Starting phenix.real_space_refine
on Thu Mar  5 16:34:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7u46_26330/03_2026/7u46_26330.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7u46_26330/03_2026/7u46_26330.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7u46_26330/03_2026/7u46_26330.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7u46_26330/03_2026/7u46_26330.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7u46_26330/03_2026/7u46_26330.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7u46_26330/03_2026/7u46_26330.map"
  }
  resolution = 2.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.030
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P     288      5.49       5
     S      16      5.16       5
     C    7565      2.51       5
     N    2453      2.21       5
     O    3038      1.98       5
     H   11015      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 24375
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 1503
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 1503
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 2, 'TRANS': 86}
    Chain: "B"
      Number of atoms: 1307
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 1307
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "C"
      Number of atoms: 1573
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 1573
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "D"
      Number of atoms: 1458
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 1458
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 1539
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 1539
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 2, 'TRANS': 88}
    Chain: "F"
      Number of atoms: 1283
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 1283
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "G"
      Number of atoms: 1589
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 1589
          Classifications: {'peptide': 100}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
    Chain: "H"
      Number of atoms: 1458
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 1458
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "K"
      Number of atoms: 3451
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 205, 3451
          Classifications: {'peptide': 205}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 199}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 4607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 4607
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 4607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 4607
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 4.39, per 1000 atoms: 0.18
  Number of scatterers: 24375
  At special positions: 0
  Unit cell: (108.385, 128.092, 119.881, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      16     16.00
     P     288     15.00
     O    3038      8.00
     N    2453      7.00
     C    7565      6.00
     H   11015      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.12
  Conformation dependent library (CDL) restraints added in 556.1 milliseconds
  

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1740

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 11 sheets defined
      69.0% alpha, 5.9% beta
      139 base pairs and 262 stacking pairs defined.
    Time for finding SS restraints: 4.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 57
      removed outlier: 3.604A  pdb=" N   GLU A  50 " --> pdb=" O   GLY A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 76
      removed outlier: 3.701A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 116
      removed outlier: 3.891A  pdb=" N   LEU A  91 " --> pdb=" O   GLN A  87 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LEU A  92 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ALA A  93 " --> pdb=" O   GLN A  89 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   LEU A 112 " --> pdb=" O   ASP A 108 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LEU A 114 " --> pdb=" O   TYR A 110 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   HIS A 115 " --> pdb=" O   LEU A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 134
      removed outlier: 3.550A  pdb=" N   VAL A 126 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LEU A 128 " --> pdb=" O   LYS A 124 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ALA A 129 " --> pdb=" O   ASP A 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.840A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ARG B  55 " --> pdb=" O   TYR B  51 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.686A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
      removed outlier: 3.929A  pdb=" N   ARG C  20 " --> pdb=" O   SER C  16 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 36
