Starting phenix.real_space_refine
on Wed Mar  4 09:05:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9wc0_65853/03_2026/9wc0_65853.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9wc0_65853/03_2026/9wc0_65853.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9wc0_65853/03_2026/9wc0_65853.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9wc0_65853/03_2026/9wc0_65853.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9wc0_65853/03_2026/9wc0_65853.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9wc0_65853/03_2026/9wc0_65853.cif"
  }
  resolution = 2.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     308      5.49       5
     S      12      5.16       5
     C    6840      2.51       5
     N    2339      2.21       5
     O    2932      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12431
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "B"
      Number of atoms: 703
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 703
          Classifications: {'peptide': 87}
          Link IDs: {'PTRANS': 1, 'TRANS': 85}
    Chain: "C"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 811
          Classifications: {'peptide': 107}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 12
    Chain: "D"
      Number of atoms: 717
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 717
          Classifications: {'peptide': 93}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "E"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "F"
      Number of atoms: 672
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 672
          Classifications: {'peptide': 86}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 84}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 15
    Chain: "G"
      Number of atoms: 828
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 828
          Classifications: {'peptide': 108}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "H"
      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: "I"
      Number of atoms: 3139
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 3139
          Classifications: {'DNA': 154}
          Link IDs: {'rna3p': 153}
    Chain: "J"
      Number of atoms: 3175
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 3175
          Classifications: {'DNA': 154}
          Link IDs: {'rna3p': 153}
    Chain: "K"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 801
          Classifications: {'peptide': 98}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "O"
      Number of atoms: 81
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 81
          Classifications: {'peptide': 10}
          Link IDs: {'TRANS': 9}
  Time building chain proxies: 2.65, per 1000 atoms: 0.21
  Number of scatterers: 12431
  At special positions: 0
  Unit cell: (80.6462, 122.323, 117.451, 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      12     16.00
     P     308     15.00
     O    2932      8.00
     N    2339      7.00
     C    6840      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.93
  Conformation dependent library (CDL) restraints added in 359.4 milliseconds
  

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1460

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      70.7% alpha, 3.1% beta
      153 base pairs and 279 stacking pairs defined.
    Time for finding SS restraints: 2.08
  Creating SS restraints...
    Processing helix  chain 'B' and resid 16 through 22
      removed outlier: 3.744A  pdb=" N   LYS B  20 " --> pdb=" O   LYS B  16 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   VAL B  21 " --> pdb=" O   ARG B  17 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LEU B  22 " --> pdb=" O   HIS B  18 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 16 through 22'
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.760A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.424A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 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 124
      removed outlier: 3.541A  pdb=" N   HIS D 109 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ALA D 124 " --> pdb=" O   LYS D 120 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 3.634A  pdb=" N   SER E  57 " --> pdb=" O   ARG E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.533A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.505A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.762A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 22
      removed outlier: 3.509A  pdb=" N   ARG G  20 " --> pdb=" O   THR G  16 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.487A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    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
    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 124
    Processing helix  chain 'K' and resid 44 through 49
    Processing helix  chain 'K' and resid 50 through 53
    Processing helix  chain 'K' and resid 63 through 79
      removed outlier: 4.045A  pdb=" N   ASP K  77 " --> pdb=" O   GLU K  73 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   PHE K  78 " --> pdb=" O   ILE K  74 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 85 through 114
      removed outlier: 3.507A  pdb=" N   ALA K 114 " --> pdb=" O   CYS K 110 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 120 through 131
    Processing helix  chain 'O' and resid 10 through 15
    Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 46
      removed outlier: 7.362A  pdb=" N   ARG B  45 " --> pdb=" O   ILE K 119 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.048A  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 100 through 102
      removed outlier: 6.807A  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 83 through 84
      removed outlier: 6.830A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.044A  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

    395 hydrogen bonds defined for protein.
