Starting phenix.real_space_refine
on Sat May 17 23:24:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dwl_47254/05_2025/9dwl_47254.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dwl_47254/05_2025/9dwl_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dwl_47254/05_2025/9dwl_47254.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dwl_47254/05_2025/9dwl_47254.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dwl_47254/05_2025/9dwl_47254.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dwl_47254/05_2025/9dwl_47254.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.60, per 1000 atoms: 0.64
  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: 3.01
  Conformation dependent library (CDL) restraints added in 960.6 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: 5.42
  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: 4.08

  Time building geometry restraints manager: 3.53 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=" N   ILE C 111 "
       pdb=" CA  ILE C 111 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.19e-02 7.06e+03 9.57e+00
  bond pdb=" N   ILE F  46 "
       pdb=" CA  ILE F  46 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.033 1.14e-02 7.69e+03 8.27e+00
  bond pdb=" N   VAL B  86 "
       pdb=" CA  VAL B  86 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.034 1.19e-02 7.06e+03 7.97e+00
  bond pdb=" N   ILE G  87 "
       pdb=" CA  ILE G  87 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.033 1.19e-02 7.06e+03 7.59e+00
  ... (remaining 12680 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 17569
        1.60 -     3.20: 714
        3.20 -     4.80: 72
        4.80 -     6.40: 25
        6.40 -     8.00: 10
  Bond angle restraints: 18390
  Sorted by residual:
  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=" 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
  angle pdb=" C   HIS A  39 "
        pdb=" CA  HIS A  39 "
        pdb=" CB  HIS A  39 "
      ideal   model   delta    sigma   weight residual
     110.67  117.52   -6.85 1.52e+00 4.33e-01 2.03e+01
  angle pdb=" N   ARG A  40 "
        pdb=" CA  ARG A  40 "
        pdb=" C   ARG A  40 "
      ideal   model   delta    sigma   weight residual
     108.73  101.77    6.96 1.63e+00 3.76e-01 1.82e+01
  angle pdb=" CA  GLU B  63 "
        pdb=" CB  GLU B  63 "
        pdb=" CG  GLU B  63 "
      ideal   model   delta    sigma   weight residual
     114.10  122.10   -8.00 2.00e+00 2.50e-01 1.60e+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 -    0.127: 2070
       0.127 -    0.255: 23
       0.255 -    0.382: 2
       0.382 -    0.510: 0
       0.510 -    0.637: 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       2.35   -2.98   -0.64 2.00e-01 2.50e+01 1.01e+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:             2.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.110
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.080
  Set scattering table:                    0.130
  Process input model:                     32.150
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.050
  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:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8619
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      :  0.005   0.114  12685  Z= 0.265
  Angle     :  0.725   7.999  18390  Z= 0.429
  Chirality :  0.045   0.637   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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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
 HIS   0.004   0.001   HIS B  75 
 PHE   0.022   0.002   PHE E 104 
 TYR   0.025   0.002   TYR B  98 
 ARG   0.010   0.001   ARG B  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11362 (  738)
  hydrogen bonds       : angle       4.08529 ( 1835)
  covalent geometry    : bond        0.00534 (12685)
  covalent geometry    : angle       0.72521 (18390)

*********************** 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  : 0.842 
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: 0.9205 (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: 0.8252 (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: 0.9227 (mmm) cc_final: 0.9018 (mmp)
REVERT: E  120 MET cc_start: 0.8375 (mpp) cc_final: 0.8166 (mpp)
REVERT: F   67 ARG cc_start: 0.9494 (ttm170) cc_final: 0.9242 (ttp-110)
REVERT: F   93 GLN cc_start: 0.9080 (mp10) cc_final: 0.8819 (mp10)
REVERT: G   75 LYS cc_start: 0.9246 (mmpt) cc_final: 0.9011 (mmmm)
REVERT: H   71 GLU cc_start: 0.9234 (tp30) cc_final: 0.8731 (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: 0.2705
  time to fit residues: 73.4134
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  : 0.809 
-------------------------------------------------------------------------------
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 81 optimal weight:    7.9990
   chunk 73 optimal weight:    8.9990
   chunk 40 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 49 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9980
   chunk 76 optimal weight:    7.9990
   chunk 29 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 88 optimal weight:    6.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
A 108 ASN
E  55 GLN
E  68 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.060610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.041198 restraints weight = 68554.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.042112 restraints weight = 34405.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.042724 restraints weight = 22959.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.1499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12685  Z= 0.167
  Angle     :  0.589   7.019  18390  Z= 0.348
  Chirality :  0.034   0.142   2096
  Planarity :  0.004   0.045   1312
  Dihedral  : 30.240 142.156   4021
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 14.12 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.31), residues: 726
  helix:  2.12 (0.23), residues: 514
  sheet:  None (None), residues: 0
  loop : -1.23 (0.39), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.008   0.001   PHE E 104 
 TYR   0.014   0.001   TYR H  40 
 ARG   0.011   0.001   ARG H  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04008 (  738)
  hydrogen bonds       : angle       2.88446 ( 1835)
  covalent geometry    : bond        0.00361 (12685)
  covalent geometry    : angle       0.58889 (18390)