      removed outlier: 3.704A  pdb=" N   VAL C  30 " --> pdb=" O   PRO C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 73
    Processing helix  chain 'C' and resid 79 through 89
      removed outlier: 3.541A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 123
    Processing helix  chain 'E' and resid 46 through 56
    Processing helix  chain 'E' and resid 63 through 78
      removed outlier: 3.715A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LYS E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 116
      removed outlier: 3.606A  pdb=" N   LEU E  91 " --> pdb=" O   GLN E  87 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LEU E 111 " --> pdb=" O   GLU E 107 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   LEU E 112 " --> pdb=" O   ASP E 108 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   THR E 113 " --> pdb=" O   ALA E 109 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LEU E 114 " --> pdb=" O   TYR E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 134
      removed outlier: 3.949A  pdb=" N   VAL E 126 " --> pdb=" O   PHE E 122 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.668A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ASN F  64 " --> pdb=" O   VAL F  60 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
      removed outlier: 3.630A  pdb=" N   VAL G  30 " --> pdb=" O   PRO G  26 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 73
      removed outlier: 3.734A  pdb=" N   LEU G  65 " --> pdb=" O   GLU G  61 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
      removed outlier: 3.524A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
      removed outlier: 3.576A  pdb=" N   LYS G  95 " --> pdb=" O   GLU G  91 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 104 through 123
    Processing helix  chain 'K' and resid 2 through 15
      removed outlier: 3.673A  pdb=" N   GLU K   7 " --> pdb=" O   GLU K   3 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   PHE K   8 " --> pdb=" O   THR K   4 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LYS K  15 " --> pdb=" O   ARG K  11 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 20 through 29
    Processing helix  chain 'K' and resid 32 through 39
    Processing helix  chain 'K' and resid 44 through 59
    Processing helix  chain 'K' and resid 62 through 77
      removed outlier: 3.612A  pdb=" N   PHE K  76 " --> pdb=" O   ILE K  72 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 78 through 81
    Processing helix  chain 'K' and resid 100 through 116
    Processing helix  chain 'K' and resid 171 through 183
    Processing helix  chain 'K' and resid 197 through 211
    Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86
      removed outlier: 6.970A  pdb=" N   ASN A  85 " --> 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 120 through 121
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97
      removed outlier: 6.407A  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: 7.057A  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 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.751A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 85 through 86
      removed outlier: 7.070A  pdb=" N   ASN E  85 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 120 through 121
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.146A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 120 through 126
      removed outlier: 5.300A  pdb=" N   TYR K 151 " --> pdb=" O   SER K 164 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   TYR K 155 " --> pdb=" O   TYR K 160 " (cutoff:3.500A)
      removed outlier: 4.945A  pdb=" N   TYR K 160 " --> pdb=" O   TYR K 155 " (cutoff:3.500A)
      removed outlier: 7.571A  pdb=" N   TRP K  83 " --> pdb=" O   LEU K 193 " (cutoff:3.500A)
      removed outlier: 7.524A  pdb=" N   LEU K 193 " --> pdb=" O   TRP K  83 " (cutoff:3.500A)
      removed outlier: 5.661A  pdb=" N   VAL K  85 " --> pdb=" O   MET K 191 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   GLN K 187 " --> pdb=" O   SER K  89 " (cutoff:3.500A)

    464 hydrogen bonds defined for protein.
    1380 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      335 hydrogen bonds
      670 hydrogen bond angles
      0 basepair planarities
      139 basepair parallelities
      262 stacking parallelities
  Total time for adding SS restraints: 5.57

  Time building geometry restraints manager: 3.00 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 11012
        1.03 -     1.22: 125
        1.22 -     1.42: 6172
        1.42 -     1.61: 7880
        1.61 -     1.81: 30
  Bond restraints: 25219
  Sorted by residual:
  bond pdb=" CB  VAL G  49 "
       pdb=" CG2 VAL G  49 "
    ideal  model  delta    sigma   weight residual
    1.521  1.431  0.090 3.30e-02 9.18e+02 7.45e+00
  bond pdb=" CB  THR B  73 "
       pdb=" CG2 THR B  73 "
