Starting phenix.real_space_refine
on Tue Aug 26 10:20:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hal_51982/08_2025/9hal_51982.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hal_51982/08_2025/9hal_51982.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hal_51982/08_2025/9hal_51982.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hal_51982/08_2025/9hal_51982.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hal_51982/08_2025/9hal_51982.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hal_51982/08_2025/9hal_51982.map"
  }
  resolution = 4.49
  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=  -0.013 sd=   0.109
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    1329      5.49       5
     S      20      5.16       5
     C   17868      2.51       5
     N    6829      2.21       5
     O   10671      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 36717
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "J"
      Number of atoms: 1129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 1129
          Classifications: {'peptide': 142}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 135}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 961
          Classifications: {'peptide': 120}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 115}
    Chain: "Q"
      Number of atoms: 947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 947
          Classifications: {'peptide': 117}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 116}
    Chain: "R"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 816
          Classifications: {'peptide': 103}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 101}
    Chain: "A"
      Number of atoms: 28562
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1329, 28562
          Classifications: {'RNA': 1329}
          Modifications used: {'rna2p_pur': 127, 'rna2p_pyr': 68, 'rna3p_pur': 654, 'rna3p_pyr': 480}
          Link IDs: {'rna2p': 195, 'rna3p': 1133}
          Chain breaks: 6
    Chain: "D"
      Number of atoms: 1306
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 175, 1306
          Classifications: {'peptide': 175}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 170}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 187, 1438
          Classifications: {'peptide': 187}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 182}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 778
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 778
          Classifications: {'peptide': 109}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 106}
          Chain breaks: 1
    Chain: "U"
      Number of atoms: 780
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 780
          Classifications: {'peptide': 102}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 98}
  Time building chain proxies: 6.30, per 1000 atoms: 0.17
  Number of scatterers: 36717
  At special positions: 0
  Unit cell: (133.866, 215.784, 175.824, 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      20     16.00
     P    1329     15.00
     O   10671      8.00
     N    6829      7.00
     C   17868      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: 2.32
  Conformation dependent library (CDL) restraints added in 566.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1918

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 14 sheets defined
      34.2% alpha, 15.7% beta
      436 base pairs and 626 stacking pairs defined.
    Time for finding SS restraints: 5.40
  Creating SS restraints...
    Processing helix  chain 'J' and resid 24 through 38
    Processing helix  chain 'J' and resid 58 through 62
    Processing helix  chain 'J' and resid 67 through 72
    Processing helix  chain 'J' and resid 89 through 96
    Processing helix  chain 'J' and resid 96 through 109
      removed outlier: 3.671A  pdb=" N   VAL J 100 " --> pdb=" O   ARG J  96 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 112 through 121
    Processing helix  chain 'J' and resid 130 through 136
      removed outlier: 4.330A  pdb=" N   ALA J 134 " --> pdb=" O   ASN J 131 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 13 through 32
    Processing helix  chain 'N' and resid 37 through 55
      removed outlier: 3.834A  pdb=" N   GLU N  43 " --> pdb=" O   PRO N  39 " (cutoff:3.500A)
      Proline residue:  N  50  - end of helix
    Processing helix  chain 'N' and resid 59 through 71
    Processing helix  chain 'N' and resid 72 through 79
    Processing helix  chain 'N' and resid 82 through 87
    Processing helix  chain 'Q' and resid 5 through 19
      removed outlier: 4.018A  pdb=" N   GLN Q  19 " --> pdb=" O   LYS Q  15 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 25 through 30
    Processing helix  chain 'Q' and resid 30 through 72
      removed outlier: 4.616A  pdb=" N   GLN Q  36 " --> pdb=" O   ARG Q  32 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ARG Q  50 " --> pdb=" O   TYR Q  46 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   LYS Q  53 " --> pdb=" O   ARG Q  49 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   ARG Q  54 " --> pdb=" O   ARG Q  50 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 74 through 85