*********************** 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
  170 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 157
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8585 (pt0)
REVERT: A   59 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7482 (tm-30)
REVERT: A   60 LEU cc_start: 0.9190 (mm) cc_final: 0.8804 (mm)
REVERT: A   61 LEU cc_start: 0.9471 (mp) cc_final: 0.9127 (mp)
REVERT: A   90 MET cc_start: 0.9320 (mmp) cc_final: 0.9114 (mmp)
REVERT: B   35 ARG cc_start: 0.9494 (mtp85) cc_final: 0.8759 (mtm-85)
REVERT: B   98 TYR cc_start: 0.9130 (m-80) cc_final: 0.8876 (m-80)
REVERT: C   38 ASN cc_start: 0.8080 (t0) cc_final: 0.7827 (t0)
REVERT: C   42 ARG cc_start: 0.9039 (ptm160) cc_final: 0.8131 (ptm160)
REVERT: C   64 GLU cc_start: 0.8990 (tp30) cc_final: 0.8643 (tp30)
REVERT: C   71 ARG cc_start: 0.9062 (ttp80) cc_final: 0.8810 (ttp80)
REVERT: D   71 GLU cc_start: 0.9147 (tt0) cc_final: 0.8923 (tm-30)
REVERT: E   60 LEU cc_start: 0.9199 (tp) cc_final: 0.8776 (tt)
REVERT: E  120 MET cc_start: 0.8535 (mpp) cc_final: 0.8306 (mpp)
REVERT: F   84 MET cc_start: 0.8959 (mmm) cc_final: 0.8292 (mmm)
REVERT: F   93 GLN cc_start: 0.8922 (mp10) cc_final: 0.8674 (mp10)
REVERT: G   35 ARG cc_start: 0.8412 (ttp-170) cc_final: 0.8143 (ttm110)
REVERT: G   75 LYS cc_start: 0.9196 (mmpt) cc_final: 0.8971 (mmmm)
REVERT: G   95 LYS cc_start: 0.9493 (tppp) cc_final: 0.9158 (tppt)
REVERT: H  105 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8144 (tm-30)
REVERT: H  106 LEU cc_start: 0.9633 (mt) cc_final: 0.9129 (mt)
  outliers start: 13
  outliers final: 8
  residues processed: 162
  average time/residue: 0.2669
  time to fit residues: 58.8264
Evaluate side-chains
  141 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 133
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain B residue   70 VAL
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 F residue   37 LEU
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain G residue   49 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 88 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9980
   chunk 63 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 90 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   chunk 2 optimal weight:    7.9990
   chunk 14 optimal weight:   10.0000
   chunk 51 optimal weight:   10.0000
   chunk 91 optimal weight:    6.9990
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
E  55 GLN
** 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 = 0.3329 r_free = 0.3329 target = 0.058590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.037741 restraints weight = 71134.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.038560 restraints weight = 36817.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.039100 restraints weight = 25310.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8727
moved from start:          0.2102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  12685  Z= 0.274
  Angle     :  0.650   9.755  18390  Z= 0.379
  Chirality :  0.036   0.185   2096
  Planarity :  0.005   0.053   1312
  Dihedral  : 30.391 142.072   4020
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 17.37 %
    Favored  : 79.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.76 (0.31), residues: 726
  helix:  2.05 (0.22), residues: 516
  sheet:  None (None), residues: 0
  loop : -1.12 (0.40), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B  75 
 PHE   0.011   0.001   PHE A 104 
 TYR   0.022   0.002   TYR F  88 
 ARG   0.005   0.001   ARG G  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05716 (  738)
  hydrogen bonds       : angle       3.25553 ( 1835)
  covalent geometry    : bond        0.00603 (12685)
  covalent geometry    : angle       0.65029 (18390)