    ideal  model  delta    sigma   weight residual
    1.521  1.437  0.084 3.30e-02 9.18e+02 6.50e+00
  bond pdb=" CB  THR A 113 "
       pdb=" CG2 THR A 113 "
    ideal  model  delta    sigma   weight residual
    1.521  1.442  0.079 3.30e-02 9.18e+02 5.76e+00
  bond pdb=" CB  VAL F  57 "
       pdb=" CG1 VAL F  57 "
    ideal  model  delta    sigma   weight residual
    1.521  1.446  0.075 3.30e-02 9.18e+02 5.20e+00
  bond pdb=" CG1 ILE D  61 "
       pdb=" CD1 ILE D  61 "
    ideal  model  delta    sigma   weight residual
    1.513  1.427  0.086 3.90e-02 6.57e+02 4.81e+00
  ... (remaining 25214 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 44810
        2.19 -     4.38: 855
        4.38 -     6.57: 28
        6.57 -     8.76: 8
        8.76 -    10.95: 4
  Bond angle restraints: 45705
  Sorted by residual:
  angle pdb=" N   VAL A 119 "
        pdb=" CA  VAL A 119 "
        pdb=" C   VAL A 119 "
      ideal   model   delta    sigma   weight residual
     113.53  109.43    4.10 9.80e-01 1.04e+00 1.75e+01
  angle pdb=" N   ILE F  26 "
        pdb=" CA  ILE F  26 "
        pdb=" C   ILE F  26 "
      ideal   model   delta    sigma   weight residual
     113.43  109.09    4.34 1.09e+00 8.42e-01 1.58e+01
  angle pdb=" N   GLY H 104 "
        pdb=" CA  GLY H 104 "
        pdb=" C   GLY H 104 "
      ideal   model   delta    sigma   weight residual
     111.02  118.01   -6.99 1.86e+00 2.89e-01 1.41e+01
  angle pdb=" N   GLY D 104 "
        pdb=" CA  GLY D 104 "
        pdb=" C   GLY D 104 "
      ideal   model   delta    sigma   weight residual
     111.02  117.96   -6.94 1.86e+00 2.89e-01 1.39e+01
  angle pdb=" OP1  DC I -24 "
        pdb=" P    DC I -24 "
        pdb=" OP2  DC I -24 "
      ideal   model   delta    sigma   weight residual
     120.00  110.20    9.80 3.00e+00 1.11e-01 1.07e+01
  ... (remaining 45700 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.26: 8823
       32.26 -    64.52: 1843
       64.52 -    96.78: 61
       96.78 -   129.04: 2
      129.04 -   161.30: 3
  Dihedral angle restraints: 10732
    sinusoidal: 7617
      harmonic: 3115
  Sorted by residual:
  dihedral pdb=" CA  HIS F  75 "
           pdb=" C   HIS F  75 "
           pdb=" N   ALA F  76 "
           pdb=" CA  ALA F  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.48   22.52     0      5.00e+00 4.00e-02 2.03e+01
  dihedral pdb=" CA  TYR B  98 "
           pdb=" C   TYR B  98 "
           pdb=" N   GLY B  99 "
           pdb=" CA  GLY B  99 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.20  -19.80     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" C4'  DT J -22 "
           pdb=" C3'  DT J -22 "
           pdb=" O3'  DT J -22 "
           pdb=" P    DC J -21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   58.70  161.30     1      3.50e+01 8.16e-04 1.53e+01
  ... (remaining 10729 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 1767
       0.067 -    0.134: 513
       0.134 -    0.200: 32
       0.200 -    0.267: 2
       0.267 -    0.334: 2
  Chirality restraints: 2316
  Sorted by residual:
  chirality pdb=" P    DC I -24 "
            pdb=" OP1  DC I -24 "
            pdb=" OP2  DC I -24 "
            pdb=" O5'  DC I -24 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.68   -0.33 2.00e-01 2.50e+01 2.79e+00
  chirality pdb=" P    DC J -24 "
            pdb=" OP1  DC J -24 "
            pdb=" OP2  DC J -24 "
            pdb=" O5'  DC J -24 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.64   -0.30 2.00e-01 2.50e+01 2.21e+00
  chirality pdb=" CB  VAL F  81 "
            pdb=" CA  VAL F  81 "
            pdb=" CG1 VAL F  81 "
            pdb=" CG2 VAL F  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.03e+00
  ... (remaining 2313 not shown)

  Planarity restraints: 2666
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR G  50 "   -0.028 2.00e-02 2.50e+03   2.35e-02 1.66e+01
        pdb=" CG  TYR G  50 "    0.063 2.00e-02 2.50e+03
        pdb=" CD1 TYR G  50 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD2 TYR G  50 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR G  50 "    0.012 2.00e-02 2.50e+03
        pdb=" CE2 TYR G  50 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR G  50 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR G  50 "   -0.000 2.00e-02 2.50e+03
        pdb=" HD1 TYR G  50 "    0.008 2.00e-02 2.50e+03
        pdb=" HD2 TYR G  50 "    0.004 2.00e-02 2.50e+03
        pdb=" HE1 TYR G  50 "    0.000 2.00e-02 2.50e+03
        pdb=" HE2 TYR G  50 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  98 "    0.035 2.00e-02 2.50e+03   1.59e-02 7.61e+00
        pdb=" CG  TYR B  98 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  98 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  98 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  98 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  98 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  98 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B  98 "    0.010 2.00e-02 2.50e+03
