  60 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5   DT I  60 "    0.004 2.00e-02 2.50e+03
        pdb=" C7   DT I  60 "    0.005 2.00e-02 2.50e+03
        pdb=" C6   DT I  60 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE G  79 "    0.046 5.00e-02 4.00e+02   7.00e-02 7.84e+00
        pdb=" N   PRO G  80 "   -0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO G  80 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO G  80 "    0.039 5.00e-02 4.00e+02
  ... (remaining 1581 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2703
        2.78 -     3.31: 11633
        3.31 -     3.84: 27034
        3.84 -     4.37: 31845
        4.37 -     4.90: 45229
  Nonbonded interactions: 118444
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D  29 "
            pdb=" OP1  DT I  30 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OG1 THR H  87 "
            pdb=" OE1 GLU H  90 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   GLY K 174 "
            pdb=" OG  SER K 178 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" NE2 GLN G  24 "
            pdb=" OE1 GLN H  44 "
     model   vdw
     2.302 3.120
  nonbonded pdb=" OD2 ASP E 106 "
            pdb=" NH1 ARG E 131 "
     model   vdw
     2.322 3.120
  ... (remaining 118439 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'
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 24 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 27 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=0.00 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     13.240
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
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      :  0.006   0.084  14254  Z= 0.541
  Angle     :  0.964  10.276  20486  Z= 0.765
  Chirality :  0.053   0.364   2336
  Planarity :  0.007   0.070   1584
  Dihedral  : 28.695 104.782   6091
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  4.32 %
    Favored  : 94.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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: -2.05 (0.23), residues: 925
  helix: -1.01 (0.18), residues: 588
  sheet: -0.37 (0.82), residues: 41
  loop : -1.97 (0.29), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG H  96 
 TYR   0.039   0.002   TYR G  50 
 PHE   0.025   0.002   PHE K  99 
 HIS   0.005   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00643 /  0.54 (14254)
  covalent geometry    : angle       0.96420 /  0.77 (20486)
  hydrogen bonds       : bond        0.12750 /  8.33 (  840)
  hydrogen bonds       : angle       5.17632 /  3.73 ( 2125)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 192
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.7946 (t0) cc_final: 0.7505 (t70)
REVERT: B   25 ASN cc_start: 0.8125 (m-40) cc_final: 0.7878 (m110)
REVERT: C   36 LYS cc_start: 0.8709 (mmtp) cc_final: 0.8461 (mmmm)
REVERT: C   74 LYS cc_start: 0.8764 (mppt) cc_final: 0.8531 (mptt)
REVERT: E  106 ASP cc_start: 0.7443 (m-30) cc_final: 0.7178 (m-30)
REVERT: F   74 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7766 (mt-10)
REVERT: G   91 GLU cc_start: 0.8047 (tt0) cc_final: 0.7818 (tt0)
REVERT: H   33 SER cc_start: 0.8880 (t) cc_final: 0.8493 (p)
REVERT: H   34 TYR cc_start: 0.8858 (m-80) cc_final: 0.8608 (m-80)
REVERT: K   69 ASN cc_start: 0.7863 (t0) cc_final: 0.6797 (m110)
REVERT: K  121 MET cc_start: 0.7527 (tpt) cc_final: 0.7034 (mtm)
  outliers start: 7
  outliers final: 1
  residues processed: 196
  average time/residue: 0.1417
  time to fit residues: 37.9923
Evaluate side-chains
  146 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:   20.0000
   chunk 113 optimal weight:   20.0000
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:   10.0000
   overall best weight:    1.0182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E  76 GLN
E 113 HIS
F  93 GLN
G 112 GLN
H  81 ASN
K  95 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.090987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.055379 restraints weight = 38266.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.2877 rms_B_bonded: 2.04
r_work: 0.2667 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8805
moved from start:          0.1304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14254  Z= 0.159
  Angle     :  0.700   8.302  20486  Z= 0.398
  Chirality :  0.048   0.225   2336
  Planarity :  0.005   0.048   1584