    Processing helix  chain 'Q' and resid 90 through 101
      removed outlier: 3.905A  pdb=" N   VAL Q  99 " --> pdb=" O   ALA Q  95 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   PHE Q 100 " --> pdb=" O   ASP Q  96 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 102 through 117
      removed outlier: 4.117A  pdb=" N   ALA Q 117 " --> pdb=" O   LYS Q 113 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 61 through 72
    Processing helix  chain 'D' and resid 98 through 102
      removed outlier: 4.097A  pdb=" N   ALA D 102 " --> pdb=" O   GLU D  99 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 120 through 125
    Processing helix  chain 'E' and resid 15 through 21
      removed outlier: 3.705A  pdb=" N   PHE E  19 " --> pdb=" O   SER E  15 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 24 through 39
      removed outlier: 3.600A  pdb=" N   VAL E  28 " --> pdb=" O   ASN E  24 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 97 through 115
    Processing helix  chain 'E' and resid 130 through 142
    Processing helix  chain 'E' and resid 154 through 162
    Processing helix  chain 'E' and resid 176 through 183
    Processing helix  chain 'E' and resid 190 through 199
    Processing helix  chain 'L' and resid 29 through 33
    Processing helix  chain 'L' and resid 70 through 74
    Processing helix  chain 'L' and resid 128 through 138
    Processing sheet with id=AA1, first strand: chain 'J' and resid 122 through 124
      removed outlier: 6.290A  pdb=" N   ILE J  54 " --> pdb=" O   LYS J 123 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   TYR J  16 " --> pdb=" O   ILE J  55 " (cutoff:3.500A)
      removed outlier: 7.725A  pdb=" N   LEU J  57 " --> pdb=" O   TYR J  16 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   VAL J  18 " --> pdb=" O   LEU J  57 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'J' and resid 73 through 75
    Processing sheet with id=AA3, first strand: chain 'N' and resid 33 through 36
      removed outlier: 5.776A  pdb=" N   ALA N 108 " --> pdb=" O   PHE N 102 " (cutoff:3.500A)
      removed outlier: 4.823A  pdb=" N   PHE N 102 " --> pdb=" O   ALA N 108 " (cutoff:3.500A)
      removed outlier: 4.940A  pdb=" N   MET N 110 " --> pdb=" O   CYS N 100 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'R' and resid 3 through 6
    Processing sheet with id=AA5, first strand: chain 'R' and resid 19 through 22
      removed outlier: 6.706A  pdb=" N   PHE R  93 " --> pdb=" O   HIS R  66 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   HIS R  66 " --> pdb=" O   PHE R  93 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   ASP R  95 " --> pdb=" O   VAL R  64 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   THR R  99 " --> pdb=" O   LYS R  60 " (cutoff:3.500A)
      removed outlier: 5.877A  pdb=" N   LYS R  60 " --> pdb=" O   THR R  99 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'R' and resid 72 through 77
    Processing sheet with id=AA7, first strand: chain 'D' and resid 108 through 111
      removed outlier: 6.344A  pdb=" N   LYS D   8 " --> pdb=" O   GLU D  28 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   GLU D  28 " --> pdb=" O   LYS D   8 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 80 through 83
      removed outlier: 6.671A  pdb=" N   THR D  51 " --> pdb=" O   VAL D  34 " (cutoff:3.500A)
      removed outlier: 5.826A  pdb=" N   VAL D  34 " --> pdb=" O   THR D  51 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ASN D  32 " --> pdb=" O   ILE D  96 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ILE D  96 " --> pdb=" O   ASN D  32 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 4
    Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 121
      removed outlier: 6.271A  pdb=" N   ILE E 119 " --> pdb=" O   MET E 188 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   THR E 189 " --> pdb=" O   ILE E 149 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   ASP E 168 " --> pdb=" O   VAL E 146 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ARG E 170 " --> pdb=" O   ILE E 148 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 77 through 78
      removed outlier: 6.491A  pdb=" N   ILE L  77 " --> pdb=" O   ILE L 111 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'U' and resid 63 through 65
      removed outlier: 6.746A  pdb=" N   LYS U  32 " --> pdb=" O   VAL U  27 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   VAL U  27 " --> pdb=" O   LYS U  32 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ILE U  34 " --> pdb=" O   LYS U  25 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLU U  36 " --> pdb=" O   LYS U  23 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   LYS U  23 " --> pdb=" O   GLU U  36 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   GLU U   9 " --> pdb=" O   PHE U  72 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ASN U  73 " --> pdb=" O   LYS U  78 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LYS U  78 " --> pdb=" O   ASN U  73 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'U' and resid 40 through 44
    Processing sheet with id=AB5, first strand: chain 'U' and resid 82 through 86

    303 hydrogen bonds defined for protein.