        pdb=" HD1 TYR B  98 "   -0.003 2.00e-02 2.50e+03
        pdb=" HD2 TYR B  98 "   -0.003 2.00e-02 2.50e+03
        pdb=" HE1 TYR B  98 "    0.003 2.00e-02 2.50e+03
        pdb=" HE2 TYR B  98 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE E 122 "    0.038 5.00e-02 4.00e+02   5.77e-02 5.32e+00
        pdb=" N   PRO E 123 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO E 123 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO E 123 "    0.032 5.00e-02 4.00e+02
  ... (remaining 2663 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.17: 959
        2.17 -     2.78: 41187
        2.78 -     3.38: 59937
        3.38 -     3.99: 87001
        3.99 -     4.60: 134856
  Nonbonded interactions: 323940
  Sorted by model distance:
  nonbonded pdb=" O4   DT I  23 "
            pdb=" H62  DA J -23 "
     model   vdw
     1.559 2.450
  nonbonded pdb=" OD2 ASP K  70 "
            pdb=" HH  TYR K 151 "
     model   vdw
     1.594 2.450
  nonbonded pdb="HH11 ARG A  80 "
            pdb=" OE1 GLU K   7 "
     model   vdw
     1.627 2.450
  nonbonded pdb=" HG  SER K  32 "
            pdb=" OE1 GLN K  35 "
     model   vdw
     1.651 2.450
  nonbonded pdb=" OE1 GLU E  73 "
            pdb="HD21 ASN F  25 "
     model   vdw
     1.655 2.450
  ... (remaining 323935 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' and resid 46 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 24 through 101)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 15 through 112)
  selection = (chain 'G' and resid 15 through 112)
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}
ncs_group {
  reference = (chain 'I' and (resid -72 through -1 or resid 1 through 72))
  selection = (chain 'J' and (resid -72 through -1 or resid 1 through 72))
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.120
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     26.130
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:5.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
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      :  0.011   0.090  14204  Z= 0.434
  Angle     :  0.791  10.948  20430  Z= 0.471
  Chirality :  0.057   0.334   2316
  Planarity :  0.005   0.058   1569
  Dihedral  : 26.919 161.305   6092
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  0.77 %
    Favored  : 98.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.27), residues: 905
  helix:  0.57 (0.21), residues: 620
  sheet: -1.15 (0.70), residues: 43
  loop : -1.72 (0.32), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.001   ARG E  69 
 TYR   0.065   0.003   TYR G  50 
 PHE   0.013   0.002   PHE H  70 
 TRP   0.014   0.002   TRP A  86 
 HIS   0.007   0.002   HIS K 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.01106 (14204)
  covalent geometry    : angle       0.79074 (20430)
  hydrogen bonds       : bond        0.15720 (  799)
  hydrogen bonds       : angle       4.55970 ( 2050)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   91 LYS cc_start: 0.7783 (ttpt) cc_final: 0.7566 (ttpt)
REVERT: K  140 GLN cc_start: 0.8563 (tt0) cc_final: 0.7648 (tp-100)
  outliers start: 6
  outliers final: 0
  residues processed: 85
  average time/residue: 1.9956
  time to fit residues: 178.9338
Evaluate side-chains
  60 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.2980
   chunk 100 optimal weight:    3.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS
C  73 ASN
** K 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.185522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.118535 restraints weight = 32715.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 1.26
r_work: 0.3273 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.1458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  14204  Z= 0.170
  Angle     :  0.616   4.966  20430  Z= 0.381
  Chirality :  0.037   0.137   2316
  Planarity :  0.004   0.052   1569
  Dihedral  : 30.249 160.633   4266
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  5.74 %
    Favored  : 93.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.27), residues: 905
  helix:  1.65 (0.21), residues: 636
  sheet: -0.20 (0.73), residues: 45
  loop : -1.25 (0.34), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  99 
 TYR   0.017   0.001   TYR B  98 
 PHE   0.009   0.001   PHE K 123 
 TRP   0.005   0.001   TRP E  86 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (14204)
  covalent geometry    : angle       0.61632 (20430)
  hydrogen bonds       : bond        0.05124 (  799)
  hydrogen bonds       : angle       3.05270 ( 2050)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
REVERT: B   91 LYS cc_start: 0.7846 (ttpt) cc_final: 0.7621 (ttpt)