  Dihedral  : 31.656  98.848   4227
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 10.93 %
    Favored  : 87.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.01 (0.25), residues: 925
  helix:  0.83 (0.20), residues: 601
  sheet:  0.10 (0.72), residues: 47
  loop : -1.78 (0.31), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  40 
 TYR   0.018   0.002   TYR K 231 
 PHE   0.012   0.001   PHE D  62 
 HIS   0.014   0.001   HIS D 106 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.16 (14254)
  covalent geometry    : angle       0.70004 /  0.40 (20486)
  hydrogen bonds       : bond        0.04738 /  3.18 (  840)
  hydrogen bonds       : angle       3.68686 /  2.66 ( 2125)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 155
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8964 (pm20) cc_final: 0.8575 (pm20)
REVERT: A   81 ASP cc_start: 0.8703 (t0) cc_final: 0.8338 (t70)
REVERT: B   25 ASN cc_start: 0.8207 (m-40) cc_final: 0.7886 (m110)
REVERT: C   74 LYS cc_start: 0.8980 (mppt) cc_final: 0.8753 (mptt)
REVERT: F   74 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8482 (mt-10)
REVERT: H   30 ARG cc_start: 0.8215 (mtp85) cc_final: 0.7952 (mtp85)
REVERT: H   33 SER cc_start: 0.8837 (t) cc_final: 0.8464 (p)
REVERT: H  105 LYS cc_start: 0.8831 (mmtt) cc_final: 0.8600 (mmtm)
REVERT: K   69 ASN cc_start: 0.7845 (t0) cc_final: 0.6544 (m110)
  outliers start: 11
  outliers final: 8
  residues processed: 160
  average time/residue: 0.1243
  time to fit residues: 27.9798
Evaluate side-chains
  149 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 141
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain K residue  164 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 64 optimal weight:    5.9990
   chunk 91 optimal weight:   20.0000
   chunk 84 optimal weight:   40.0000
   chunk 45 optimal weight:    0.4980
   chunk 43 optimal weight:    4.9990
   chunk 104 optimal weight:   50.0000
   chunk 87 optimal weight:   20.0000
   chunk 34 optimal weight:    2.9990
   overall best weight:    1.8386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  93 GLN
** G  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  38 ASN
G 112 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.090029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.053863 restraints weight = 38220.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.2827 rms_B_bonded: 2.07
r_work: 0.2614 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8835
moved from start:          0.1717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  14254  Z= 0.192
  Angle     :  0.658   8.042  20486  Z= 0.377
  Chirality :  0.046   0.224   2336
  Planarity :  0.005   0.047   1584
  Dihedral  : 31.388  92.832   4226
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 13.60 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.92 (0.27), residues: 925
  helix:  1.61 (0.21), residues: 599
  sheet:  0.10 (0.70), residues: 47
  loop : -1.54 (0.33), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  40 
 TYR   0.016   0.002   TYR K 139 
 PHE   0.011   0.001   PHE K  99 
 HIS   0.004   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00393 /  0.19 (14254)
  covalent geometry    : angle       0.65848 /  0.38 (20486)
  hydrogen bonds       : bond        0.04515 /  3.02 (  840)
  hydrogen bonds       : angle       3.38648 /  2.44 ( 2125)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 149
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9093 (pm20) cc_final: 0.8605 (pm20)
REVERT: A   81 ASP cc_start: 0.8707 (t0) cc_final: 0.8363 (t70)
REVERT: C   74 LYS cc_start: 0.9109 (mppt) cc_final: 0.8851 (mptt)
REVERT: D   30 ARG cc_start: 0.8048 (mtm110) cc_final: 0.7757 (ttm170)
REVERT: E  115 LYS cc_start: 0.9211 (mmtp) cc_final: 0.8986 (mmtp)
REVERT: F   74 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8493 (mt-10)
REVERT: H   33 SER cc_start: 0.8951 (t) cc_final: 0.8652 (p)
REVERT: K  195 TYR cc_start: 0.8396 (t80) cc_final: 0.7900 (t80)
  outliers start: 13
  outliers final: 11
  residues processed: 157
  average time/residue: 0.1325
  time to fit residues: 28.9805
Evaluate side-chains
  147 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 136
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain D residue   65 ASP
Chi-restraints excluded: chain D residue   88 SER
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue   57 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 111 optimal weight:    8.9990
