Starting phenix.real_space_refine
on Fri Jul  3 21:01:23 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dwl_47254/07_2026/9dwl_47254.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dwl_47254/07_2026/9dwl_47254.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dwl_47254/07_2026/9dwl_47254.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dwl_47254/07_2026/9dwl_47254.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dwl_47254/07_2026/9dwl_47254.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dwl_47254/07_2026/9dwl_47254.map"
  }
  resolution = 3.9
  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=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5748 atoms to isotropic.
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     293      5.49       5
     S      10      5.16       5
     C    6554      2.51       5
     N    2217      2.21       5
     O    2803      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11877
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 800
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "C"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 821
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "D"
      Number of atoms: 725
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 725
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "E"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 800
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "G"
      Number of atoms: 784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 784
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 5, 'TRANS': 96}
    Chain: "H"
      Number of atoms: 699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 699
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 2, 'TRANS': 87}
    Chain: "I"
      Number of atoms: 2587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 2587
          Classifications: {'DNA': 127}
          Link IDs: {'rna3p': 126}
    Chain: "J"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "K"
      Number of atoms: 386
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 386
          Classifications: {'DNA': 19}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 18}
  Time building chain proxies: 2.70, per 1000 atoms: 0.23
  Number of scatterers: 11877
  At special positions: 0
  Unit cell: (79.54, 120.28, 123.19, 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      10     16.00
     P     293     15.00
     O    2803      8.00
     N    2217      7.00
     C    6554      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: 0.98
  Conformation dependent library (CDL) restraints added in 241.3 milliseconds
  

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1384

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 8 sheets defined
      73.7% alpha, 2.4% beta
      143 base pairs and 250 stacking pairs defined.
    Time for finding SS restraints: 1.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 49
    Processing helix  chain 'A' and resid 50 through 57
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.892A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.724A  pdb=" N   HIS A 113 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   ALA A 114 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.570A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.714A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
      removed outlier: 3.530A  pdb=" N   ILE B  34 " --> pdb=" O   THR B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.118A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.584A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 27 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.521A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   TYR C  50 " --> pdb=" O   GLY C  46 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.516A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 4.011A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 124
      removed outlier: 3.843A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   HIS D 109 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ALA D 110 " --> pdb=" O   LEU D 106 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LYS D 120 " --> pdb=" O   LYS D 116 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 45 through 56
      removed outlier: 3.749A  pdb=" N   ARG E  49 " --> pdb=" O   THR E  45 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 76
      removed outlier: 3.921A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.549A  pdb=" N   ALA E 114 " --> pdb=" O   ALA E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.749A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.504A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.121A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.639A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 17 through 22
    Processing helix  chain 'G' and resid 26 through 37
      removed outlier: 3.747A  pdb=" N   VAL G  30 " --> pdb=" O   PRO G  26 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 72
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
      removed outlier: 3.612A  pdb=" N   VAL H  41 " --> pdb=" O   TYR H  37 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   TYR H  42 " --> pdb=" O   SER H  38 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.594A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.627A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 124
      removed outlier: 3.878A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   HIS H 109 " --> pdb=" O   GLU H 105 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   SER H 124 " --> pdb=" O   LYS H 120 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.440A  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: 6.449A  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: 7.776A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.278A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.559A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78

    371 hydrogen bonds defined for protein.
    1101 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      367 hydrogen bonds
      734 hydrogen bond angles
      0 basepair planarities
      143 basepair parallelities
      250 stacking parallelities
  Total time for adding SS restraints: 2.08

  Time building geometry restraints manager: 1.33 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: 2297
        1.33 -     1.45: 4201