REVERT: C   73 ASN cc_start: 0.6659 (m-40) cc_final: 0.6116 (t0)
REVERT: K   54 HIS cc_start: 0.7445 (t-90) cc_final: 0.6944 (t70)
REVERT: K  140 GLN cc_start: 0.8724 (tt0) cc_final: 0.7717 (tp-100)
REVERT: K  167 MET cc_start: 0.7097 (ttt) cc_final: 0.6787 (ttt)
  outliers start: 5
  outliers final: 1
  residues processed: 84
  average time/residue: 1.8427
  time to fit residues: 163.9855
Evaluate side-chains
  72 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  117 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   overall best weight:    1.1184

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.180448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.111492 restraints weight = 32510.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 1.27
r_work: 0.3181 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3061 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14204  Z= 0.193
  Angle     :  0.620   7.271  20430  Z= 0.381
  Chirality :  0.039   0.140   2316
  Planarity :  0.004   0.046   1569
  Dihedral  : 30.112 162.518   4266
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 2.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  8.29 %
    Favored  : 91.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.72 (0.28), residues: 905
  helix:  2.02 (0.20), residues: 637
  sheet:  0.06 (0.74), residues: 45
  loop : -1.25 (0.35), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  69 
 TYR   0.019   0.001   TYR B  98 
 PHE   0.008   0.001   PHE F  61 
 TRP   0.009   0.001   TRP E  86 
 HIS   0.005   0.001   HIS K 185 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 (14204)
  covalent geometry    : angle       0.62033 (20430)
  hydrogen bonds       : bond        0.05354 (  799)
  hydrogen bonds       : angle       2.86622 ( 2050)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 0.492 
Fit side-chains
REVERT: B   91 LYS cc_start: 0.7800 (ttpt) cc_final: 0.7593 (ttpt)
REVERT: C   61 GLU cc_start: 0.7291 (tp30) cc_final: 0.7082 (tp30)
REVERT: C   64 GLU cc_start: 0.7776 (tt0) cc_final: 0.7502 (tt0)
REVERT: C   73 ASN cc_start: 0.6630 (m-40) cc_final: 0.5787 (t0)
REVERT: D   85 LYS cc_start: 0.8134 (mttp) cc_final: 0.7885 (mttt)
REVERT: K   54 HIS cc_start: 0.7444 (t-90) cc_final: 0.6934 (t70)
REVERT: K  140 GLN cc_start: 0.8716 (tt0) cc_final: 0.7712 (tp-100)
  outliers start: 5
  outliers final: 3
  residues processed: 88
  average time/residue: 1.8465
  time to fit residues: 171.8415
Evaluate side-chains
  84 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain K residue  117 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 112 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 109 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9980
   chunk 88 optimal weight:   30.0000
   chunk 101 optimal weight:   10.0000
   chunk 67 optimal weight:    1.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
** K 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.178089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.108264 restraints weight = 32445.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 1.27
r_work: 0.3109 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2989 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.2397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  14204  Z= 0.219
  Angle     :  0.636   5.046  20430  Z= 0.389
  Chirality :  0.041   0.145   2316
  Planarity :  0.005   0.045   1569
  Dihedral  : 30.068 161.973   4266
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  9.95 %
    Favored  : 88.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.61 (0.27), residues: 905
  helix:  1.93 (0.20), residues: 639
  sheet:  0.14 (0.74), residues: 45
  loop : -1.34 (0.36), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  69 
 TYR   0.019   0.002   TYR B  98 
 PHE   0.010   0.001   PHE K 162 
 TRP   0.009   0.001   TRP E  86 
 HIS   0.004   0.001   HIS H 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 (14204)
  covalent geometry    : angle       0.63645 (20430)
  hydrogen bonds       : bond        0.05837 (  799)
  hydrogen bonds       : angle       2.88516 ( 2050)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.446 
Fit side-chains
REVERT: C   64 GLU cc_start: 0.7725 (tt0) cc_final: 0.7481 (tt0)
REVERT: C   73 ASN cc_start: 0.6547 (m-40) cc_final: 0.5803 (t0)
REVERT: K  140 GLN cc_start: 0.8764 (tt0) cc_final: 0.7693 (tp-100)
  outliers start: 10
  outliers final: 6
  residues processed: 95
  average time/residue: 1.8900
  time to fit residues: 189.4948
Evaluate side-chains
  87 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain F residue   67 ARG
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain K residue  117 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 89 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 76 optimal weight:    7.9990