    1176 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      391 hydrogen bonds
      762 hydrogen bond angles
      0 basepair planarities
      153 basepair parallelities
      279 stacking parallelities
  Total time for adding SS restraints: 1.99

  Time building geometry restraints manager: 1.28 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: 2342
        1.33 -     1.45: 4435
        1.45 -     1.57: 5865
        1.57 -     1.69: 614
        1.69 -     1.81: 22
  Bond restraints: 13278
  Sorted by residual:
  bond pdb=" C3'  DT J  15 "
       pdb=" O3'  DT J  15 "
    ideal  model  delta    sigma   weight residual
    1.422  1.463 -0.041 3.00e-02 1.11e+03 1.84e+00
  bond pdb=" C3'  DC J 126 "
       pdb=" O3'  DC J 126 "
    ideal  model  delta    sigma   weight residual
    1.422  1.463 -0.041 3.00e-02 1.11e+03 1.82e+00
  bond pdb=" C2'  DT I  27 "
       pdb=" C1'  DT I  27 "
    ideal  model  delta    sigma   weight residual
    1.525  1.502  0.023 2.00e-02 2.50e+03 1.36e+00
  bond pdb=" CA  LEU B  22 "
       pdb=" CB  LEU B  22 "
    ideal  model  delta    sigma   weight residual
    1.524  1.538 -0.014 1.31e-02 5.83e+03 1.22e+00
  bond pdb=" CG  LYS G  36 "
       pdb=" CD  LYS G  36 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 9.85e-01
  ... (remaining 13273 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 18672
        1.56 -     3.11: 562
        3.11 -     4.67: 20
        4.67 -     6.23: 7
        6.23 -     7.78: 2
  Bond angle restraints: 19263
  Sorted by residual:
  angle pdb=" CB  MET F  84 "
        pdb=" CG  MET F  84 "
        pdb=" SD  MET F  84 "
      ideal   model   delta    sigma   weight residual
     112.70  120.13   -7.43 3.00e+00 1.11e-01 6.14e+00
  angle pdb=" N   GLY D 104 "
        pdb=" CA  GLY D 104 "
        pdb=" C   GLY D 104 "
      ideal   model   delta    sigma   weight residual
     113.18  119.03   -5.85 2.37e+00 1.78e-01 6.09e+00
  angle pdb=" CB  LYS G  36 "
        pdb=" CG  LYS G  36 "
        pdb=" CD  LYS G  36 "
      ideal   model   delta    sigma   weight residual
     111.30  116.71   -5.41 2.30e+00 1.89e-01 5.52e+00
  angle pdb=" CA  LEU B  22 "
        pdb=" CB  LEU B  22 "
        pdb=" CG  LEU B  22 "
      ideal   model   delta    sigma   weight residual
     116.30  124.08   -7.78 3.50e+00 8.16e-02 4.94e+00
  angle pdb=" C3'  DG I  16 "
        pdb=" C2'  DG I  16 "
        pdb=" C1'  DG I  16 "
      ideal   model   delta    sigma   weight residual
     101.60   98.44    3.16 1.50e+00 4.44e-01 4.44e+00
  ... (remaining 19258 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.32: 5612
       35.32 -    70.64: 1544
       70.64 -   105.96: 13
      105.96 -   141.28: 0
      141.28 -   176.60: 3
  Dihedral angle restraints: 7172
    sinusoidal: 4914
      harmonic: 2258
  Sorted by residual:
  dihedral pdb=" CA  ARG K  53 "
           pdb=" C   ARG K  53 "
           pdb=" N   TYR K  54 "
           pdb=" CA  TYR K  54 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.67  -24.33     0      5.00e+00 4.00e-02 2.37e+01
  dihedral pdb=" C4'  DT J  15 "
           pdb=" C3'  DT J  15 "
           pdb=" O3'  DT J  15 "
           pdb=" P    DC J  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   36.60 -176.60     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DC I  12 "
           pdb=" C3'  DC I  12 "
           pdb=" O3'  DC I  12 "
           pdb=" P    DG I  13 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   52.71  167.29     1      3.50e+01 8.16e-04 1.55e+01
  ... (remaining 7169 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1317
       0.026 -    0.052: 589
       0.052 -    0.079: 205
       0.079 -    0.105: 64
       0.105 -    0.131: 25
  Chirality restraints: 2200
  Sorted by residual:
  chirality pdb=" P    DG I  13 "
            pdb=" OP1  DG I  13 "
            pdb=" OP2  DG I  13 "
            pdb=" O5'  DG I  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.48   -0.13 2.00e-01 2.50e+01 4.28e-01
  chirality pdb=" CA  ILE B  29 "
            pdb=" N   ILE B  29 "
            pdb=" C   ILE B  29 "
            pdb=" CB  ILE B  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.23e-01
  chirality pdb=" CA  ILE E  62 "
            pdb=" N   ILE E  62 "
            pdb=" C   ILE E  62 "
            pdb=" CB  ILE E  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.11e-01
  ... (remaining 2197 not shown)

  Planarity restraints: 1372
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I 100 "   -0.031 2.00e-02 2.50e+03   1.30e-02 5.07e+00
        pdb=" N9   DG I 100 "    0.030 2.00e-02 2.50e+03
        pdb=" C8   DG I 100 "    0.004 2.00e-02 2.50e+03
        pdb=" N7   DG I 100 "    0.001 2.00e-02 2.50e+03
        pdb=" C5   DG I 100 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I 100 "   -0.003 2.00e-02 2.50e+03
        pdb=" O6   DG I 100 "   -0.011 2.00e-02 2.50e+03
        pdb=" N1   DG I 100 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DG I 100 "    0.001 2.00e-02 2.50e+03
        pdb=" N2   DG I 100 "    0.003 2.00e-02 2.50e+03