        1.45 -     1.57: 5583
        1.57 -     1.69: 584
        1.69 -     1.81: 20
  Bond restraints: 12685
  Sorted by residual:
  bond pdb=" P    DT K 129 "
       pdb=" OP3  DT K 129 "
    ideal  model  delta    sigma   weight residual
    1.480  1.594 -0.114 2.00e-02 2.50e+03 3.23e+01
  bond pdb=" C3'  DT J  15 "
       pdb=" C2'  DT J  15 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.10e+01
  bond pdb=" C3'  DG J  95 "
       pdb=" C2'  DG J  95 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.86e+00
  bond pdb=" C3'  DG I  21 "
       pdb=" C2'  DG I  21 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.69e+00
  bond pdb=" C3'  DG J  39 "
       pdb=" O3'  DG J  39 "
    ideal  model  delta    sigma   weight residual
    1.435  1.395  0.040 1.30e-02 5.92e+03 9.60e+00
  ... (remaining 12680 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 16953
        1.60 -     3.20: 1310
        3.20 -     4.80: 93
        4.80 -     6.40: 24
        6.40 -     8.00: 10
  Bond angle restraints: 18390
  Sorted by residual:
  angle pdb=" O4'  DC I 111 "
        pdb=" C4'  DC I 111 "
        pdb=" C3'  DC I 111 "
      ideal   model   delta    sigma   weight residual
     106.00  103.06    2.94 6.00e-01 2.78e+00 2.39e+01
  angle pdb=" C   TYR F  88 "
        pdb=" CA  TYR F  88 "
        pdb=" CB  TYR F  88 "
      ideal   model   delta    sigma   weight residual
     110.79  103.07    7.72 1.66e+00 3.63e-01 2.16e+01
  angle pdb=" N3   DT I  32 "
        pdb=" C4   DT I  32 "
        pdb=" O4   DT I  32 "
      ideal   model   delta    sigma   weight residual
     119.90  122.68   -2.78 6.00e-01 2.78e+00 2.14e+01
  angle pdb=" N3   DT J  51 "
        pdb=" C4   DT J  51 "
        pdb=" O4   DT J  51 "
      ideal   model   delta    sigma   weight residual
     119.90  122.64   -2.74 6.00e-01 2.78e+00 2.09e+01
  angle pdb=" N   GLU B  63 "
        pdb=" CA  GLU B  63 "
        pdb=" CB  GLU B  63 "
      ideal   model   delta    sigma   weight residual
     110.28  117.36   -7.08 1.55e+00 4.16e-01 2.08e+01
  ... (remaining 18385 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.36: 5130
       28.36 -    56.72: 1556
       56.72 -    85.08: 167
       85.08 -   113.44: 4
      113.44 -   141.80: 4
  Dihedral angle restraints: 6861
    sinusoidal: 4713
      harmonic: 2148
  Sorted by residual:
  dihedral pdb=" CD  ARG B  92 "
           pdb=" NE  ARG B  92 "
           pdb=" CZ  ARG B  92 "
           pdb=" NH1 ARG B  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   41.78  -41.78     1      1.00e+01 1.00e-02 2.44e+01
  dihedral pdb=" N   ARG A  40 "
           pdb=" C   ARG A  40 "
           pdb=" CA  ARG A  40 "
           pdb=" CB  ARG A  40 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  111.76   11.04     0      2.50e+00 1.60e-01 1.95e+01
  dihedral pdb=" CD  ARG C  71 "
           pdb=" NE  ARG C  71 "
           pdb=" CZ  ARG C  71 "
           pdb=" NH1 ARG C  71 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   35.46  -35.46     1      1.00e+01 1.00e-02 1.78e+01
  ... (remaining 6858 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.129: 2063
       0.129 -    0.259: 30
       0.259 -    0.388: 2
       0.388 -    0.518: 0
       0.518 -    0.647: 1
  Chirality restraints: 2096
  Sorted by residual:
  chirality pdb=" P    DA I   1 "
            pdb=" OP1  DA I   1 "
            pdb=" OP2  DA I   1 "
            pdb=" O5'  DA I   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.98   -0.65 2.00e-01 2.50e+01 1.05e+01
  chirality pdb=" CA  ARG A  40 "
            pdb=" N   ARG A  40 "
            pdb=" C   ARG A  40 "
            pdb=" CB  ARG A  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.86   -0.35 2.00e-01 2.50e+01 3.13e+00
  chirality pdb=" CA  PRO A  38 "
            pdb=" N   PRO A  38 "
            pdb=" C   PRO A  38 "
            pdb=" CB  PRO A  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.37    0.35 2.00e-01 2.50e+01 3.11e+00
  ... (remaining 2093 not shown)

  Planarity restraints: 1312
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  92 "    0.753 9.50e-02 1.11e+02   3.38e-01 6.97e+01
        pdb=" NE  ARG B  92 "   -0.042 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  92 "   -0.018 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  92 "    0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  92 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C  71 "   -0.634 9.50e-02 1.11e+02   2.84e-01 4.93e+01
        pdb=" NE  ARG C  71 "    0.038 2.00e-02 2.50e+03
        pdb=" CZ  ARG C  71 "    0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG C  71 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG C  71 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  63 "   -0.489 9.50e-02 1.11e+02   2.19e-01 2.95e+01
        pdb=" NE  ARG A  63 "    0.029 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  63 "    0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  63 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  63 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1309 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2757
        2.82 -     3.34: 10722
        3.34 -     3.86: 23122
        3.86 -     4.38: 25677
        4.38 -     4.90: 35714
  Nonbonded interactions: 97992
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A  40 "
            pdb=" O3'  DT J  83 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" O   ILE C  78 "
            pdb=" OG  SER D  55 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" NZ  LYS E  79 "
            pdb=" O   THR E  80 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" NH1 ARG G  32 "
            pdb=" OP2  DG J  30 "
     model   vdw
     2.337 3.120
  nonbonded pdb=" N   THR D  90 "
            pdb=" OE2 GLU D  93 "
     model   vdw
     2.344 3.120
  ... (remaining 97987 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'
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 16 through 117)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 35 through 124)
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             2.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.990
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.114  12685  Z= 0.573
  Angle     :  0.864   7.999  18390  Z= 0.719
  Chirality :  0.053   0.647   2096
  Planarity :  0.015   0.338   1312
  Dihedral  : 27.704 141.801   5477
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  1.14 %