*********************** 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
  146 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.9309 (mmp) cc_final: 0.9063 (mmp)
REVERT: B   35 ARG cc_start: 0.9511 (mtp85) cc_final: 0.8738 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8618 (pm20)
REVERT: B   98 TYR cc_start: 0.9107 (m-80) cc_final: 0.8879 (m-80)
REVERT: C   64 GLU cc_start: 0.8873 (tp30) cc_final: 0.8521 (tp30)
REVERT: C   71 ARG cc_start: 0.9137 (ttp80) cc_final: 0.8832 (ttp80)
REVERT: D   71 GLU cc_start: 0.9199 (tt0) cc_final: 0.8981 (tm-30)
REVERT: E   68 GLN cc_start: 0.9369 (OUTLIER) cc_final: 0.9120 (tt0)
REVERT: E  120 MET cc_start: 0.8567 (mpp) cc_final: 0.8190 (mpp)
REVERT: F   37 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9401 (mm)
REVERT: F   53 GLU cc_start: 0.9182 (mp0) cc_final: 0.8848 (mp0)
REVERT: F   93 GLN cc_start: 0.9059 (mp10) cc_final: 0.8762 (mp10)
REVERT: G   35 ARG cc_start: 0.8457 (ttp-170) cc_final: 0.7827 (ttm-80)
REVERT: G   41 GLU cc_start: 0.9300 (mt-10) cc_final: 0.8548 (pt0)
REVERT: G   95 LYS cc_start: 0.9489 (tppp) cc_final: 0.9218 (tppt)
REVERT: H  105 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8173 (tm-30)
REVERT: H  106 LEU cc_start: 0.9627 (mt) cc_final: 0.9116 (mt)
  outliers start: 18
  outliers final: 10
  residues processed: 139
  average time/residue: 0.2537
  time to fit residues: 48.5864
Evaluate side-chains
  132 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 119
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain D residue   94 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   85 ASP
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 90 optimal weight:    6.9990
   chunk 59 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 63 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 87 optimal weight:    7.9990
   chunk 22 optimal weight:    0.0870
   chunk 95 optimal weight:    8.9990
   overall best weight:    0.7360

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
E  68 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.061008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.041043 restraints weight = 68014.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.042002 restraints weight = 34294.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.042646 restraints weight = 22922.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12685  Z= 0.150
  Angle     :  0.591   8.902  18390  Z= 0.343
  Chirality :  0.034   0.143   2096
  Planarity :  0.004   0.064   1312
  Dihedral  : 30.250 143.160   4020
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.81 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.13 (0.32), residues: 726
  helix:  2.33 (0.23), residues: 512
  sheet:  None (None), residues: 0
  loop : -0.93 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS F  75 
 PHE   0.005   0.001   PHE B 100 
 TYR   0.012   0.001   TYR H  40 
 ARG   0.004   0.000   ARG G  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03478 (  738)
  hydrogen bonds       : angle       2.67024 ( 1835)
  covalent geometry    : bond        0.00321 (12685)
  covalent geometry    : angle       0.59050 (18390)

*********************** 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
  161 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 147
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8831 (pt0) cc_final: 0.8557 (pm20)
REVERT: A   56 LYS cc_start: 0.9572 (ptpt) cc_final: 0.9286 (ptpp)
REVERT: A   59 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7509 (tm-30)
REVERT: A   61 LEU cc_start: 0.9362 (mp) cc_final: 0.9150 (mp)
REVERT: A  120 MET cc_start: 0.8927 (mmm) cc_final: 0.8573 (mmm)
REVERT: B   35 ARG cc_start: 0.9508 (mtp85) cc_final: 0.8786 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8544 (pm20)
REVERT: B   98 TYR cc_start: 0.9182 (m-80) cc_final: 0.8906 (m-80)
REVERT: C   64 GLU cc_start: 0.9006 (tp30) cc_final: 0.8632 (tp30)
REVERT: D   68 ASP cc_start: 0.9033 (t0) cc_final: 0.8830 (t0)
REVERT: D   71 GLU cc_start: 0.9140 (tt0) cc_final: 0.8898 (tm-30)
REVERT: E   60 LEU cc_start: 0.9417 (tp) cc_final: 0.9022 (tt)
REVERT: E   90 MET cc_start: 0.9277 (mmm) cc_final: 0.9058 (mmp)
REVERT: E  120 MET cc_start: 0.8607 (mpp) cc_final: 0.8197 (mpp)
REVERT: F   37 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9325 (mm)
REVERT: G   35 ARG cc_start: 0.8340 (ttp-170) cc_final: 0.8033 (ttm110)
REVERT: G   61 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8570 (tm-30)
REVERT: G   95 LYS cc_start: 0.9452 (tppp) cc_final: 0.9156 (tppt)
REVERT: H  105 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8373 (tm-30)
REVERT: H  106 LEU cc_start: 0.9639 (mt) cc_final: 0.9245 (mt)
  outliers start: 14
  outliers final: 9
  residues processed: 156
  average time/residue: 0.2353
  time to fit residues: 51.7517
Evaluate side-chains
  147 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 136
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   77 ASP
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 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  111 ILE
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 83 optimal weight:   10.0000
   chunk 40 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 45 optimal weight:    7.9990
   chunk 96 optimal weight:   10.0000
   chunk 32 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   chunk 86 optimal weight:    7.9990
   chunk 9 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.4786