   chunk 34 optimal weight:    0.9980
   chunk 112 optimal weight:   20.0000
   chunk 98 optimal weight:   30.0000
   chunk 18 optimal weight:    3.9990
   chunk 68 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 99 optimal weight:   10.0000
   chunk 12 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   overall best weight:    1.5184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 113 HIS
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 159 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.089998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.053662 restraints weight = 38291.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.2826 rms_B_bonded: 2.01
r_work: 0.2616 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8835
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14254  Z= 0.168
  Angle     :  0.638   9.269  20486  Z= 0.367
  Chirality :  0.045   0.228   2336
  Planarity :  0.004   0.044   1584
  Dihedral  : 31.211  93.305   4226
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 15.88 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.25 (0.27), residues: 925
  helix:  1.91 (0.21), residues: 599
  sheet: -0.01 (0.70), residues: 47
  loop : -1.50 (0.33), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  29 
 TYR   0.013   0.001   TYR H  37 
 PHE   0.009   0.001   PHE A  67 
 HIS   0.006   0.001   HIS D 106 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.17 (14254)
  covalent geometry    : angle       0.63779 /  0.37 (20486)
  hydrogen bonds       : bond        0.04171 /  2.82 (  840)
  hydrogen bonds       : angle       3.26153 /  2.35 ( 2125)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 148
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9104 (pm20) cc_final: 0.8613 (pm20)
REVERT: A   76 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8487 (mm-40)
REVERT: A   81 ASP cc_start: 0.8691 (t0) cc_final: 0.8383 (t70)
REVERT: D   30 ARG cc_start: 0.8046 (mtm110) cc_final: 0.7661 (mtm-85)
REVERT: E  115 LYS cc_start: 0.9195 (mmtp) cc_final: 0.8985 (mmtp)
REVERT: F   74 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8505 (mt-10)
REVERT: H   30 ARG cc_start: 0.8252 (mtp85) cc_final: 0.7912 (mtp85)
REVERT: H   33 SER cc_start: 0.8969 (t) cc_final: 0.8735 (p)
REVERT: H   42 LEU cc_start: 0.9440 (tp) cc_final: 0.9225 (tp)
REVERT: K  195 TYR cc_start: 0.8447 (t80) cc_final: 0.7869 (t80)
  outliers start: 17
  outliers final: 10
  residues processed: 158
  average time/residue: 0.1296
  time to fit residues: 28.9072
Evaluate side-chains
  150 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 140
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain K residue  205 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 54 optimal weight:    0.4980
   chunk 41 optimal weight:    0.6980
   chunk 83 optimal weight:   20.0000
   chunk 62 optimal weight:    0.9980
   chunk 106 optimal weight:    9.9990
   chunk 63 optimal weight:    0.9980
   chunk 111 optimal weight:   30.0000
   chunk 39 optimal weight:    0.8980
   chunk 91 optimal weight:   10.0000
   chunk 88 optimal weight:   10.0000
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E  85 GLN
** G  24 GLN ** 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 = 0.3749 r_free = 0.3749 target = 0.090830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.054755 restraints weight = 38630.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.2857 rms_B_bonded: 1.99
r_work: 0.2650 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8807
moved from start:          0.2156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  14254  Z= 0.138
  Angle     :  0.612   8.460  20486  Z= 0.358
  Chirality :  0.044   0.217   2336
  Planarity :  0.004   0.043   1584
  Dihedral  : 30.956  94.389   4226
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 16.77 %
    Favored  : 81.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.56 (0.27), residues: 925
  helix:  2.18 (0.21), residues: 599
  sheet: -0.04 (0.69), residues: 47
  loop : -1.38 (0.34), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  83 
 TYR   0.021   0.001   TYR K 139 
 PHE   0.010   0.001   PHE E  67 
 HIS   0.004   0.001   HIS H 106 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00249 /  0.14 (14254)
  covalent geometry    : angle       0.61222 /  0.36 (20486)