    Favored  : 98.21 %
  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:  1.14 (0.31), residues: 726
  helix:  1.69 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -1.47 (0.37), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  92 
 TYR   0.025   0.002   TYR B  98 
 PHE   0.022   0.002   PHE E 104 
 HIS   0.004   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00661 /  0.57 (12685)
  covalent geometry    : angle       0.86404 /  0.72 (18390)
  hydrogen bonds       : bond        0.11362 /  7.93 (  738)
  hydrogen bonds       : angle       4.08529 /  2.87 ( 1835)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 196
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.9364 (mm) cc_final: 0.8866 (mm)
REVERT: A   61 LEU cc_start: 0.9521 (mp) cc_final: 0.9204 (mp)
REVERT: B   35 ARG cc_start: 0.9493 (mtp85) cc_final: 0.8755 (mtm-85)
REVERT: C   38 ASN cc_start: 0.8175 (t0) cc_final: 0.7933 (t0)
REVERT: C   42 ARG cc_start: 0.9052 (ptm160) cc_final: 0.8253 (ptm160)
REVERT: C   64 GLU cc_start: 0.9021 (tp30) cc_final: 0.8658 (tp30)
REVERT: C   72 ASP cc_start: 0.8727 (m-30) cc_final: 0.8344 (m-30)
REVERT: E   90 MET cc_start: 0.9226 (mmm) cc_final: 0.9019 (mmp)
REVERT: E  120 MET cc_start: 0.8375 (mpp) cc_final: 0.8164 (mpp)
REVERT: F   67 ARG cc_start: 0.9494 (ttm170) cc_final: 0.9241 (ttp-110)
REVERT: F   93 GLN cc_start: 0.9080 (mp10) cc_final: 0.8820 (mp10)
REVERT: G   75 LYS cc_start: 0.9246 (mmpt) cc_final: 0.9010 (mmmm)
REVERT: H   71 GLU cc_start: 0.9234 (tp30) cc_final: 0.8730 (tp30)
REVERT: H   87 SER cc_start: 0.9366 (OUTLIER) cc_final: 0.9067 (p)
REVERT: H  105 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8216 (tm-30)
REVERT: H  106 LEU cc_start: 0.9642 (mt) cc_final: 0.9205 (mt)
  outliers start: 4
  outliers final: 0
  residues processed: 200
  average time/residue: 0.1241
  time to fit residues: 34.2998
Evaluate side-chains
  143 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   87 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:   20.0000
   overall best weight:    1.7184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  93 GLN
A 108 ASN
E  68 GLN
** F  25 ASN ** 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 = 0.3372 r_free = 0.3372 target = 0.060873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.040507 restraints weight = 70507.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.041372 restraints weight = 36189.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.041964 restraints weight = 24454.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.042335 restraints weight = 19867.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.042501 restraints weight = 17862.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.1172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12685  Z= 0.176
  Angle     :  0.660   9.284  18390  Z= 0.397
  Chirality :  0.043   0.237   2096
  Planarity :  0.005   0.058   1312
  Dihedral  : 30.756 143.827   4021
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 13.15 %
    Favored  : 83.60 %
  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:  1.38 (0.31), residues: 726
  helix:  1.79 (0.22), residues: 513
  sheet:  None (None), residues: 0
  loop : -1.30 (0.39), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  86 
 TYR   0.025   0.002   TYR F  88 
 PHE   0.010   0.001   PHE E 104 
 HIS   0.005   0.001   HIS D 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.18 (12685)
  covalent geometry    : angle       0.66028 /  0.40 (18390)
  hydrogen bonds       : bond        0.05040 /  3.37 (  738)
  hydrogen bonds       : angle       3.24958 /  2.28 ( 1835)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 154
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8544 (pt0)
REVERT: A   56 LYS cc_start: 0.9538 (ptpt) cc_final: 0.9326 (tptt)
REVERT: A   59 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7538 (tm-30)
REVERT: A   60 LEU cc_start: 0.9194 (mm) cc_final: 0.8770 (mm)
REVERT: A   61 LEU cc_start: 0.9501 (mp) cc_final: 0.9186 (mp)
REVERT: A  120 MET cc_start: 0.8719 (mmm) cc_final: 0.8471 (mmm)
REVERT: B   35 ARG cc_start: 0.9501 (mtp85) cc_final: 0.8847 (mtm-85)
REVERT: B   98 TYR cc_start: 0.8994 (m-80) cc_final: 0.8764 (m-80)
REVERT: C   38 ASN cc_start: 0.8173 (t0) cc_final: 0.7898 (t0)
REVERT: C   42 ARG cc_start: 0.9081 (ptm160) cc_final: 0.8220 (ptm160)
REVERT: C   64 GLU cc_start: 0.9006 (tp30) cc_final: 0.8670 (tp30)
REVERT: D   71 GLU cc_start: 0.9113 (tt0) cc_final: 0.8834 (tm-30)
REVERT: E   59 GLU cc_start: 0.8372 (mp0) cc_final: 0.8159 (mp0)
REVERT: E   60 LEU cc_start: 0.9340 (tp) cc_final: 0.8981 (tt)
REVERT: E   93 GLN cc_start: 0.9412 (mm110) cc_final: 0.9141 (mm110)
REVERT: F   37 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9381 (mm)
REVERT: F   67 ARG cc_start: 0.9449 (ttm170) cc_final: 0.8973 (mtm-85)
REVERT: F   74 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8557 (tm-30)
REVERT: F   84 MET cc_start: 0.8859 (mmm) cc_final: 0.8500 (mmm)
REVERT: G   35 ARG cc_start: 0.8442 (ttp-170) cc_final: 0.8109 (ttm110)
REVERT: G   75 LYS cc_start: 0.9183 (mmpt) cc_final: 0.8959 (mmmm)
REVERT: H  105 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8152 (tm-30)
REVERT: H  106 LEU cc_start: 0.9660 (mt) cc_final: 0.9145 (mt)
  outliers start: 20
  outliers final: 14
  residues processed: 163
  average time/residue: 0.1190
  time to fit residues: 27.0435
Evaluate side-chains
  151 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 136
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   85 ASP
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain H residue   52 THR
Chi-restraints excluded: chain H residue   87 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 75 optimal weight:   30.0000
   chunk 90 optimal weight:   20.0000
   chunk 49 optimal weight:    3.9990
   chunk 84 optimal weight:   40.0000
   chunk 0 optimal weight:    9.9990
   chunk 62 optimal weight:    5.9990
   chunk 68 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 60 optimal weight:   10.0000
   chunk 91 optimal weight:   20.0000
   overall best weight:    3.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 108 ASN