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.060683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.040080 restraints weight = 69310.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.040977 restraints weight = 35950.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.041563 restraints weight = 24625.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8656
moved from start:          0.2454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12685  Z= 0.167
  Angle     :  0.582   7.758  18390  Z= 0.341
  Chirality :  0.033   0.154   2096
  Planarity :  0.004   0.058   1312
  Dihedral  : 30.234 142.805   4020
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 21.59 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.32), residues: 726
  helix:  2.37 (0.23), residues: 514
  sheet:  None (None), residues: 0
  loop : -0.88 (0.40), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.004   0.001   PHE B 100 
 TYR   0.009   0.001   TYR F  88 
 ARG   0.004   0.000   ARG G  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03835 (  738)
  hydrogen bonds       : angle       2.68666 ( 1835)
  covalent geometry    : bond        0.00365 (12685)
  covalent geometry    : angle       0.58231 (18390)

*********************** 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
  162 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 145
  time to evaluate  : 0.825 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8829 (pt0) cc_final: 0.8616 (pm20)
REVERT: A   56 LYS cc_start: 0.9555 (ptpt) cc_final: 0.9269 (ptpp)
REVERT: A   59 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7497 (tm-30)
REVERT: A   61 LEU cc_start: 0.9283 (mp) cc_final: 0.8994 (mp)
REVERT: A  120 MET cc_start: 0.8944 (mmm) cc_final: 0.8607 (mmm)
REVERT: B   35 ARG cc_start: 0.9520 (mtp85) cc_final: 0.8803 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8554 (pm20)
REVERT: B   98 TYR cc_start: 0.9159 (m-80) cc_final: 0.8897 (m-80)
REVERT: C   64 GLU cc_start: 0.9002 (tp30) cc_final: 0.8754 (tp30)
REVERT: C   72 ASP cc_start: 0.9177 (p0) cc_final: 0.8976 (p0)
REVERT: D   71 GLU cc_start: 0.9137 (tt0) cc_final: 0.8914 (tm-30)
REVERT: E   60 LEU cc_start: 0.9425 (tp) cc_final: 0.9019 (tt)
REVERT: E  129 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8353 (ttp80)
REVERT: F   37 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9351 (mm)
REVERT: G   35 ARG cc_start: 0.8365 (ttp-170) cc_final: 0.8051 (ttm110)
REVERT: G   41 GLU cc_start: 0.9245 (mt-10) cc_final: 0.8496 (pt0)
REVERT: G   61 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8583 (tm-30)
REVERT: G   95 LYS cc_start: 0.9456 (tppp) cc_final: 0.9180 (tppt)
REVERT: H  105 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8185 (tm-30)
REVERT: H  106 LEU cc_start: 0.9663 (mt) cc_final: 0.9086 (mt)
  outliers start: 17
  outliers final: 10
  residues processed: 155
  average time/residue: 0.2865
  time to fit residues: 61.6786
Evaluate side-chains
  147 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 134
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   77 ASP
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 B residue   85 ASP
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain E residue  129 ARG
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   52 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 80 optimal weight:    8.9990
   chunk 88 optimal weight:    7.9990
   chunk 33 optimal weight:    0.0980
   chunk 36 optimal weight:    2.9990
   chunk 17 optimal weight:    0.3980
   chunk 51 optimal weight:    8.9990
   chunk 12 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 8 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   chunk 83 optimal weight:   10.0000
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
C 104 GLN
E  68 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.060280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.039683 restraints weight = 70623.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.040591 restraints weight = 36174.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.041218 restraints weight = 24605.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8663
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12685  Z= 0.184
  Angle     :  0.605   8.163  18390  Z= 0.350
  Chirality :  0.033   0.155   2096
  Planarity :  0.004   0.061   1312
  Dihedral  : 30.265 143.007   4020
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 21.92 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.23 (0.31), residues: 726
  helix:  2.38 (0.23), residues: 514
  sheet:  None (None), residues: 0
  loop : -0.85 (0.40), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.016   0.001   PHE E  67 
 TYR   0.009   0.001   TYR F  88 
 ARG   0.005   0.000   ARG C  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04129 (  738)
  hydrogen bonds       : angle       2.74588 ( 1835)
  covalent geometry    : bond        0.00405 (12685)
  covalent geometry    : angle       0.60472 (18390)