  hydrogen bonds       : bond        0.03958 /  2.66 (  840)
  hydrogen bonds       : angle       3.11629 /  2.25 ( 2125)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 156
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9040 (pm20) cc_final: 0.8546 (pm20)
REVERT: A   76 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8481 (mm-40)
REVERT: A   81 ASP cc_start: 0.8651 (t0) cc_final: 0.8366 (t70)
REVERT: D   30 ARG cc_start: 0.7990 (mtm110) cc_final: 0.7672 (mtm-85)
REVERT: E  115 LYS cc_start: 0.9198 (mmtp) cc_final: 0.8988 (mmtp)
REVERT: F   24 ASP cc_start: 0.7469 (p0) cc_final: 0.7178 (p0)
REVERT: F   27 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8712 (mp10)
REVERT: F   74 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8446 (mt-10)
REVERT: H   33 SER cc_start: 0.8915 (t) cc_final: 0.8701 (p)
REVERT: H   42 LEU cc_start: 0.9375 (tp) cc_final: 0.9164 (tp)
REVERT: K   69 ASN cc_start: 0.7734 (t0) cc_final: 0.6392 (m110)
REVERT: K  195 TYR cc_start: 0.8427 (t80) cc_final: 0.7835 (t80)
  outliers start: 13
  outliers final: 11
  residues processed: 164
  average time/residue: 0.1295
  time to fit residues: 29.6112
Evaluate side-chains
  156 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 145
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain D residue   88 SER
Chi-restraints excluded: chain E residue   79 LYS
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue   68 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 104 optimal weight:   50.0000
   chunk 31 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 106 optimal weight:    7.9990
   chunk 13 optimal weight:    0.8980
   chunk 95 optimal weight:   10.0000
   chunk 59 optimal weight:    0.6980
   chunk 86 optimal weight:   30.0000
   chunk 68 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  92 GLN
F  93 GLN
** G  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 159 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.090921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.055010 restraints weight = 38141.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.2862 rms_B_bonded: 1.98
r_work: 0.2654 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8801
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14254  Z= 0.138
  Angle     :  0.609   8.512  20486  Z= 0.354
  Chirality :  0.043   0.215   2336
  Planarity :  0.004   0.039   1584
  Dihedral  : 30.858  94.337   4226
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.03 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.70 (0.27), residues: 925
  helix:  2.30 (0.21), residues: 599
  sheet: -0.21 (0.68), residues: 47
  loop : -1.34 (0.34), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  83 
 TYR   0.023   0.001   TYR K 139 
 PHE   0.010   0.001   PHE E  67 
 HIS   0.002   0.001   HIS H 106 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00251 /  0.14 (14254)
  covalent geometry    : angle       0.60860 /  0.35 (20486)
  hydrogen bonds       : bond        0.03907 /  2.63 (  840)
  hydrogen bonds       : angle       3.04085 /  2.19 ( 2125)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 148
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9056 (pm20) cc_final: 0.8617 (pm20)
REVERT: A   76 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8424 (mm-40)
REVERT: A   81 ASP cc_start: 0.8600 (t0) cc_final: 0.8290 (t0)
REVERT: D   30 ARG cc_start: 0.7981 (mtm110) cc_final: 0.7698 (mtm-85)
REVERT: E  115 LYS cc_start: 0.9193 (mmtp) cc_final: 0.8992 (mmtp)
REVERT: F   24 ASP cc_start: 0.7586 (p0) cc_final: 0.7362 (p0)
REVERT: F   27 GLN cc_start: 0.9022 (mm-40) cc_final: 0.8678 (mp10)
REVERT: F   74 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8436 (mt-10)
REVERT: H   30 ARG cc_start: 0.8181 (mtp85) cc_final: 0.7847 (mtp85)
REVERT: H   42 LEU cc_start: 0.9375 (tp) cc_final: 0.9174 (tp)
REVERT: H   43 LYS cc_start: 0.9061 (mmtm) cc_final: 0.8838 (mptt)
REVERT: K   69 ASN cc_start: 0.7915 (t0) cc_final: 0.6479 (m-40)
REVERT: K  195 TYR cc_start: 0.8440 (t80) cc_final: 0.7820 (t80)
  outliers start: 17
  outliers final: 13
  residues processed: 158
  average time/residue: 0.1282
  time to fit residues: 28.2182
Evaluate side-chains
  158 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 145
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain D residue   88 SER
Chi-restraints excluded: chain E residue   79 LYS