** F  25 ASN ** 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 = 0.3341 r_free = 0.3341 target = 0.059514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.039861 restraints weight = 70189.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.040762 restraints weight = 35650.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.041373 restraints weight = 23751.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.041734 restraints weight = 19066.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.041909 restraints weight = 17018.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8634
moved from start:          0.1536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12685  Z= 0.219
  Angle     :  0.663   7.484  18390  Z= 0.396
  Chirality :  0.043   0.247   2096
  Planarity :  0.005   0.047   1312
  Dihedral  : 30.817 143.111   4021
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 18.02 %
    Favored  : 78.90 %
  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:  1.45 (0.31), residues: 726
  helix:  1.82 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -1.25 (0.40), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  20 
 TYR   0.025   0.002   TYR H  83 
 PHE   0.006   0.001   PHE A  67 
 HIS   0.008   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00412 /  0.22 (12685)
  covalent geometry    : angle       0.66290 /  0.40 (18390)
  hydrogen bonds       : bond        0.05610 /  3.80 (  738)
  hydrogen bonds       : angle       3.26724 /  2.27 ( 1835)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.9198 (mm) cc_final: 0.8886 (mm)
REVERT: A   61 LEU cc_start: 0.9519 (mp) cc_final: 0.9136 (mp)
REVERT: A   90 MET cc_start: 0.9318 (mmp) cc_final: 0.9039 (mmp)
REVERT: B   35 ARG cc_start: 0.9494 (mtp85) cc_final: 0.8727 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8599 (pm20)
REVERT: C   38 ASN cc_start: 0.8198 (t0) cc_final: 0.7925 (t0)
REVERT: C   64 GLU cc_start: 0.9019 (tp30) cc_final: 0.8711 (tp30)
REVERT: C   71 ARG cc_start: 0.9088 (ttp80) cc_final: 0.8791 (ttp80)
REVERT: D   71 GLU cc_start: 0.9150 (tt0) cc_final: 0.8888 (tm-30)
REVERT: E   59 GLU cc_start: 0.8484 (mp0) cc_final: 0.8238 (mp0)
REVERT: E   60 LEU cc_start: 0.9399 (tp) cc_final: 0.9037 (tt)
REVERT: E   97 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8210 (mt-10)
REVERT: F   37 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9312 (mm)
REVERT: F   67 ARG cc_start: 0.9451 (ttm170) cc_final: 0.8901 (mtm-85)
REVERT: F   84 MET cc_start: 0.8971 (mmm) cc_final: 0.8413 (mmm)
REVERT: G   35 ARG cc_start: 0.8464 (ttp-170) cc_final: 0.8160 (ttm110)
REVERT: G   41 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8613 (pt0)
REVERT: G   75 LYS cc_start: 0.9254 (mmpt) cc_final: 0.9045 (mmmm)
REVERT: G   95 LYS cc_start: 0.9502 (tppp) cc_final: 0.9188 (tppt)
REVERT: H  105 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8140 (tm-30)
REVERT: H  106 LEU cc_start: 0.9656 (mt) cc_final: 0.9103 (mt)
  outliers start: 19
  outliers final: 9
  residues processed: 144
  average time/residue: 0.1155
  time to fit residues: 23.4120
Evaluate side-chains
  137 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 126
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain H residue   52 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 78 optimal weight:   20.0000
   chunk 42 optimal weight:    1.9990
   chunk 92 optimal weight:   20.0000
   chunk 32 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0070
   chunk 93 optimal weight:   20.0000
   chunk 96 optimal weight:   50.0000
   chunk 46 optimal weight:    0.2980
   chunk 47 optimal weight:    0.9990
   chunk 84 optimal weight:   40.0000
   overall best weight:    0.6200

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.060847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.040970 restraints weight = 67877.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.041945 restraints weight = 34154.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.042615 restraints weight = 22693.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.042988 restraints weight = 17998.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.043220 restraints weight = 15968.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.1745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  12685  Z= 0.146
  Angle     :  0.620   8.509  18390  Z= 0.371
  Chirality :  0.042   0.245   2096
  Planarity :  0.004   0.043   1312
  Dihedral  : 30.797 143.832   4020
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 18.99 %
    Favored  : 79.06 %
  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:  1.85 (0.32), residues: 726
  helix:  2.09 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -1.02 (0.41), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  86 
 TYR   0.014   0.001   TYR H  40 
 PHE   0.007   0.001   PHE A  78 
 HIS   0.003   0.001   HIS H  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00237 /  0.15 (12685)
  covalent geometry    : angle       0.62046 /  0.37 (18390)
  hydrogen bonds       : bond        0.04146 /  2.77 (  738)
  hydrogen bonds       : angle       2.80771 /  1.95 ( 1835)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 150
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8740 (pt0) cc_final: 0.8433 (pm20)
REVERT: A   59 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7421 (tm-30)
REVERT: A   60 LEU cc_start: 0.9176 (mm) cc_final: 0.8887 (mm)
REVERT: A   61 LEU cc_start: 0.9498 (mp) cc_final: 0.9144 (mp)
REVERT: A   90 MET cc_start: 0.9338 (mmp) cc_final: 0.9026 (mmp)
REVERT: A  120 MET cc_start: 0.8814 (mmm) cc_final: 0.8538 (mmm)
REVERT: B   35 ARG cc_start: 0.9498 (mtp85) cc_final: 0.8804 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8515 (pm20)
REVERT: B   98 TYR cc_start: 0.9118 (m-80) cc_final: 0.8798 (m-80)
REVERT: C   38 ASN cc_start: 0.8214 (t0) cc_final: 0.7915 (t0)
REVERT: C   64 GLU cc_start: 0.9018 (tp30) cc_final: 0.8754 (tp30)
REVERT: D   71 GLU cc_start: 0.9158 (tt0) cc_final: 0.8906 (tm-30)
REVERT: E   59 GLU cc_start: 0.8540 (mp0) cc_final: 0.8252 (mp0)
REVERT: E   60 LEU cc_start: 0.9403 (tp) cc_final: 0.9051 (tt)
REVERT: E   90 MET cc_start: 0.9253 (mmm) cc_final: 0.9048 (mmp)
REVERT: E   97 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8019 (mt-10)
REVERT: E  103 LEU cc_start: 0.9446 (tp) cc_final: 0.9243 (tp)
REVERT: E  120 MET cc_start: 0.8579 (mpp) cc_final: 0.8366 (mpp)
REVERT: F   37 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9335 (mm)
REVERT: F   67 ARG cc_start: 0.9463 (ttm110) cc_final: 0.8883 (mtm-85)
REVERT: F   84 MET cc_start: 0.9013 (mmm) cc_final: 0.8246 (mmm)
REVERT: F   92 ARG cc_start: 0.9465 (mmm-85) cc_final: 0.9222 (tpp80)