*********************** 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: 21
    poor density    : 137
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7438 (tm-30)
REVERT: A   61 LEU cc_start: 0.9265 (mp) cc_final: 0.8796 (mp)
REVERT: A  120 MET cc_start: 0.8994 (mmm) cc_final: 0.8665 (mmm)
REVERT: B   35 ARG cc_start: 0.9510 (mtp85) cc_final: 0.8850 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8557 (pm20)
REVERT: B   98 TYR cc_start: 0.9176 (m-80) cc_final: 0.8943 (m-80)
REVERT: C   64 GLU cc_start: 0.8957 (tp30) cc_final: 0.8688 (tp30)
REVERT: D   68 ASP cc_start: 0.9065 (t0) cc_final: 0.8851 (t0)
REVERT: D   71 GLU cc_start: 0.9135 (tt0) cc_final: 0.8929 (tm-30)
REVERT: E   59 GLU cc_start: 0.8438 (mp0) cc_final: 0.8169 (mp0)
REVERT: E   60 LEU cc_start: 0.9420 (tp) cc_final: 0.9028 (tt)
REVERT: E  129 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8345 (ttp80)
REVERT: F   37 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9370 (mm)
REVERT: F   53 GLU cc_start: 0.9069 (mp0) cc_final: 0.8867 (mp0)
REVERT: F   67 ARG cc_start: 0.9407 (ttp-110) cc_final: 0.8839 (mtm-85)
REVERT: G   35 ARG cc_start: 0.8330 (ttp-170) cc_final: 0.8022 (ttm110)
REVERT: G   41 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8511 (pt0)
REVERT: G   61 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8552 (tm-30)
REVERT: G   75 LYS cc_start: 0.9399 (mmmm) cc_final: 0.9035 (mmmm)
REVERT: G   95 LYS cc_start: 0.9458 (tppp) cc_final: 0.9190 (tppt)
REVERT: H  105 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8210 (tm-30)
REVERT: H  106 LEU cc_start: 0.9668 (mt) cc_final: 0.9086 (mt)
  outliers start: 21
  outliers final: 14
  residues processed: 151
  average time/residue: 0.2564
  time to fit residues: 53.5202
Evaluate side-chains
  149 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   77 ASP
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 B residue   85 ASP
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain E residue  129 ARG
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   85 ASP
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   52 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 71 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9980
   chunk 51 optimal weight:    8.9990
   chunk 25 optimal weight:    3.9990
   chunk 22 optimal weight:    6.9990
   chunk 88 optimal weight:    6.9990
   chunk 30 optimal weight:    4.9990
   chunk 75 optimal weight:    8.9990
   chunk 26 optimal weight:    0.9980
   chunk 92 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    2.5986

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.059876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.038976 restraints weight = 70664.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.039875 restraints weight = 36350.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.040466 restraints weight = 24902.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.2723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  12685  Z= 0.217
  Angle     :  0.622   8.161  18390  Z= 0.361
  Chirality :  0.034   0.190   2096
  Planarity :  0.004   0.059   1312
  Dihedral  : 30.338 143.433   4020
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.15 (0.31), residues: 726
  helix:  2.33 (0.23), residues: 513
  sheet:  None (None), residues: 0
  loop : -0.88 (0.40), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.006   0.001   PHE B 100 
 TYR   0.020   0.002   TYR H  83 
 ARG   0.004   0.000   ARG G  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04688 (  738)
  hydrogen bonds       : angle       2.94500 ( 1835)
  covalent geometry    : bond        0.00480 (12685)
  covalent geometry    : angle       0.62233 (18390)

*********************** 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
  147 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7522 (tm-30)
REVERT: A   61 LEU cc_start: 0.9299 (mp) cc_final: 0.8798 (mp)
REVERT: B   35 ARG cc_start: 0.9516 (mtp85) cc_final: 0.8868 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8582 (pm20)
REVERT: B   98 TYR cc_start: 0.9176 (m-80) cc_final: 0.8898 (m-80)
REVERT: C   64 GLU cc_start: 0.8978 (tp30) cc_final: 0.8716 (tp30)
REVERT: D   68 ASP cc_start: 0.9095 (t0) cc_final: 0.8869 (t0)
REVERT: D   71 GLU cc_start: 0.9175 (tt0) cc_final: 0.8965 (tm-30)
REVERT: E   60 LEU cc_start: 0.9445 (tp) cc_final: 0.9077 (tt)
REVERT: E   90 MET cc_start: 0.9319 (mmm) cc_final: 0.9105 (mmp)
REVERT: E  129 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.8349 (ttp80)
REVERT: F   37 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9369 (mm)
REVERT: F   53 GLU cc_start: 0.9106 (mp0) cc_final: 0.8852 (mp0)
REVERT: F   84 MET cc_start: 0.9136 (mmm) cc_final: 0.8161 (mmm)
REVERT: G   35 ARG cc_start: 0.8358 (ttp-170) cc_final: 0.8039 (ttm110)
REVERT: G   41 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8555 (pt0)
REVERT: G   61 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8574 (tm-30)
REVERT: G   75 LYS cc_start: 0.9410 (mmmm) cc_final: 0.9007 (mmmm)
REVERT: G   95 LYS cc_start: 0.9465 (tppp) cc_final: 0.9209 (tppt)
REVERT: H  105 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8226 (tm-30)
REVERT: H  106 LEU cc_start: 0.9669 (mt) cc_final: 0.9079 (mt)
  outliers start: 17
  outliers final: 12
  residues processed: 141
  average time/residue: 0.2521
  time to fit residues: 49.3481
Evaluate side-chains
  139 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 124
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   77 ASP
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 B residue   85 ASP
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain E residue  129 ARG
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   52 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 51 optimal weight:    7.9990
   chunk 64 optimal weight:    1.9990
   chunk 96 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 73 optimal weight:    8.9990
   chunk 24 optimal weight:    0.0370
   chunk 66 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.7058