        pdb=" N3   DG I 100 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DG I 100 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  91 "    0.022 2.00e-02 2.50e+03   1.01e-02 2.80e+00
        pdb=" N9   DA I  91 "   -0.023 2.00e-02 2.50e+03
        pdb=" C8   DA I  91 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7   DA I  91 "    0.001 2.00e-02 2.50e+03
        pdb=" C5   DA I  91 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DA I  91 "    0.002 2.00e-02 2.50e+03
        pdb=" N6   DA I  91 "    0.006 2.00e-02 2.50e+03
        pdb=" N1   DA I  91 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I  91 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3   DA I  91 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DA I  91 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I 121 "   -0.022 2.00e-02 2.50e+03   9.50e-03 2.71e+00
        pdb=" N9   DG I 121 "    0.023 2.00e-02 2.50e+03
        pdb=" C8   DG I 121 "    0.003 2.00e-02 2.50e+03
        pdb=" N7   DG I 121 "    0.000 2.00e-02 2.50e+03
        pdb=" C5   DG I 121 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DG I 121 "   -0.002 2.00e-02 2.50e+03
        pdb=" O6   DG I 121 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1   DG I 121 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DG I 121 "   -0.000 2.00e-02 2.50e+03
        pdb=" N2   DG I 121 "    0.002 2.00e-02 2.50e+03
        pdb=" N3   DG I 121 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DG I 121 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1369 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.59: 83
        2.59 -     3.17: 9000
        3.17 -     3.75: 22812
        3.75 -     4.32: 32392
        4.32 -     4.90: 44743
  Nonbonded interactions: 109030
  Sorted by model distance:
  nonbonded pdb=" N2   DG I  14 "
            pdb=" O2   DC J 134 "
     model   vdw
     2.018 2.496
  nonbonded pdb=" O2   DC I  95 "
            pdb=" N2   DG J  53 "
     model   vdw
     2.081 2.496
  nonbonded pdb=" O2   DC I  53 "
            pdb=" N2   DG J  95 "
     model   vdw
     2.097 2.496
  nonbonded pdb=" O2   DC I  23 "
            pdb=" N2   DG J 125 "
     model   vdw
     2.146 2.496
  nonbonded pdb=" O2   DC I  70 "
            pdb=" N2   DG J  78 "
     model   vdw
     2.153 2.496
  ... (remaining 109025 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 'B' and ((resid 17 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 18 or (resid 19 through 20 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 24 through 101))
  selection = (chain 'F' and resid 17 through 101)
}
ncs_group {
  reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 75 through 118))
  selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 37 through 117 or (resid 118 and (name N or  \ 
name CA or name C or name O or name CB ))))
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'H' and (resid 32 through 33 or (resid 34 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 35 through 56 or (resid 57 through 58 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 59 through 124))
}
ncs_group {
  reference = chain 'E'
  selection = (chain 'K' and resid 40 through 134)
}

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:             4.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.790
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  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:5.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
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      :  0.004   0.041  13278  Z= 0.199
  Angle     :  0.604   7.782  19263  Z= 0.367
  Chirality :  0.036   0.131   2200
  Planarity :  0.005   0.041   1372
  Dihedral  : 28.804 176.600   5712
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 14.98 %
    Favored  : 84.07 %
  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:  2.25 (0.29), residues: 759
  helix:  2.36 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop : -0.58 (0.34), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG K  52 
 TYR   0.019   0.002   TYR F  88 
 PHE   0.009   0.002   PHE G  25 
 HIS   0.008   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (13278)
  covalent geometry    : angle       0.60360 (19263)
  hydrogen bonds       : bond        0.11867 (  786)
  hydrogen bonds       : angle       3.68589 ( 1938)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 179
  time to evaluate  : 0.322 
Fit side-chains
  outliers start: 6
  outliers final: 2
  residues processed: 181
  average time/residue: 1.0803
  time to fit residues: 204.2181
Evaluate side-chains
  159 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 157
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain H residue   88 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.4980
   overall best weight:    1.8988

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

Flipped N/Q/H residues before XYZ refinement:
D  95 GLN
E  76 GLN
F  93 GLN
G 110 ASN
H  84 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.115406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.080082 restraints weight = 21086.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 1.68