REVERT: G   35 ARG cc_start: 0.8432 (ttp-170) cc_final: 0.8121 (ttm110)
REVERT: G   95 LYS cc_start: 0.9457 (tppp) cc_final: 0.9169 (tppt)
REVERT: H   76 GLU cc_start: 0.9280 (tp30) cc_final: 0.8720 (tp30)
REVERT: H  105 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8183 (tm-30)
REVERT: H  106 LEU cc_start: 0.9663 (mt) cc_final: 0.9148 (mt)
  outliers start: 12
  outliers final: 7
  residues processed: 157
  average time/residue: 0.1079
  time to fit residues: 23.6875
Evaluate side-chains
  144 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 135
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain H residue   52 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 51 optimal weight:   10.0000
   chunk 35 optimal weight:   10.0000
   chunk 25 optimal weight:    7.9990
   chunk 44 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 52 optimal weight:    0.6980
   chunk 19 optimal weight:    5.9990
   chunk 56 optimal weight:    8.9990
   chunk 69 optimal weight:    0.9980
   chunk 96 optimal weight:   50.0000
   overall best weight:    2.7386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E  68 GLN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.059510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.039593 restraints weight = 69098.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.040473 restraints weight = 35439.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.041058 restraints weight = 23850.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.041417 restraints weight = 19265.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.041609 restraints weight = 17156.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.1895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  12685  Z= 0.197
  Angle     :  0.637   6.910  18390  Z= 0.379
  Chirality :  0.041   0.252   2096
  Planarity :  0.004   0.066   1312
  Dihedral  : 30.825 143.422   4020
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 19.64 %
    Favored  : 77.44 %
  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:  1.90 (0.32), residues: 726
  helix:  2.12 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -0.99 (0.41), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  86 
 TYR   0.013   0.002   TYR H  83 
 PHE   0.006   0.001   PHE A 104 
 HIS   0.007   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00367 /  0.20 (12685)
  covalent geometry    : angle       0.63712 /  0.38 (18390)
  hydrogen bonds       : bond        0.05047 /  3.43 (  738)
  hydrogen bonds       : angle       2.99747 /  2.07 ( 1835)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8771 (pt0) cc_final: 0.8551 (pm20)
REVERT: A   56 LYS cc_start: 0.9494 (ptmt) cc_final: 0.9083 (ptpp)
REVERT: A   59 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7461 (tm-30)
REVERT: A   90 MET cc_start: 0.9341 (mmp) cc_final: 0.9085 (mmp)
REVERT: B   35 ARG cc_start: 0.9520 (mtp85) cc_final: 0.8823 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8554 (pm20)
REVERT: C   38 ASN cc_start: 0.8306 (t0) cc_final: 0.8028 (t0)
REVERT: C   64 GLU cc_start: 0.8977 (tp30) cc_final: 0.8685 (tp30)
REVERT: D   68 ASP cc_start: 0.9026 (t0) cc_final: 0.8823 (t0)
REVERT: D   71 GLU cc_start: 0.9181 (tt0) cc_final: 0.8911 (tm-30)
REVERT: E   59 GLU cc_start: 0.8503 (mp0) cc_final: 0.8200 (mp0)
REVERT: E   60 LEU cc_start: 0.9426 (tp) cc_final: 0.9072 (tt)
REVERT: E   90 MET cc_start: 0.9294 (mmm) cc_final: 0.9092 (mmp)
REVERT: E   94 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8976 (mm-30)
REVERT: E   97 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8052 (mt-10)
REVERT: E  120 MET cc_start: 0.8532 (mpp) cc_final: 0.8115 (mpp)
REVERT: F   37 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9348 (mm)
REVERT: F   67 ARG cc_start: 0.9470 (ttm110) cc_final: 0.8942 (mtm-85)
REVERT: F   84 MET cc_start: 0.9081 (mmm) cc_final: 0.8251 (mmm)
REVERT: G   35 ARG cc_start: 0.8456 (ttp-170) cc_final: 0.8169 (ttm110)
REVERT: G   95 LYS cc_start: 0.9466 (tppp) cc_final: 0.9170 (tppt)
REVERT: H   76 GLU cc_start: 0.9375 (tp30) cc_final: 0.8873 (tp30)
REVERT: H  105 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8195 (tm-30)
REVERT: H  106 LEU cc_start: 0.9650 (mt) cc_final: 0.9097 (mt)
  outliers start: 18
  outliers final: 9
  residues processed: 143
  average time/residue: 0.1074
  time to fit residues: 21.7973
Evaluate side-chains
  136 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 125
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain H residue   52 THR
Chi-restraints excluded: chain H residue   63 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 86 optimal weight:   20.0000
   chunk 65 optimal weight:    1.9990
   chunk 79 optimal weight:   20.0000
   chunk 13 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 91 optimal weight:   20.0000
   chunk 44 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  25 ASN
H  63 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.060751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.040121 restraints weight = 69887.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.041004 restraints weight = 36474.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.041615 restraints weight = 24954.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.041977 restraints weight = 20308.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.042177 restraints weight = 18259.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.2029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  12685  Z= 0.146
  Angle     :  0.614   7.967  18390  Z= 0.366
  Chirality :  0.041   0.312   2096
  Planarity :  0.004   0.046   1312
  Dihedral  : 30.822 143.534   4020
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 22.08 %
    Favored  : 75.81 %
  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:  1.91 (0.32), residues: 726
  helix:  2.10 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -0.87 (0.42), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  71 
 TYR   0.015   0.001   TYR H  40 
 PHE   0.006   0.001   PHE E  67 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.15 (12685)
  covalent geometry    : angle       0.61438 /  0.37 (18390)
  hydrogen bonds       : bond        0.04249 /  2.87 (  738)
  hydrogen bonds       : angle       2.82128 /  1.96 ( 1835)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 145
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7531 (tm-30)
REVERT: A   60 LEU cc_start: 0.9228 (mm) cc_final: 0.8966 (mm)