   chunk 96 optimal weight:    2.9990
   chunk 104 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.179170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.109570 restraints weight = 32386.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 1.25
r_work: 0.3151 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3031 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.2653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  14204  Z= 0.200
  Angle     :  0.618   4.961  20430  Z= 0.380
  Chirality :  0.040   0.139   2316
  Planarity :  0.004   0.046   1569
  Dihedral  : 30.005 161.111   4266
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 11.10 %
    Favored  : 87.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.75 (0.28), residues: 905
  helix:  2.04 (0.20), residues: 639
  sheet:  0.30 (0.77), residues: 45
  loop : -1.36 (0.36), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  80 
 TYR   0.011   0.001   TYR K 209 
 PHE   0.009   0.001   PHE K 108 
 TRP   0.008   0.001   TRP E  86 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 (14204)
  covalent geometry    : angle       0.61816 (20430)
  hydrogen bonds       : bond        0.05277 (  799)
  hydrogen bonds       : angle       2.78872 ( 2050)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
REVERT: C   64 GLU cc_start: 0.7724 (tt0) cc_final: 0.7484 (tt0)
REVERT: C   73 ASN cc_start: 0.6379 (m-40) cc_final: 0.5618 (t0)
REVERT: D   85 LYS cc_start: 0.8129 (mttp) cc_final: 0.7810 (mttt)
REVERT: K  140 GLN cc_start: 0.8771 (tt0) cc_final: 0.7709 (tp-100)
REVERT: K  167 MET cc_start: 0.7607 (ttm) cc_final: 0.7402 (ttm)
  outliers start: 10
  outliers final: 8
  residues processed: 86
  average time/residue: 1.8706
  time to fit residues: 170.0502
Evaluate side-chains
  87 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain E residue  113 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   67 ARG
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain K residue  117 LYS
Chi-restraints excluded: chain K residue  158 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 77 optimal weight:    7.9990
   chunk 52 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0970
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.178470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.108773 restraints weight = 32547.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 1.26
r_work: 0.3139 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3022 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.2818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  14204  Z= 0.205
  Angle     :  0.622   5.228  20430  Z= 0.381
  Chirality :  0.040   0.141   2316
  Planarity :  0.005   0.046   1569
  Dihedral  : 29.943 161.312   4266
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 10.84 %
    Favored  : 87.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.82 (0.28), residues: 905
  helix:  2.09 (0.20), residues: 639
  sheet:  0.55 (0.77), residues: 45
  loop : -1.38 (0.36), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  99 
 TYR   0.010   0.001   TYR F  51 
 PHE   0.008   0.001   PHE K 108 
 TRP   0.009   0.001   TRP A  86 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 (14204)
  covalent geometry    : angle       0.62199 (20430)
  hydrogen bonds       : bond        0.05458 (  799)
  hydrogen bonds       : angle       2.77455 ( 2050)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 GLU cc_start: 0.7732 (tt0) cc_final: 0.7486 (tt0)
REVERT: C   73 ASN cc_start: 0.6408 (m-40) cc_final: 0.5701 (t0)
REVERT: K  140 GLN cc_start: 0.8813 (tt0) cc_final: 0.7727 (tp-100)
  outliers start: 12
  outliers final: 8
  residues processed: 88
  average time/residue: 1.8692
  time to fit residues: 174.0250
Evaluate side-chains
  87 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   67 ARG
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain K residue  117 LYS
Chi-restraints excluded: chain K residue  158 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 102 optimal weight:   30.0000
   chunk 7 optimal weight:    0.3980
   chunk 24 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0050
   chunk 107 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.6794

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

Flipped N/Q/H residues before XYZ refinement:
K  37 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.179614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.109913 restraints weight = 32463.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 1.25
r_work: 0.3158 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.2858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  14204  Z= 0.164
  Angle     :  0.608   5.066  20430  Z= 0.376
  Chirality :  0.038   0.139   2316
  Planarity :  0.004   0.046   1569
  Dihedral  : 29.939 161.596   4266