r_work: 0.2961 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.2812 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8555
moved from start:          0.1531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13278  Z= 0.194
  Angle     :  0.540   5.497  19263  Z= 0.329
  Chirality :  0.033   0.133   2200
  Planarity :  0.004   0.038   1372
  Dihedral  : 30.715 173.759   4218
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 14.83 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.92 (0.30), residues: 759
  helix:  2.79 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.36 (0.36), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG K  42 
 TYR   0.009   0.001   TYR B  51 
 PHE   0.008   0.001   PHE C  25 
 HIS   0.003   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (13278)
  covalent geometry    : angle       0.53956 (19263)
  hydrogen bonds       : bond        0.05731 (  786)
  hydrogen bonds       : angle       2.75738 ( 1938)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 168
  time to evaluate  : 0.350 
Fit side-chains
REVERT: B   79 LYS cc_start: 0.9007 (mtpp) cc_final: 0.8512 (mttp)
REVERT: C   92 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8650 (mp0)
REVERT: C   99 ARG cc_start: 0.8914 (mmm-85) cc_final: 0.8276 (mmm160)
REVERT: D   68 ASP cc_start: 0.9196 (t0) cc_final: 0.8931 (t0)
REVERT: D  108 LYS cc_start: 0.8570 (mtpp) cc_final: 0.8276 (tttm)
REVERT: E   59 GLU cc_start: 0.8349 (pm20) cc_final: 0.8007 (pm20)
REVERT: F   92 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8488 (ttp80)
REVERT: F   93 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8242 (mm-40)
REVERT: G   19 SER cc_start: 0.9213 (p) cc_final: 0.9011 (p)
REVERT: G   92 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8195 (mt-10)
REVERT: H   68 ASP cc_start: 0.8980 (t0) cc_final: 0.8731 (t0)
REVERT: H  116 LYS cc_start: 0.9194 (ttmt) cc_final: 0.8905 (ttmt)
  outliers start: 16
  outliers final: 3
  residues processed: 173
  average time/residue: 0.9794
  time to fit residues: 177.7280
Evaluate side-chains
  170 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 163
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue   95 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 101 optimal weight:    0.9990
   chunk 100 optimal weight:    0.4980
   chunk 14 optimal weight:    0.6980
   chunk 77 optimal weight:   20.0000
   chunk 38 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 86 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 90 optimal weight:    7.9990
   chunk 24 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
E  76 GLN
G 110 ASN
H  63 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.115659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.080253 restraints weight = 21298.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 1.72
r_work: 0.2964 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work: 0.2816 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.1776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13278  Z= 0.176
  Angle     :  0.522   5.037  19263  Z= 0.319
  Chirality :  0.033   0.129   2200
  Planarity :  0.004   0.035   1372
  Dihedral  : 30.593 175.459   4217
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 15.77 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.17 (0.30), residues: 759
  helix:  2.96 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.23 (0.36), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  33 
 TYR   0.008   0.001   TYR B  51 
 PHE   0.008   0.001   PHE F  61 
 HIS   0.002   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (13278)
  covalent geometry    : angle       0.52159 (19263)
  hydrogen bonds       : bond        0.05471 (  786)
  hydrogen bonds       : angle       2.68067 ( 1938)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 167
  time to evaluate  : 0.316 
Fit side-chains
REVERT: B   79 LYS cc_start: 0.8989 (mtpp) cc_final: 0.8485 (mttp)
REVERT: C   99 ARG cc_start: 0.8934 (mmm-85) cc_final: 0.8269 (mmm160)
REVERT: D   68 ASP cc_start: 0.9191 (t0) cc_final: 0.8848 (t0)
REVERT: E   59 GLU cc_start: 0.8362 (pm20) cc_final: 0.7913 (pm20)
REVERT: E  122 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8438 (pttp)
REVERT: F   24 ASP cc_start: 0.7558 (t0) cc_final: 0.7246 (t0)
REVERT: F   92 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8334 (ttp80)
REVERT: F   93 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8438 (mm-40)
REVERT: G   73 ASN cc_start: 0.8446 (m-40) cc_final: 0.8024 (t160)
REVERT: G   92 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8160 (mt-10)
REVERT: H   68 ASP cc_start: 0.8989 (t0) cc_final: 0.8714 (t0)
REVERT: H  116 LYS cc_start: 0.9192 (ttmt) cc_final: 0.8919 (ttmt)
  outliers start: 15
  outliers final: 4
  residues processed: 173
  average time/residue: 0.9333
  time to fit residues: 169.6468
Evaluate side-chains
  170 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 162
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue   71 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 7 optimal weight:    5.9990
   chunk 95 optimal weight:    4.9990
   chunk 100 optimal weight:    3.9990