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.061645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.041325 restraints weight = 68815.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.042289 restraints weight = 34941.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.042925 restraints weight = 23415.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.2928

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= 0.151
  Angle     :  0.616  12.547  18390  Z= 0.349
  Chirality :  0.033   0.174   2096
  Planarity :  0.004   0.060   1312
  Dihedral  : 30.237 143.163   4020
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 23.38 %
    Favored  : 73.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.27 (0.31), residues: 726
  helix:  2.38 (0.23), residues: 512
  sheet:  None (None), residues: 0
  loop : -0.72 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS B  75 
 PHE   0.007   0.001   PHE B 100 
 TYR   0.015   0.001   TYR H  83 
 ARG   0.008   0.000   ARG G  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03492 (  738)
  hydrogen bonds       : angle       2.65805 ( 1835)
  covalent geometry    : bond        0.00325 (12685)
  covalent geometry    : angle       0.61601 (18390)

*********************** 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
  166 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 149
  time to evaluate  : 0.874 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7322 (tm-30)
REVERT: A   61 LEU cc_start: 0.9253 (mp) cc_final: 0.8632 (mt)
REVERT: A  120 MET cc_start: 0.9095 (mmm) cc_final: 0.8835 (mmt)
REVERT: B   35 ARG cc_start: 0.9522 (mtp85) cc_final: 0.8921 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8530 (pm20)
REVERT: B   98 TYR cc_start: 0.9166 (m-10) cc_final: 0.8909 (m-80)
REVERT: C   64 GLU cc_start: 0.9024 (tp30) cc_final: 0.8737 (tp30)
REVERT: D   52 THR cc_start: 0.8845 (p) cc_final: 0.8557 (p)
REVERT: D   68 ASP cc_start: 0.9030 (t0) cc_final: 0.8806 (t0)
REVERT: D   71 GLU cc_start: 0.9110 (tt0) cc_final: 0.8888 (tm-30)
REVERT: E   60 LEU cc_start: 0.9438 (tp) cc_final: 0.9005 (tt)
REVERT: E   90 MET cc_start: 0.9228 (mmm) cc_final: 0.9022 (mmp)
REVERT: E  107 THR cc_start: 0.9043 (m) cc_final: 0.8721 (p)
REVERT: E  119 ILE cc_start: 0.9339 (pt) cc_final: 0.9080 (pt)
REVERT: E  120 MET cc_start: 0.8673 (mpp) cc_final: 0.8386 (mpp)
REVERT: E  129 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8418 (ttp80)
REVERT: F   37 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9321 (mm)
REVERT: F   67 ARG cc_start: 0.9454 (ttp-110) cc_final: 0.8866 (mtm-85)
REVERT: F   84 MET cc_start: 0.9108 (mmm) cc_final: 0.8110 (mmm)
REVERT: G   35 ARG cc_start: 0.8362 (ttp-170) cc_final: 0.8082 (ttm110)
REVERT: G   41 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8566 (pt0)
REVERT: G   61 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8525 (tm-30)
REVERT: G   75 LYS cc_start: 0.9381 (mmmm) cc_final: 0.8987 (mmmm)
REVERT: G   95 LYS cc_start: 0.9441 (tppp) cc_final: 0.9158 (tppt)
REVERT: H  105 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8253 (tm-30)
REVERT: H  106 LEU cc_start: 0.9668 (mt) cc_final: 0.9089 (mt)
  outliers start: 17
  outliers final: 12
  residues processed: 159
  average time/residue: 0.2434
  time to fit residues: 53.9412
Evaluate side-chains
  154 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 139
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   77 ASP
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 B residue   85 ASP
Chi-restraints excluded: chain D residue   88 THR
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 G residue  101 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   52 THR
Chi-restraints excluded: chain H residue   80 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 9 optimal weight:    0.2980
   chunk 8 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 96 optimal weight:   10.0000
   chunk 6 optimal weight:    2.9990
   chunk 81 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 28 optimal weight:    0.1980
   chunk 18 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
H  63 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.062434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.041622 restraints weight = 69534.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.042593 restraints weight = 35547.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.043241 restraints weight = 24132.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          0.3110