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain K residue  205 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 52 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 96 optimal weight:   20.0000
   chunk 105 optimal weight:   10.0000
   chunk 74 optimal weight:   20.0000
   chunk 48 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   chunk 85 optimal weight:   50.0000
   chunk 33 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  85 GLN
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  24 GLN ** 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 = 0.3703 r_free = 0.3703 target = 0.088486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.051832 restraints weight = 38246.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.2775 rms_B_bonded: 1.96
r_work: 0.2566 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8868
moved from start:          0.2515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.094  14254  Z= 0.286
  Angle     :  0.714   9.688  20486  Z= 0.395
  Chirality :  0.047   0.240   2336
  Planarity :  0.005   0.038   1584
  Dihedral  : 31.160  92.391   4226
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 17.53 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.20 (0.27), residues: 925
  helix:  1.89 (0.21), residues: 599
  sheet: -0.14 (0.68), residues: 47
  loop : -1.52 (0.33), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG G  29 
 TYR   0.015   0.002   TYR K 139 
 PHE   0.015   0.002   PHE E 104 
 HIS   0.007   0.001   HIS D  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00621 /  0.29 (14254)
  covalent geometry    : angle       0.71377 /  0.39 (20486)
  hydrogen bonds       : bond        0.04831 /  3.24 (  840)
  hydrogen bonds       : angle       3.33224 /  2.42 ( 2125)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 138
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9097 (pm20) cc_final: 0.8617 (pm20)
REVERT: A   76 GLN cc_start: 0.8954 (mm-40) cc_final: 0.8620 (mm-40)
REVERT: A   81 ASP cc_start: 0.8761 (t0) cc_final: 0.8438 (t70)
REVERT: F   74 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8555 (mt-10)
REVERT: H   48 ASP cc_start: 0.8203 (p0) cc_final: 0.7989 (p0)
REVERT: K  121 MET cc_start: 0.8298 (tpt) cc_final: 0.7485 (mpp)
REVERT: K  195 TYR cc_start: 0.8444 (t80) cc_final: 0.7982 (t80)
REVERT: K  199 LYS cc_start: 0.6924 (OUTLIER) cc_final: 0.6718 (pptt)
  outliers start: 23
  outliers final: 19
  residues processed: 154
  average time/residue: 0.1256
  time to fit residues: 26.9770
Evaluate side-chains
  155 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 135
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue   13 LYS
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain D residue   88 SER
Chi-restraints excluded: chain E residue   79 LYS
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   72 ASP
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain K residue  199 LYS
Chi-restraints excluded: chain K residue  205 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 73 optimal weight:   20.0000
   chunk 15 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   chunk 102 optimal weight:   10.0000
   chunk 105 optimal weight:   30.0000
   chunk 36 optimal weight:    6.9990
   chunk 90 optimal weight:   20.0000
   overall best weight:    0.8980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  92 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.090248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.053981 restraints weight = 38028.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.2832 rms_B_bonded: 1.98
r_work: 0.2625 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8823
moved from start:          0.2574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14254  Z= 0.143
  Angle     :  0.622   8.708  20486  Z= 0.359
  Chirality :  0.043   0.221   2336
  Planarity :  0.004   0.041   1584
  Dihedral  : 30.885  93.404   4226
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 19.06 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.56 (0.27), residues: 925
  helix:  2.19 (0.21), residues: 599
  sheet: -0.17 (0.69), residues: 47
  loop : -1.40 (0.34), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D  30 
 TYR   0.014   0.001   TYR G  57 
 PHE   0.009   0.001   PHE E  67 
 HIS   0.003   0.001   HIS H 106 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.14 (14254)