   chunk 87 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 63 optimal weight:   40.0000
   chunk 67 optimal weight:    6.9990
   chunk 29 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 71 optimal weight:    4.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
E  76 GLN
E 125 GLN
H  63 ASN
K  68 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.111905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.076405 restraints weight = 21130.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.3127 rms_B_bonded: 1.69
r_work: 0.2881 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2729 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8640
moved from start:          0.1700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.051  13278  Z= 0.359
  Angle     :  0.591   5.871  19263  Z= 0.356
  Chirality :  0.039   0.131   2200
  Planarity :  0.005   0.043   1372
  Dihedral  : 30.998 177.661   4215
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 15.77 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.83 (0.30), residues: 759
  helix:  2.76 (0.22), residues: 541
  sheet:  None (None), residues: 0
  loop : -0.47 (0.36), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  33 
 TYR   0.011   0.002   TYR E  54 
 PHE   0.010   0.002   PHE C  25 
 HIS   0.004   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00819 (13278)
  covalent geometry    : angle       0.59138 (19263)
  hydrogen bonds       : bond        0.07134 (  786)
  hydrogen bonds       : angle       2.90265 ( 1938)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 165
  time to evaluate  : 0.338 
Fit side-chains
REVERT: B   79 LYS cc_start: 0.8995 (mtpp) cc_final: 0.8524 (mttp)
REVERT: D  108 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8270 (tttm)
REVERT: E   59 GLU cc_start: 0.8546 (pm20) cc_final: 0.8169 (pm20)
REVERT: E  122 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8577 (pttp)
REVERT: F   77 LYS cc_start: 0.9279 (mmtt) cc_final: 0.9038 (mmtt)
REVERT: G   92 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8164 (mt-10)
REVERT: G  110 ASN cc_start: 0.8941 (t0) cc_final: 0.8673 (t0)
REVERT: H   68 ASP cc_start: 0.9056 (t0) cc_final: 0.8818 (t0)
REVERT: H  116 LYS cc_start: 0.9209 (ttmt) cc_final: 0.8931 (ttmt)
  outliers start: 15
  outliers final: 9
  residues processed: 170
  average time/residue: 0.9738
  time to fit residues: 173.5125
Evaluate side-chains
  173 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 162
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain K residue   87 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 80 optimal weight:   10.0000
   chunk 72 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 99 optimal weight:    0.9990
   chunk 78 optimal weight:   30.0000
   chunk 88 optimal weight:    4.9990
   chunk 74 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   chunk 76 optimal weight:   10.0000
   chunk 48 optimal weight:    0.7980
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
E  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.113562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.078225 restraints weight = 21196.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 1.70
r_work: 0.2914 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.2762 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.1750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13278  Z= 0.174
  Angle     :  0.552   5.310  19263  Z= 0.337
  Chirality :  0.034   0.132   2200
  Planarity :  0.004   0.046   1372
  Dihedral  : 31.040 177.405   4215
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 17.19 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.98 (0.30), residues: 759
  helix:  2.86 (0.22), residues: 541
  sheet:  None (None), residues: 0
  loop : -0.42 (0.36), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG H  33 
 TYR   0.013   0.002   TYR D  83 
 PHE   0.008   0.001   PHE F  61 
 HIS   0.003   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 (13278)
  covalent geometry    : angle       0.55156 (19263)
  hydrogen bonds       : bond        0.06381 (  786)
  hydrogen bonds       : angle       2.85353 ( 1938)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 163
  time to evaluate  : 0.323 
Fit side-chains
REVERT: B   79 LYS cc_start: 0.8957 (mtpp) cc_final: 0.8476 (mttp)
REVERT: C   99 ARG cc_start: 0.8895 (mmm-85) cc_final: 0.8265 (mmm160)
REVERT: D   68 ASP cc_start: 0.9141 (t0) cc_final: 0.8935 (t0)
REVERT: D  108 LYS cc_start: 0.8527 (mtpp) cc_final: 0.8212 (tttm)
REVERT: E   59 GLU cc_start: 0.8511 (pm20) cc_final: 0.8118 (pm20)
REVERT: F   24 ASP cc_start: 0.7306 (t0) cc_final: 0.6874 (t0)
REVERT: F   93 GLN cc_start: 0.8580 (mt0) cc_final: 0.8330 (mm-40)
REVERT: G   92 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8174 (mt-10)
REVERT: G  110 ASN cc_start: 0.8899 (t0) cc_final: 0.8623 (t0)
REVERT: H   68 ASP cc_start: 0.9021 (t0) cc_final: 0.8767 (t0)
REVERT: H  116 LYS cc_start: 0.9196 (ttmt) cc_final: 0.8929 (ttmt)
  outliers start: 14
  outliers final: 9
  residues processed: 169
  average time/residue: 0.9227
  time to fit residues: 163.6618
Evaluate side-chains
  172 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 162