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 10.71 %
    Favored  : 88.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.92 (0.28), residues: 905
  helix:  2.16 (0.20), residues: 639
  sheet:  0.65 (0.78), residues: 45
  loop : -1.32 (0.37), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  39 
 TYR   0.010   0.001   TYR K 155 
 PHE   0.007   0.001   PHE F  61 
 TRP   0.007   0.001   TRP A  86 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (14204)
  covalent geometry    : angle       0.60820 (20430)
  hydrogen bonds       : bond        0.04894 (  799)
  hydrogen bonds       : angle       2.80703 ( 2050)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.513 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 GLU cc_start: 0.7715 (tt0) cc_final: 0.7470 (tt0)
REVERT: C   73 ASN cc_start: 0.6341 (m-40) cc_final: 0.5637 (t0)
REVERT: K  140 GLN cc_start: 0.8816 (tt0) cc_final: 0.7723 (tp-100)
  outliers start: 10
  outliers final: 9
  residues processed: 84
  average time/residue: 2.0163
  time to fit residues: 178.8503
Evaluate side-chains
  87 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain E residue  113 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   67 ARG
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain K residue  117 LYS
Chi-restraints excluded: chain K residue  158 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 102 optimal weight:   20.0000
   chunk 105 optimal weight:    3.9990
   chunk 99 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 109 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    1.1988

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.181065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.112079 restraints weight = 32135.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 1.22
r_work: 0.3173 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3052 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.2899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14204  Z= 0.190
  Angle     :  0.609   5.421  20430  Z= 0.374
  Chirality :  0.039   0.141   2316
  Planarity :  0.004   0.046   1569
  Dihedral  : 29.928 160.619   4266
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 10.97 %
    Favored  : 87.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.97 (0.28), residues: 905
  helix:  2.20 (0.20), residues: 639
  sheet:  0.80 (0.78), residues: 45
  loop : -1.33 (0.37), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  99 
 TYR   0.010   0.001   TYR F  51 
 PHE   0.007   0.001   PHE F  61 
 TRP   0.008   0.001   TRP A  86 
 HIS   0.003   0.001   HIS H 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (14204)
  covalent geometry    : angle       0.60874 (20430)
  hydrogen bonds       : bond        0.05062 (  799)
  hydrogen bonds       : angle       2.72510 ( 2050)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 GLU cc_start: 0.7925 (tt0) cc_final: 0.7725 (tt0)
REVERT: C   73 ASN cc_start: 0.6582 (m-40) cc_final: 0.5939 (t0)
REVERT: K  117 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7413 (tmmm)
REVERT: K  140 GLN cc_start: 0.8821 (tt0) cc_final: 0.7735 (tp-100)
  outliers start: 10
  outliers final: 8
  residues processed: 85
  average time/residue: 1.9091
  time to fit residues: 171.5150
Evaluate side-chains
  87 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain E residue  113 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   67 ARG
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain K residue  117 LYS
Chi-restraints excluded: chain K residue  158 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 71 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   chunk 69 optimal weight:    0.5980
   chunk 77 optimal weight:   10.0000
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
K  37 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.181448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.112476 restraints weight = 32214.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 1.21
r_work: 0.3182 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3061 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.2910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14204  Z= 0.170
  Angle     :  0.604   5.541  20430  Z= 0.372
  Chirality :  0.038   0.139   2316
  Planarity :  0.004   0.046   1569
  Dihedral  : 29.921 160.837   4266
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 11.10 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.01 (0.28), residues: 905
  helix:  2.22 (0.20), residues: 639
  sheet:  0.83 (0.78), residues: 45
  loop : -1.30 (0.37), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  80 
 TYR   0.010   0.001   TYR F  51 
 PHE   0.007   0.001   PHE F  61 
 TRP   0.007   0.001   TRP E  86 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (14204)
  covalent geometry    : angle       0.60358 (20430)