  covalent geometry    : angle       0.62166 /  0.36 (20486)
  hydrogen bonds       : bond        0.03861 /  2.59 (  840)
  hydrogen bonds       : angle       3.10579 /  2.25 ( 2125)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 146
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9029 (pm20) cc_final: 0.8626 (pm20)
REVERT: A   76 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8595 (mm-40)
REVERT: A   81 ASP cc_start: 0.8650 (t0) cc_final: 0.8377 (t70)
REVERT: C   91 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7784 (tp30)
REVERT: D   30 ARG cc_start: 0.8336 (mtm110) cc_final: 0.7935 (mtm180)
REVERT: F   74 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8458 (mt-10)
REVERT: H   30 ARG cc_start: 0.8295 (mtp85) cc_final: 0.8008 (mtp85)
REVERT: K  112 THR cc_start: 0.7068 (m) cc_final: 0.6834 (p)
REVERT: K  121 MET cc_start: 0.8363 (tpt) cc_final: 0.7683 (mmp)
REVERT: K  159 ASN cc_start: 0.7680 (t0) cc_final: 0.7243 (t0)
REVERT: K  195 TYR cc_start: 0.8470 (t80) cc_final: 0.7967 (t80)
  outliers start: 15
  outliers final: 11
  residues processed: 156
  average time/residue: 0.1401
  time to fit residues: 30.4549
Evaluate side-chains
  150 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 138
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain E residue   79 LYS
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain K residue  205 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 89 optimal weight:   20.0000
   chunk 48 optimal weight:    0.8980
   chunk 58 optimal weight:    6.9990
   chunk 107 optimal weight:    9.9990
   chunk 3 optimal weight:    0.6980
   chunk 23 optimal weight:    5.9990
   chunk 75 optimal weight:   20.0000
   chunk 16 optimal weight:    0.3980
   chunk 42 optimal weight:    0.6980
   chunk 9 optimal weight:    4.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 104 GLN
E  85 GLN
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 225 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.090698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.054478 restraints weight = 38523.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 1.99
r_work: 0.2639 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8813
moved from start:          0.2674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14254  Z= 0.139
  Angle     :  0.631   9.435  20486  Z= 0.361
  Chirality :  0.043   0.259   2336
  Planarity :  0.004   0.039   1584
  Dihedral  : 30.775  93.593   4226
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 19.44 %
    Favored  : 79.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.70 (0.27), residues: 925
  helix:  2.32 (0.21), residues: 599
  sheet: -0.23 (0.68), residues: 47
  loop : -1.40 (0.34), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  30 
 TYR   0.027   0.001   TYR K 231 
 PHE   0.011   0.001   PHE E  67 
 HIS   0.002   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.14 (14254)
  covalent geometry    : angle       0.63067 /  0.36 (20486)
  hydrogen bonds       : bond        0.03807 /  2.56 (  840)
  hydrogen bonds       : angle       3.05370 /  2.21 ( 2125)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 144
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9005 (pm20) cc_final: 0.8689 (pm20)
REVERT: A   76 GLN cc_start: 0.8870 (mm-40) cc_final: 0.8572 (mm-40)
REVERT: A   81 ASP cc_start: 0.8588 (t0) cc_final: 0.8273 (t0)
REVERT: C   91 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7728 (tp30)
REVERT: D   30 ARG cc_start: 0.8309 (mtm110) cc_final: 0.7907 (mtm180)
REVERT: D   73 GLU cc_start: 0.8988 (tp30) cc_final: 0.8698 (tp30)
REVERT: E   90 MET cc_start: 0.8852 (mmm) cc_final: 0.8496 (mmp)
REVERT: F   74 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8465 (mt-10)
REVERT: H   30 ARG cc_start: 0.8318 (mtp85) cc_final: 0.7995 (mtp85)
REVERT: K  112 THR cc_start: 0.7005 (m) cc_final: 0.6628 (m)
REVERT: K  121 MET cc_start: 0.8306 (tpt) cc_final: 0.7643 (mmp)
REVERT: K  195 TYR cc_start: 0.8394 (t80) cc_final: 0.7922 (t80)
  outliers start: 11
  outliers final: 10
  residues processed: 152
  average time/residue: 0.1374
  time to fit residues: 29.2604
Evaluate side-chains
  152 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 141
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain K residue  205 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 77 optimal weight:   20.0000