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain F residue   59 LYS
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain K residue   87 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 68 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 75 optimal weight:    8.9990
   chunk 51 optimal weight:    0.8980
   chunk 63 optimal weight:   40.0000
   chunk 47 optimal weight:    0.4980
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
E  76 GLN
H  63 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.113895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.078602 restraints weight = 21064.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 1.68
r_work: 0.2929 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.2776 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.1791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  13278  Z= 0.180
  Angle     :  0.546   5.521  19263  Z= 0.333
  Chirality :  0.034   0.175   2200
  Planarity :  0.004   0.057   1372
  Dihedral  : 30.953 177.061   4215
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 17.35 %
    Favored  : 80.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.10 (0.30), residues: 759
  helix:  2.95 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.33 (0.37), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG H  33 
 TYR   0.014   0.002   TYR D  83 
 PHE   0.008   0.001   PHE E  67 
 HIS   0.002   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 (13278)
  covalent geometry    : angle       0.54644 (19263)
  hydrogen bonds       : bond        0.05930 (  786)
  hydrogen bonds       : angle       2.79503 ( 1938)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 162
  time to evaluate  : 0.329 
Fit side-chains
REVERT: B   79 LYS cc_start: 0.8965 (mtpp) cc_final: 0.8492 (mttp)
REVERT: C   99 ARG cc_start: 0.8915 (mmm-85) cc_final: 0.8265 (mmm160)
REVERT: D  108 LYS cc_start: 0.8535 (mtpp) cc_final: 0.8210 (tttm)
REVERT: E   59 GLU cc_start: 0.8501 (pm20) cc_final: 0.8107 (pm20)
REVERT: F   24 ASP cc_start: 0.7306 (t0) cc_final: 0.6883 (t0)
REVERT: G   92 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8163 (mt-10)
REVERT: G  110 ASN cc_start: 0.8865 (t0) cc_final: 0.8609 (t0)
REVERT: H   68 ASP cc_start: 0.9027 (t0) cc_final: 0.8753 (t0)
REVERT: H  116 LYS cc_start: 0.9203 (ttmt) cc_final: 0.8936 (ttmt)
  outliers start: 11
  outliers final: 7
  residues processed: 168
  average time/residue: 0.9415
  time to fit residues: 166.0548
Evaluate side-chains
  170 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 162
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain K residue   87 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 73 optimal weight:    5.9990
   chunk 64 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 91 optimal weight:   10.0000
   chunk 56 optimal weight:    2.9990
   chunk 46 optimal weight:    6.9990
   chunk 51 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 43 optimal weight:    5.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
E  76 GLN
H  63 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.114493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.079255 restraints weight = 21064.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 1.68
r_work: 0.2944 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.2795 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.1930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13278  Z= 0.189
  Angle     :  0.530   5.843  19263  Z= 0.324
  Chirality :  0.033   0.146   2200
  Planarity :  0.004   0.049   1372
  Dihedral  : 30.716 176.709   4215
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 17.35 %
    Favored  : 80.76 %
  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:  3.20 (0.30), residues: 759
  helix:  3.00 (0.22), residues: 541
  sheet:  None (None), residues: 0
  loop : -0.24 (0.37), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG H  33 
 TYR   0.011   0.001   TYR D  83 
 PHE   0.008   0.001   PHE E  67 
 HIS   0.002   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 (13278)
  covalent geometry    : angle       0.52955 (19263)
  hydrogen bonds       : bond        0.05642 (  786)
  hydrogen bonds       : angle       2.70133 ( 1938)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 160
  time to evaluate  : 0.267 
Fit side-chains
REVERT: B   79 LYS cc_start: 0.8976 (mtpp) cc_final: 0.8484 (mttp)
REVERT: C   99 ARG cc_start: 0.8912 (mmm-85) cc_final: 0.8281 (mmm160)
REVERT: D  108 LYS cc_start: 0.8543 (mtpp) cc_final: 0.8208 (tttm)
REVERT: E   59 GLU cc_start: 0.8455 (pm20) cc_final: 0.8050 (pm20)
REVERT: E  122 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8439 (pttp)
REVERT: F   24 ASP cc_start: 0.7373 (t0) cc_final: 0.7003 (t0)
REVERT: F   93 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8464 (mm-40)
REVERT: G   73 ASN cc_start: 0.8544 (m-40) cc_final: 0.8084 (t160)
REVERT: G   92 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8145 (mt-10)
REVERT: G  110 ASN cc_start: 0.8866 (t0) cc_final: 0.8637 (t0)
REVERT: H   68 ASP cc_start: 0.9019 (t0) cc_final: 0.8762 (t0)
REVERT: H  116 LYS cc_start: 0.9204 (ttmt) cc_final: 0.8936 (ttmt)