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= 0.151
  Angle     :  0.621  12.486  18390  Z= 0.349
  Chirality :  0.033   0.161   2096
  Planarity :  0.004   0.061   1312
  Dihedral  : 30.185 142.655   4020
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 25.32 %
    Favored  : 71.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.35 (0.32), residues: 726
  helix:  2.44 (0.23), residues: 514
  sheet:  None (None), residues: 0
  loop : -0.72 (0.41), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.000   HIS F  75 
 PHE   0.011   0.001   PHE E  67 
 TYR   0.015   0.001   TYR H  83 
 ARG   0.014   0.000   ARG H  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03504 (  738)
  hydrogen bonds       : angle       2.61527 ( 1835)
  covalent geometry    : bond        0.00328 (12685)
  covalent geometry    : angle       0.62148 (18390)

*********************** 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
  167 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 149
  time to evaluate  : 0.852 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.9548 (ptmt) cc_final: 0.9131 (ptpp)
REVERT: A   59 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7352 (tm-30)
REVERT: A   61 LEU cc_start: 0.9259 (mp) cc_final: 0.8594 (mt)
REVERT: A  120 MET cc_start: 0.9073 (mmm) cc_final: 0.8765 (mmm)
REVERT: B   35 ARG cc_start: 0.9519 (mtp85) cc_final: 0.8948 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8520 (pm20)
REVERT: B   98 TYR cc_start: 0.9134 (m-10) cc_final: 0.8836 (m-80)
REVERT: C   64 GLU cc_start: 0.9020 (tp30) cc_final: 0.8752 (tp30)
REVERT: D   52 THR cc_start: 0.8821 (p) cc_final: 0.8476 (p)
REVERT: D   71 GLU cc_start: 0.9067 (tt0) cc_final: 0.8864 (tm-30)
REVERT: D  113 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8672 (mt-10)
REVERT: E   60 LEU cc_start: 0.9441 (tp) cc_final: 0.9020 (tt)
REVERT: E   90 MET cc_start: 0.9213 (mmm) cc_final: 0.8779 (mmp)
REVERT: E   94 GLU cc_start: 0.9327 (mm-30) cc_final: 0.8961 (mm-30)
REVERT: E  107 THR cc_start: 0.9009 (m) cc_final: 0.8703 (p)
REVERT: E  119 ILE cc_start: 0.9356 (pt) cc_final: 0.9088 (pt)
REVERT: E  120 MET cc_start: 0.8674 (mpp) cc_final: 0.8405 (mpp)
REVERT: E  129 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8386 (ttp80)
REVERT: F   37 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9339 (mm)
REVERT: F   67 ARG cc_start: 0.9436 (ttp-110) cc_final: 0.8817 (mtm-85)
REVERT: F   84 MET cc_start: 0.9084 (mmm) cc_final: 0.8098 (mmm)
REVERT: G   35 ARG cc_start: 0.8253 (ttp-170) cc_final: 0.8046 (ttm110)
REVERT: G   61 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8509 (tm-30)
REVERT: G   75 LYS cc_start: 0.9396 (mmmm) cc_final: 0.8999 (mmmm)
REVERT: G   95 LYS cc_start: 0.9439 (tppp) cc_final: 0.9152 (tppt)
REVERT: H  105 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8386 (tm-30)
  outliers start: 18
  outliers final: 12
  residues processed: 160
  average time/residue: 0.2536
  time to fit residues: 56.8733
Evaluate side-chains
  155 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 140
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   77 ASP
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 B residue   85 ASP
Chi-restraints excluded: chain D residue   88 THR
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 G residue  101 THR
Chi-restraints excluded: chain G residue  111 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 79 optimal weight:    8.9990
   chunk 92 optimal weight:    6.9990
   chunk 25 optimal weight:    0.3980
   chunk 55 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 67 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 35 optimal weight:   10.0000
   chunk 61 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0470
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
E  55 GLN
H  63 ASN
H  84 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.062708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.042193 restraints weight = 69134.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.043143 restraints weight = 35401.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.043789 restraints weight = 23987.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
moved from start:          0.3273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12685  Z= 0.152
  Angle     :  0.637  12.100  18390  Z= 0.359
  Chirality :  0.033   0.159   2096
  Planarity :  0.004   0.061   1312
  Dihedral  : 30.173 142.515   4020
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 25.97 %
    Favored  : 71.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.23 (0.32), residues: 726
  helix:  2.32 (0.23), residues: 515
  sheet:  None (None), residues: 0
  loop : -0.72 (0.42), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS H  82 
 PHE   0.013   0.001   PHE E  67 
 TYR   0.011   0.001   TYR D  40 
 ARG   0.006   0.000   ARG G  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03443 (  738)
  hydrogen bonds       : angle       2.61221 ( 1835)
  covalent geometry    : bond        0.00328 (12685)
  covalent geometry    : angle       0.63740 (18390)