   chunk 79 optimal weight:    9.9990
   chunk 89 optimal weight:   20.0000
   chunk 81 optimal weight:   20.0000
   chunk 57 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 105 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 106 optimal weight:    8.9990
   chunk 110 optimal weight:    8.9990
   chunk 75 optimal weight:   20.0000
   overall best weight:    5.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  24 GLN ** 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 = 0.3681 r_free = 0.3681 target = 0.087381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.050291 restraints weight = 38622.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.2732 rms_B_bonded: 1.97
r_work: 0.2525 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8896
moved from start:          0.2846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.128  14254  Z= 0.423
  Angle     :  0.820  11.227  20486  Z= 0.439
  Chirality :  0.051   0.252   2336
  Planarity :  0.005   0.039   1584
  Dihedral  : 31.241  90.808   4226
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 19.06 %
    Favored  : 79.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.88 (0.27), residues: 925
  helix:  1.62 (0.20), residues: 605
  sheet: -0.33 (0.66), residues: 47
  loop : -1.64 (0.33), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B  39 
 TYR   0.019   0.002   TYR G  39 
 PHE   0.022   0.002   PHE G  25 
 HIS   0.007   0.002   HIS D  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00943 /  0.42 (14254)
  covalent geometry    : angle       0.82045 /  0.44 (20486)
  hydrogen bonds       : bond        0.05339 /  3.57 (  840)
  hydrogen bonds       : angle       3.49957 /  2.54 ( 2125)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 130
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9082 (pm20) cc_final: 0.8653 (pm20)
REVERT: A   76 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8664 (mm-40)
REVERT: A   81 ASP cc_start: 0.8722 (t0) cc_final: 0.8426 (t70)
REVERT: C   91 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8026 (tp30)
REVERT: F   74 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8582 (mt-10)
REVERT: H   30 ARG cc_start: 0.8428 (mtp85) cc_final: 0.8069 (mtp85)
REVERT: K  112 THR cc_start: 0.7242 (m) cc_final: 0.6952 (m)
REVERT: K  121 MET cc_start: 0.8433 (tpt) cc_final: 0.7555 (mpp)
REVERT: K  195 TYR cc_start: 0.8399 (t80) cc_final: 0.7937 (t80)
  outliers start: 14
  outliers final: 12
  residues processed: 139
  average time/residue: 0.1321
  time to fit residues: 25.9566
Evaluate side-chains
  141 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue   13 LYS
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain K residue  205 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 89 optimal weight:   20.0000
   chunk 40 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 90 optimal weight:   10.0000
   chunk 36 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 75 optimal weight:   20.0000
   chunk 25 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** F  93 GLN ** 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 = 0.3728 r_free = 0.3728 target = 0.089865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.053318 restraints weight = 38263.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.2815 rms_B_bonded: 1.98
r_work: 0.2608 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8834
moved from start:          0.2817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14254  Z= 0.152
  Angle     :  0.662   9.608  20486  Z= 0.373
  Chirality :  0.044   0.230   2336
  Planarity :  0.004   0.039   1584
  Dihedral  : 30.955  92.323   4226
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 19.06 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.45 (0.27), residues: 925
  helix:  2.09 (0.21), residues: 599
  sheet: -0.19 (0.68), residues: 47
  loop : -1.43 (0.33), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  30 
 TYR   0.013   0.001   TYR G  57 
 PHE   0.008   0.001   PHE K  99 
 HIS   0.003   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.15 (14254)
  covalent geometry    : angle       0.66155 /  0.37 (20486)
  hydrogen bonds       : bond        0.03899 /  2.60 (  840)
  hydrogen bonds       : angle       3.17589 /  2.30 ( 2125)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3006.45 seconds
wall clock time: 52 minutes 12.58 seconds (3132.58 seconds total)