  outliers start: 12
  outliers final: 7
  residues processed: 165
  average time/residue: 0.9468
  time to fit residues: 163.8897
Evaluate side-chains
  168 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 159
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain K residue   87 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 80 optimal weight:   10.0000
   chunk 55 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 64 optimal weight:   10.0000
   chunk 30 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 74 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
E  76 GLN
H  63 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.114104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.078662 restraints weight = 21037.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 1.69
r_work: 0.2929 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.2780 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  13278  Z= 0.212
  Angle     :  0.535   7.636  19263  Z= 0.326
  Chirality :  0.034   0.130   2200
  Planarity :  0.004   0.044   1372
  Dihedral  : 30.706 177.171   4215
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 17.19 %
    Favored  : 80.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.16 (0.30), residues: 759
  helix:  2.98 (0.22), residues: 541
  sheet:  None (None), residues: 0
  loop : -0.27 (0.37), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG H  33 
 TYR   0.014   0.002   TYR D  83 
 PHE   0.007   0.001   PHE E  67 
 HIS   0.002   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 (13278)
  covalent geometry    : angle       0.53508 (19263)
  hydrogen bonds       : bond        0.05825 (  786)
  hydrogen bonds       : angle       2.70921 ( 1938)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 160
  time to evaluate  : 0.329 
Fit side-chains
REVERT: B   79 LYS cc_start: 0.8969 (mtpp) cc_final: 0.8486 (mttp)
REVERT: C   99 ARG cc_start: 0.8913 (mmm-85) cc_final: 0.8272 (mmm160)
REVERT: D  108 LYS cc_start: 0.8566 (mtpp) cc_final: 0.8229 (tttm)
REVERT: E   59 GLU cc_start: 0.8449 (pm20) cc_final: 0.8036 (pm20)
REVERT: E  122 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8461 (pttp)
REVERT: F   24 ASP cc_start: 0.7433 (t0) cc_final: 0.7112 (t0)
REVERT: F   53 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8294 (mm-30)
REVERT: G   73 ASN cc_start: 0.8554 (m-40) cc_final: 0.8108 (t160)
REVERT: G   92 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8146 (mt-10)
REVERT: G  110 ASN cc_start: 0.8890 (t0) cc_final: 0.8664 (t0)
REVERT: H   68 ASP cc_start: 0.9017 (t0) cc_final: 0.8750 (t0)
REVERT: H  116 LYS cc_start: 0.9207 (ttmt) cc_final: 0.8936 (ttmt)
  outliers start: 15
  outliers final: 8
  residues processed: 167
  average time/residue: 0.9095
  time to fit residues: 159.5694
Evaluate side-chains
  168 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 158
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   59 LYS
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain K residue   87 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 90 optimal weight:    7.9990
   chunk 19 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 95 optimal weight:    4.9990
   chunk 93 optimal weight:    0.0670
   chunk 44 optimal weight:   10.0000
   overall best weight:    0.7922

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

Flipped N/Q/H residues before XYZ refinement:
E  76 GLN
E 125 GLN
H  63 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.114699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.079384 restraints weight = 21140.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 1.68
r_work: 0.2946 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.2798 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  13278  Z= 0.159
  Angle     :  0.548  16.577  19263  Z= 0.327
  Chirality :  0.032   0.208   2200
  Planarity :  0.004   0.041   1372
  Dihedral  : 30.720 177.110   4215
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 17.98 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.25 (0.30), residues: 759
  helix:  3.04 (0.22), residues: 541
  sheet:  None (None), residues: 0
  loop : -0.22 (0.37), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG H  33 
 TYR   0.018   0.002   TYR D  83 
 PHE   0.008   0.001   PHE E  67 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (13278)
  covalent geometry    : angle       0.54799 (19263)
  hydrogen bonds       : bond        0.05685 (  786)
  hydrogen bonds       : angle       2.70700 ( 1938)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 160
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
REVERT: B   79 LYS cc_start: 0.8960 (mtpp) cc_final: 0.8471 (mttp)
REVERT: C   99 ARG cc_start: 0.8897 (mmm-85) cc_final: 0.8261 (mmm160)
REVERT: D  108 LYS cc_start: 0.8548 (mtpp) cc_final: 0.8223 (tttm)
REVERT: E   59 GLU cc_start: 0.8436 (pm20) cc_final: 0.8024 (pm20)
REVERT: F   24 ASP cc_start: 0.7412 (t0) cc_final: 0.7100 (t0)
REVERT: G   73 ASN cc_start: 0.8535 (m-40) cc_final: 0.8095 (t160)
REVERT: G   92 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8140 (mt-10)