REVERT: A   61 LEU cc_start: 0.9427 (mp) cc_final: 0.9016 (mp)
REVERT: A   90 MET cc_start: 0.9306 (mmp) cc_final: 0.9058 (mmp)
REVERT: A  120 MET cc_start: 0.8766 (mmm) cc_final: 0.8505 (mmm)
REVERT: B   35 ARG cc_start: 0.9508 (mtp85) cc_final: 0.8838 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8509 (pm20)
REVERT: C   64 GLU cc_start: 0.8949 (tp30) cc_final: 0.8664 (tp30)
REVERT: D   71 GLU cc_start: 0.9174 (tt0) cc_final: 0.8923 (tm-30)
REVERT: E   59 GLU cc_start: 0.8546 (mp0) cc_final: 0.8232 (mp0)
REVERT: E   60 LEU cc_start: 0.9391 (tp) cc_final: 0.9035 (tt)
REVERT: E   68 GLN cc_start: 0.9290 (tt0) cc_final: 0.8809 (tm-30)
REVERT: E   90 MET cc_start: 0.9261 (mmm) cc_final: 0.9031 (mmp)
REVERT: E   94 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8955 (mm-30)
REVERT: E   97 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7982 (mt-10)
REVERT: E  103 LEU cc_start: 0.9449 (tp) cc_final: 0.9247 (tp)
REVERT: E  120 MET cc_start: 0.8499 (mpp) cc_final: 0.8093 (mpp)
REVERT: F   37 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9345 (mm)
REVERT: F   67 ARG cc_start: 0.9462 (ttm110) cc_final: 0.8863 (mtm-85)
REVERT: F   84 MET cc_start: 0.9061 (mmm) cc_final: 0.8062 (mmm)
REVERT: G   35 ARG cc_start: 0.8403 (ttp-170) cc_final: 0.8106 (ttm110)
REVERT: G   95 LYS cc_start: 0.9445 (tppp) cc_final: 0.9178 (tppt)
REVERT: H  105 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8186 (tm-30)
REVERT: H  106 LEU cc_start: 0.9655 (mt) cc_final: 0.9102 (mt)
  outliers start: 13
  outliers final: 10
  residues processed: 152
  average time/residue: 0.1034
  time to fit residues: 22.3843
Evaluate side-chains
  147 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 135
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  106 ASP
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain H residue   52 THR
Chi-restraints excluded: chain H residue   63 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 25 optimal weight:    0.4980
   chunk 68 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 35 optimal weight:   10.0000
   chunk 95 optimal weight:   40.0000
   chunk 94 optimal weight:   20.0000
   chunk 48 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    1.4784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  63 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.060448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.040517 restraints weight = 68779.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.041465 restraints weight = 34702.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.042110 restraints weight = 23246.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.042488 restraints weight = 18514.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.042683 restraints weight = 16481.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.2119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12685  Z= 0.155
  Angle     :  0.616   8.215  18390  Z= 0.367
  Chirality :  0.041   0.252   2096
  Planarity :  0.004   0.044   1312
  Dihedral  : 30.812 143.390   4020
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 22.08 %
    Favored  : 75.49 %
  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:  1.94 (0.32), residues: 726
  helix:  2.12 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -0.88 (0.42), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  71 
 TYR   0.017   0.001   TYR H  40 
 PHE   0.007   0.001   PHE H  65 
 HIS   0.004   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.15 (12685)
  covalent geometry    : angle       0.61634 /  0.37 (18390)
  hydrogen bonds       : bond        0.04287 /  2.91 (  738)
  hydrogen bonds       : angle       2.80526 /  1.94 ( 1835)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 134
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LEU cc_start: 0.8914 (mt) cc_final: 0.8650 (mt)
REVERT: A   56 LYS cc_start: 0.9518 (ptmt) cc_final: 0.9076 (ptpp)
REVERT: A   59 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7559 (tm-30)
REVERT: A   61 LEU cc_start: 0.9423 (mp) cc_final: 0.9003 (mp)
REVERT: A   90 MET cc_start: 0.9321 (mmp) cc_final: 0.9086 (mmp)
REVERT: A  120 MET cc_start: 0.8848 (mmm) cc_final: 0.8588 (mmm)
REVERT: B   35 ARG cc_start: 0.9510 (mtp85) cc_final: 0.8830 (mtm-85)
REVERT: B   44 LYS cc_start: 0.8768 (mtpt) cc_final: 0.8528 (mttt)
REVERT: B   63 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8532 (pm20)
REVERT: C   64 GLU cc_start: 0.8983 (tp30) cc_final: 0.8710 (tp30)
REVERT: D   68 ASP cc_start: 0.9007 (t0) cc_final: 0.8797 (t0)
REVERT: D   71 GLU cc_start: 0.9168 (tt0) cc_final: 0.8934 (tm-30)
REVERT: E   59 GLU cc_start: 0.8548 (mp0) cc_final: 0.8044 (mp0)
REVERT: E   60 LEU cc_start: 0.9397 (tp) cc_final: 0.9039 (tt)
REVERT: E   90 MET cc_start: 0.9271 (mmm) cc_final: 0.9053 (mmp)
REVERT: E  103 LEU cc_start: 0.9451 (tp) cc_final: 0.9248 (tp)
REVERT: E  120 MET cc_start: 0.8494 (mpp) cc_final: 0.8134 (mpp)
REVERT: F   37 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9333 (mm)
REVERT: F   53 GLU cc_start: 0.8887 (mp0) cc_final: 0.8592 (mp0)
REVERT: F   67 ARG cc_start: 0.9465 (ttm110) cc_final: 0.8981 (mtm-85)
REVERT: F   84 MET cc_start: 0.9102 (mmm) cc_final: 0.8101 (mmm)
REVERT: G   35 ARG cc_start: 0.8401 (ttp-170) cc_final: 0.8109 (ttm110)
REVERT: G   95 LYS cc_start: 0.9446 (tppp) cc_final: 0.9171 (tppt)
REVERT: H  105 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8175 (tm-30)
REVERT: H  106 LEU cc_start: 0.9659 (mt) cc_final: 0.9101 (mt)
  outliers start: 15
  outliers final: 10
  residues processed: 143
  average time/residue: 0.1034
  time to fit residues: 20.9786
Evaluate side-chains
  144 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 132
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain H residue   52 THR
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain H residue  100 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 60 optimal weight:    3.9990
   chunk 26 optimal weight:    7.9990
   chunk 90 optimal weight:   20.0000
   chunk 77 optimal weight:   20.0000
   chunk 68 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0470
   chunk 89 optimal weight:   20.0000
   chunk 19 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   overall best weight:    1.1484