  hydrogen bonds       : bond        0.04899 (  799)
  hydrogen bonds       : angle       2.73242 ( 2050)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 GLU cc_start: 0.7916 (tt0) cc_final: 0.7715 (tt0)
REVERT: C   73 ASN cc_start: 0.6562 (m-40) cc_final: 0.5922 (t0)
REVERT: K  117 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7408 (tmmm)
REVERT: K  140 GLN cc_start: 0.8813 (tt0) cc_final: 0.7728 (tp-100)
  outliers start: 11
  outliers final: 9
  residues processed: 85
  average time/residue: 1.9477
  time to fit residues: 174.8116
Evaluate side-chains
  88 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain E residue  113 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   67 ARG
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain K residue  117 LYS
Chi-restraints excluded: chain K residue  158 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 114 optimal weight:    4.9990
   chunk 100 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 105 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 104 optimal weight:    3.9990
   chunk 86 optimal weight:    7.9990
   chunk 89 optimal weight:    6.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.178141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.108473 restraints weight = 32407.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 1.25
r_work: 0.3110 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.2952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  14204  Z= 0.213
  Angle     :  0.623   4.996  20430  Z= 0.381
  Chirality :  0.040   0.140   2316
  Planarity :  0.005   0.057   1569
  Dihedral  : 29.897 161.505   4266
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 11.10 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.89 (0.28), residues: 905
  helix:  2.11 (0.20), residues: 640
  sheet:  0.92 (0.80), residues: 45
  loop : -1.33 (0.37), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E  80 
 TYR   0.010   0.001   TYR F  51 
 PHE   0.008   0.001   PHE H  70 
 TRP   0.009   0.001   TRP A  86 
 HIS   0.003   0.001   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 (14204)
  covalent geometry    : angle       0.62250 (20430)
  hydrogen bonds       : bond        0.05516 (  799)
  hydrogen bonds       : angle       2.75663 ( 2050)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.575 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 GLU cc_start: 0.7728 (tt0) cc_final: 0.7496 (tt0)
REVERT: C   73 ASN cc_start: 0.6417 (m-40) cc_final: 0.5691 (t0)
REVERT: E   92 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7537 (mp)
REVERT: K  117 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7372 (tmmm)
REVERT: K  140 GLN cc_start: 0.8811 (tt0) cc_final: 0.7725 (tp-100)
  outliers start: 11
  outliers final: 8
  residues processed: 86
  average time/residue: 1.9470
  time to fit residues: 177.1462
Evaluate side-chains
  88 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  113 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   67 ARG
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain K residue  117 LYS
Chi-restraints excluded: chain K residue  158 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 89 optimal weight:    6.9990
   chunk 102 optimal weight:   20.0000
   chunk 56 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 90 optimal weight:    4.9990
   chunk 54 optimal weight:    0.5980
   chunk 93 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0980
   chunk 42 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0870
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.181541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.112621 restraints weight = 32173.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 1.19
r_work: 0.3175 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3055 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.2981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14204  Z= 0.157
  Angle     :  0.606   6.583  20430  Z= 0.375
  Chirality :  0.037   0.136   2316
  Planarity :  0.004   0.056   1569
  Dihedral  : 29.892 161.684   4266
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 11.35 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.98 (0.28), residues: 905
  helix:  2.17 (0.20), residues: 640
  sheet:  0.98 (0.80), residues: 45
  loop : -1.26 (0.37), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  80 
 TYR   0.010   0.001   TYR F  51 
 PHE   0.007   0.001   PHE F  61 
 TRP   0.007   0.001   TRP A  86 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (14204)
  covalent geometry    : angle       0.60641 (20430)
  hydrogen bonds       : bond        0.04811 (  799)
  hydrogen bonds       : angle       2.83548 ( 2050)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8712.18 seconds
wall clock time: 147 minutes 25.75 seconds (8845.75 seconds total)