REVERT: G  110 ASN cc_start: 0.8884 (t0) cc_final: 0.8663 (t0)
REVERT: H   68 ASP cc_start: 0.9010 (t0) cc_final: 0.8745 (t0)
REVERT: H  116 LYS cc_start: 0.9200 (ttmt) cc_final: 0.8934 (ttmt)
  outliers start: 11
  outliers final: 7
  residues processed: 165
  average time/residue: 0.9201
  time to fit residues: 159.4610
Evaluate side-chains
  167 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 159
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   59 LYS
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain K residue   87 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 74 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   chunk 102 optimal weight:    0.0270
   chunk 87 optimal weight:    5.9990
   chunk 40 optimal weight:    0.6980
   chunk 95 optimal weight:    5.9990
   chunk 96 optimal weight:    2.9990
   chunk 99 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 71 optimal weight:    5.9990
   overall best weight:    1.9444

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

Flipped N/Q/H residues before XYZ refinement:
E  76 GLN
H  63 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.114609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.079300 restraints weight = 21113.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 1.68
r_work: 0.2945 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.2797 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
moved from start:          0.2049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13278  Z= 0.191
  Angle     :  0.540  14.573  19263  Z= 0.324
  Chirality :  0.033   0.167   2200
  Planarity :  0.004   0.041   1372
  Dihedral  : 30.649 177.235   4215
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 17.82 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.21 (0.30), residues: 759
  helix:  3.01 (0.22), residues: 541
  sheet:  None (None), residues: 0
  loop : -0.24 (0.36), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG H  33 
 TYR   0.017   0.002   TYR D  83 
 PHE   0.007   0.001   PHE F  61 
 HIS   0.002   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 (13278)
  covalent geometry    : angle       0.54006 (19263)
  hydrogen bonds       : bond        0.05568 (  786)
  hydrogen bonds       : angle       2.67906 ( 1938)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 160
  time to evaluate  : 0.326 
Fit side-chains
REVERT: B   79 LYS cc_start: 0.8954 (mtpp) cc_final: 0.8472 (mttp)
REVERT: C   99 ARG cc_start: 0.8911 (mmm-85) cc_final: 0.8276 (mmm160)
REVERT: D  108 LYS cc_start: 0.8555 (mtpp) cc_final: 0.8222 (tttm)
REVERT: E   59 GLU cc_start: 0.8422 (pm20) cc_final: 0.8022 (pm20)
REVERT: E  122 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8432 (pttp)
REVERT: F   24 ASP cc_start: 0.7494 (t0) cc_final: 0.7207 (t0)
REVERT: G   73 ASN cc_start: 0.8530 (m-40) cc_final: 0.8108 (t160)
REVERT: G   92 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8130 (mt-10)
REVERT: G  110 ASN cc_start: 0.8885 (t0) cc_final: 0.8668 (t0)
REVERT: H   68 ASP cc_start: 0.9011 (t0) cc_final: 0.8749 (t0)
REVERT: H  116 LYS cc_start: 0.9201 (ttmt) cc_final: 0.8940 (ttmt)
  outliers start: 12
  outliers final: 5
  residues processed: 165
  average time/residue: 0.9501
  time to fit residues: 164.5892
Evaluate side-chains
  166 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 159
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain K residue   87 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 89 optimal weight:    6.9990
   chunk 40 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 61 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 41 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 15 optimal weight:    0.5980
   chunk 28 optimal weight:    6.9990
   chunk 72 optimal weight:    5.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
E  76 GLN
E 125 GLN
H  63 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.115155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.079709 restraints weight = 21139.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 1.70
r_work: 0.2957 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work: 0.2808 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.2071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13278  Z= 0.153
  Angle     :  0.536  14.535  19263  Z= 0.322
  Chirality :  0.032   0.155   2200
  Planarity :  0.004   0.038   1372
  Dihedral  : 30.656 177.207   4215
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 17.98 %
    Favored  : 80.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.28 (0.30), residues: 759
  helix:  3.06 (0.22), residues: 541
  sheet:  None (None), residues: 0
  loop : -0.21 (0.37), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG H  33 
 TYR   0.021   0.002   TYR D  83 
 PHE   0.008   0.001   PHE E  67 
 HIS   0.002   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (13278)
  covalent geometry    : angle       0.53628 (19263)
  hydrogen bonds       : bond        0.05513 (  786)
  hydrogen bonds       : angle       2.67457 ( 1938)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6341.06 seconds
wall clock time: 107 minutes 47.55 seconds (6467.55 seconds total)