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  63 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.060844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.041064 restraints weight = 69514.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.042011 restraints weight = 35026.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.042633 restraints weight = 23478.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.043018 restraints weight = 18861.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.043211 restraints weight = 16805.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.2213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12685  Z= 0.149
  Angle     :  0.625  13.505  18390  Z= 0.369
  Chirality :  0.041   0.394   2096
  Planarity :  0.004   0.043   1312
  Dihedral  : 30.814 143.233   4020
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 22.24 %
    Favored  : 75.16 %
  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:  1.92 (0.32), residues: 726
  helix:  2.10 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -0.87 (0.42), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  71 
 TYR   0.017   0.001   TYR H  40 
 PHE   0.007   0.001   PHE H  65 
 HIS   0.004   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.15 (12685)
  covalent geometry    : angle       0.62461 /  0.37 (18390)
  hydrogen bonds       : bond        0.04175 /  2.84 (  738)
  hydrogen bonds       : angle       2.79985 /  1.94 ( 1835)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 138
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LEU cc_start: 0.8899 (mt) cc_final: 0.8630 (mt)
REVERT: A   59 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7536 (tm-30)
REVERT: A   60 LEU cc_start: 0.9262 (mm) cc_final: 0.8992 (mm)
REVERT: A   61 LEU cc_start: 0.9419 (mp) cc_final: 0.8981 (mp)
REVERT: A   90 MET cc_start: 0.9318 (mmp) cc_final: 0.9093 (mmp)
REVERT: A  120 MET cc_start: 0.8855 (mmm) cc_final: 0.8588 (mmm)
REVERT: B   35 ARG cc_start: 0.9513 (mtp85) cc_final: 0.8867 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8516 (pm20)
REVERT: B   98 TYR cc_start: 0.8961 (m-80) cc_final: 0.8528 (m-80)
REVERT: C   64 GLU cc_start: 0.8991 (tp30) cc_final: 0.8706 (tp30)
REVERT: D   68 ASP cc_start: 0.9037 (t0) cc_final: 0.8822 (t0)
REVERT: D   71 GLU cc_start: 0.9143 (tt0) cc_final: 0.8920 (tm-30)
REVERT: E   59 GLU cc_start: 0.8530 (mp0) cc_final: 0.8004 (mp0)
REVERT: E   60 LEU cc_start: 0.9403 (tp) cc_final: 0.9064 (tt)
REVERT: E   90 MET cc_start: 0.9261 (mmm) cc_final: 0.9052 (mmp)
REVERT: E  120 MET cc_start: 0.8514 (mpp) cc_final: 0.8129 (mpp)
REVERT: E  129 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8256 (ttp80)
REVERT: F   37 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9317 (mm)
REVERT: F   53 GLU cc_start: 0.8912 (mp0) cc_final: 0.8615 (mp0)
REVERT: F   67 ARG cc_start: 0.9474 (ttm110) cc_final: 0.8873 (mtm-85)
REVERT: F   84 MET cc_start: 0.9105 (mmm) cc_final: 0.8255 (mmm)
REVERT: G   35 ARG cc_start: 0.8415 (ttp-170) cc_final: 0.8113 (ttm110)
REVERT: G   95 LYS cc_start: 0.9439 (tppp) cc_final: 0.9165 (tppt)
REVERT: H  105 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8176 (tm-30)
REVERT: H  106 LEU cc_start: 0.9670 (mt) cc_final: 0.9124 (mt)
  outliers start: 16
  outliers final: 13
  residues processed: 147
  average time/residue: 0.1136
  time to fit residues: 23.5910
Evaluate side-chains
  147 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  129 ARG
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain H residue   52 THR
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain H residue  100 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 11 optimal weight:    4.9990
   chunk 85 optimal weight:   20.0000
   chunk 62 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 82 optimal weight:   50.0000
   chunk 38 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    1.4786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  63 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.060788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.039958 restraints weight = 69003.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.040837 restraints weight = 36490.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.041417 restraints weight = 25226.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.041731 restraints weight = 20660.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.041958 restraints weight = 18710.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.2259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12685  Z= 0.155
  Angle     :  0.636  12.483  18390  Z= 0.372
  Chirality :  0.041   0.384   2096
  Planarity :  0.004   0.047   1312
  Dihedral  : 30.824 143.142   4020
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 22.08 %
    Favored  : 75.00 %
  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:  1.93 (0.32), residues: 726
  helix:  2.10 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -0.83 (0.42), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  71 
 TYR   0.017   0.001   TYR H  40 
 PHE   0.029   0.001   PHE E  67 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.16 (12685)
  covalent geometry    : angle       0.63625 /  0.37 (18390)
  hydrogen bonds       : bond        0.04219 /  2.88 (  738)
  hydrogen bonds       : angle       2.82597 /  1.96 ( 1835)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.9504 (ptmt) cc_final: 0.9062 (ptpp)
REVERT: A   59 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7558 (tm-30)
REVERT: A   60 LEU cc_start: 0.9270 (mm) cc_final: 0.9007 (mm)
REVERT: A   61 LEU cc_start: 0.9433 (mp) cc_final: 0.9009 (mp)
REVERT: A  120 MET cc_start: 0.8860 (mmm) cc_final: 0.8594 (mmm)
REVERT: B   35 ARG cc_start: 0.9513 (mtp85) cc_final: 0.8869 (mtm-85)
REVERT: B   44 LYS cc_start: 0.8979 (mmmt) cc_final: 0.8664 (mmtt)
REVERT: B   63 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8550 (pm20)
REVERT: C   64 GLU cc_start: 0.8942 (tp30) cc_final: 0.8677 (tp30)
REVERT: D  113 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8737 (mt-10)
REVERT: E   59 GLU cc_start: 0.8538 (mp0) cc_final: 0.8025 (mp0)
REVERT: E   60 LEU cc_start: 0.9411 (tp) cc_final: 0.9050 (tt)
REVERT: E   90 MET cc_start: 0.9249 (mmm) cc_final: 0.9042 (mmp)
REVERT: E  120 MET cc_start: 0.8497 (mpp) cc_final: 0.8120 (mpp)
REVERT: E  129 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8224 (ttp80)
REVERT: F   37 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9332 (mm)
REVERT: F   53 GLU cc_start: 0.8916 (mp0) cc_final: 0.8629 (mp0)
REVERT: F   67 ARG cc_start: 0.9459 (ttm110) cc_final: 0.8981 (mtm-85)