********************** 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
  169 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 152
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.9520 (ptmt) cc_final: 0.9099 (ptpp)
REVERT: A   59 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7345 (tm-30)
REVERT: A   60 LEU cc_start: 0.9239 (mm) cc_final: 0.9036 (mm)
REVERT: A   61 LEU cc_start: 0.9252 (mp) cc_final: 0.8576 (mt)
REVERT: A  120 MET cc_start: 0.9049 (mmm) cc_final: 0.8740 (mmm)
REVERT: B   35 ARG cc_start: 0.9516 (mtp85) cc_final: 0.8906 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8496 (pm20)
REVERT: B   98 TYR cc_start: 0.9147 (m-10) cc_final: 0.8823 (m-80)
REVERT: C   64 GLU cc_start: 0.9039 (tp30) cc_final: 0.8764 (tp30)
REVERT: D   68 ASP cc_start: 0.9048 (t0) cc_final: 0.8828 (t0)
REVERT: D   71 GLU cc_start: 0.9061 (tt0) cc_final: 0.8848 (tm-30)
REVERT: E   60 LEU cc_start: 0.9432 (tp) cc_final: 0.8996 (tt)
REVERT: E  119 ILE cc_start: 0.9348 (pt) cc_final: 0.9088 (pt)
REVERT: E  120 MET cc_start: 0.8717 (mpp) cc_final: 0.8418 (mpp)
REVERT: E  129 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8376 (ttp80)
REVERT: F   37 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9324 (mm)
REVERT: F   84 MET cc_start: 0.9095 (mmm) cc_final: 0.8212 (tpp)
REVERT: G   35 ARG cc_start: 0.8268 (ttp-170) cc_final: 0.7971 (ttm170)
REVERT: G   61 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8490 (tm-30)
REVERT: G   75 LYS cc_start: 0.9443 (mmmm) cc_final: 0.8993 (mmmm)
REVERT: G   95 LYS cc_start: 0.9424 (tppp) cc_final: 0.9134 (tppt)
REVERT: H  105 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8373 (tm-30)
  outliers start: 17
  outliers final: 14
  residues processed: 161
  average time/residue: 0.2320
  time to fit residues: 53.0163
Evaluate side-chains
  159 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 142
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   77 ASP
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 B residue   85 ASP
Chi-restraints excluded: chain D residue   88 THR
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 G residue   49 VAL
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   52 THR
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain H residue   84 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 92 optimal weight:    7.9990
   chunk 82 optimal weight:   20.0000
   chunk 83 optimal weight:   10.0000
   chunk 49 optimal weight:    5.9990
   chunk 9 optimal weight:    0.0980
   chunk 93 optimal weight:    6.9990
   chunk 89 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9990
   chunk 35 optimal weight:   10.0000
   chunk 31 optimal weight:    2.9990
   overall best weight:    2.4188

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

Flipped N/Q/H residues before XYZ refinement:
H  63 ASN
H  84 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.063647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.043361 restraints weight = 79576.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.044365 restraints weight = 43143.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.045048 restraints weight = 30225.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8684
moved from start:          0.3220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  12685  Z= 0.208
  Angle     :  0.657  11.477  18390  Z= 0.371
  Chirality :  0.035   0.156   2096
  Planarity :  0.004   0.060   1312
  Dihedral  : 30.248 142.845   4020
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 26.14 %
    Favored  : 71.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.17 (0.31), residues: 726
  helix:  2.30 (0.23), residues: 514
  sheet:  None (None), residues: 0
  loop : -0.77 (0.41), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.013   0.001   PHE E  67 
 TYR   0.013   0.001   TYR F  51 
 ARG   0.007   0.000   ARG G  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04553 (  738)
  hydrogen bonds       : angle       2.87123 ( 1835)
  covalent geometry    : bond        0.00461 (12685)
  covalent geometry    : angle       0.65702 (18390)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3347.72 seconds
wall clock time: 59 minutes 11.93 seconds (3551.93 seconds total)