REVERT: F   84 MET cc_start: 0.9088 (mmm) cc_final: 0.8248 (mmm)
REVERT: G   35 ARG cc_start: 0.8384 (ttp-170) cc_final: 0.8090 (ttm110)
REVERT: G   95 LYS cc_start: 0.9442 (tppp) cc_final: 0.9172 (tppt)
REVERT: H  105 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8163 (tm-30)
REVERT: H  106 LEU cc_start: 0.9670 (mt) cc_final: 0.9104 (mt)
  outliers start: 18
  outliers final: 13
  residues processed: 142
  average time/residue: 0.1133
  time to fit residues: 22.6876
Evaluate side-chains
  147 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  129 ARG
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain H residue   52 THR
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain H residue  100 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 91 optimal weight:   20.0000
   chunk 90 optimal weight:   20.0000
   chunk 1 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 31 optimal weight:    7.9990
   chunk 13 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 83 optimal weight:   40.0000
   chunk 42 optimal weight:    3.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E  68 GLN
H  63 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.060765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.040602 restraints weight = 68806.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.041581 restraints weight = 34930.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.042210 restraints weight = 23478.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.042596 restraints weight = 18864.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.042777 restraints weight = 16723.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.2335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12685  Z= 0.153
  Angle     :  0.646  12.272  18390  Z= 0.376
  Chirality :  0.041   0.370   2096
  Planarity :  0.004   0.043   1312
  Dihedral  : 30.836 143.136   4020
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 23.21 %
    Favored  : 74.03 %
  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:  1.89 (0.32), residues: 726
  helix:  2.06 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -0.81 (0.42), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  71 
 TYR   0.018   0.001   TYR H  40 
 PHE   0.013   0.001   PHE E  67 
 HIS   0.004   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.15 (12685)
  covalent geometry    : angle       0.64622 /  0.38 (18390)
  hydrogen bonds       : bond        0.04194 /  2.87 (  738)
  hydrogen bonds       : angle       2.82483 /  1.95 ( 1835)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 137
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7576 (tm-30)
REVERT: A   60 LEU cc_start: 0.9273 (mm) cc_final: 0.9001 (mm)
REVERT: A   61 LEU cc_start: 0.9429 (mp) cc_final: 0.9006 (mp)
REVERT: A  120 MET cc_start: 0.8872 (mmm) cc_final: 0.8569 (mmm)
REVERT: B   35 ARG cc_start: 0.9519 (mtp85) cc_final: 0.8866 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8538 (pm20)
REVERT: B   98 TYR cc_start: 0.8969 (m-80) cc_final: 0.8585 (m-80)
REVERT: C   64 GLU cc_start: 0.8958 (tp30) cc_final: 0.8705 (tp30)
REVERT: D  113 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8758 (mt-10)
REVERT: E   59 GLU cc_start: 0.8547 (mp0) cc_final: 0.8023 (mp0)
REVERT: E   60 LEU cc_start: 0.9414 (tp) cc_final: 0.9123 (tt)
REVERT: E   67 PHE cc_start: 0.9133 (t80) cc_final: 0.8917 (t80)
REVERT: E   90 MET cc_start: 0.9264 (mmm) cc_final: 0.9054 (mmp)
REVERT: E   97 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7866 (mt-10)
REVERT: E  120 MET cc_start: 0.8510 (mpp) cc_final: 0.8116 (mpp)
REVERT: E  129 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8257 (ttp80)
REVERT: F   37 LEU cc_start: 0.9590 (OUTLIER) cc_final: 0.9315 (mm)
REVERT: F   53 GLU cc_start: 0.8943 (mp0) cc_final: 0.8643 (mp0)
REVERT: F   67 ARG cc_start: 0.9472 (ttm110) cc_final: 0.8987 (mtm-85)
REVERT: F   84 MET cc_start: 0.9123 (mmm) cc_final: 0.8293 (mmm)
REVERT: G   35 ARG cc_start: 0.8400 (ttp-170) cc_final: 0.8104 (ttm110)
REVERT: G   95 LYS cc_start: 0.9436 (tppp) cc_final: 0.9166 (tppt)
REVERT: H  105 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8425 (tm-30)
REVERT: H  106 LEU cc_start: 0.9671 (mt) cc_final: 0.9261 (mt)
  outliers start: 17
  outliers final: 13
  residues processed: 147
  average time/residue: 0.1166
  time to fit residues: 24.2188
Evaluate side-chains
  146 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 130
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  129 ARG
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain H residue   52 THR
Chi-restraints excluded: chain H residue   63 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 93 optimal weight:   20.0000
   chunk 24 optimal weight:    4.9990
   chunk 25 optimal weight:    7.9990
   chunk 23 optimal weight:    1.9990
   chunk 79 optimal weight:   20.0000
   chunk 60 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  63 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.060883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.040370 restraints weight = 69676.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.041275 restraints weight = 35924.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.041856 restraints weight = 24450.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.042250 restraints weight = 19924.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.042444 restraints weight = 17859.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.2393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12685  Z= 0.153
  Angle     :  0.646  11.886  18390  Z= 0.375
  Chirality :  0.041   0.363   2096
  Planarity :  0.004   0.043   1312
  Dihedral  : 30.849 143.134   4020
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 23.38 %
    Favored  : 74.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.94 (0.32), residues: 726
  helix:  2.09 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -0.79 (0.42), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  71 
 TYR   0.018   0.001   TYR H  40 
 PHE   0.011   0.001   PHE E  67 
 HIS   0.003   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.15 (12685)
  covalent geometry    : angle       0.64648 /  0.37 (18390)
  hydrogen bonds       : bond        0.04155 /  2.85 (  738)
  hydrogen bonds       : angle       2.82498 /  1.95 ( 1835)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1876.01 seconds
wall clock time: 33 minutes 2.52 seconds (1982.52 seconds total)