    858 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      1109 hydrogen bonds
      1768 hydrogen bond angles
      0 basepair planarities
      436 basepair parallelities
      626 stacking parallelities
  Total time for adding SS restraints: 11.25

  Time building geometry restraints manager: 3.26 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 5211
        1.33 -     1.45: 17716
        1.45 -     1.57: 14633
        1.57 -     1.69: 2651
        1.69 -     1.81: 39
  Bond restraints: 40250
  Sorted by residual:
  bond pdb=" N   VAL N  47 "
       pdb=" CA  VAL N  47 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.28e-02 6.10e+03 6.61e+00
  bond pdb=" N   ASN N 107 "
       pdb=" CA  ASN N 107 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.033 1.29e-02 6.01e+03 6.50e+00
  bond pdb=" N   ILE N  97 "
       pdb=" CA  ILE N  97 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.029 1.17e-02 7.31e+03 6.34e+00
  bond pdb=" N   ILE N  34 "
       pdb=" CA  ILE N  34 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.028 1.11e-02 8.12e+03 6.31e+00
  bond pdb=" N   ILE N  52 "
       pdb=" CA  ILE N  52 "
    ideal  model  delta    sigma   weight residual
    1.460  1.489 -0.030 1.21e-02 6.83e+03 6.09e+00
  ... (remaining 40245 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 59873
        1.23 -     2.46: 980
        2.46 -     3.69: 102
        3.69 -     4.92: 23
        4.92 -     6.15: 2
  Bond angle restraints: 60980
  Sorted by residual:
  angle pdb=" N   ASN U  98 "
        pdb=" CA  ASN U  98 "
        pdb=" C   ASN U  98 "
      ideal   model   delta    sigma   weight residual
     114.62  110.02    4.60 1.14e+00 7.69e-01 1.63e+01
  angle pdb=" N   SER U  97 "
        pdb=" CA  SER U  97 "
        pdb=" CB  SER U  97 "
      ideal   model   delta    sigma   weight residual
     113.65  109.41    4.24 1.47e+00 4.63e-01 8.31e+00
  angle pdb=" CA  ASN U  98 "
        pdb=" C   ASN U  98 "
        pdb=" N   SER U  99 "
      ideal   model   delta    sigma   weight residual
     119.71  116.61    3.10 1.17e+00 7.31e-01 7.04e+00
  angle pdb=" CA  GLN N   9 "
        pdb=" C   GLN N   9 "
        pdb=" O   GLN N   9 "
      ideal   model   delta    sigma   weight residual
     120.82  118.09    2.73 1.05e+00 9.07e-01 6.78e+00
  angle pdb=" N   ASN N  81 "
        pdb=" CA  ASN N  81 "
        pdb=" C   ASN N  81 "
      ideal   model   delta    sigma   weight residual
     113.18  109.76    3.42 1.33e+00 5.65e-01 6.63e+00
  ... (remaining 60975 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.51: 22677
       35.51 -    71.02: 2665
       71.02 -   106.52: 350
      106.52 -   142.03: 9
      142.03 -   177.54: 3
  Dihedral angle restraints: 25704
    sinusoidal: 22723
      harmonic: 2981
  Sorted by residual:
  dihedral pdb=" O4'   U A 828 "
           pdb=" C1'   U A 828 "
           pdb=" N1    U A 828 "
           pdb=" C2    U A 828 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   49.54 -177.54     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   C A 323 "
           pdb=" C1'   C A 323 "
           pdb=" N1    C A 323 "
           pdb=" C2    C A 323 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   -3.99 -124.01     1      1.70e+01 3.46e-03 5.18e+01
  dihedral pdb=" C4'   G A2763 "
           pdb=" C3'   G A2763 "
           pdb=" O3'   G A2763 "
           pdb=" P     A A2764 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   46.11  173.89     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 25701 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 7436
       0.043 -    0.086: 311
       0.086 -    0.129: 143
       0.129 -    0.172: 14
       0.172 -    0.216: 4
  Chirality restraints: 7908
  Sorted by residual:
  chirality pdb=" CA  ILE N 113 "
            pdb=" N   ILE N 113 "
            pdb=" C   ILE N 113 "
            pdb=" CB  ILE N 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CA  ILE N  97 "
            pdb=" N   ILE N  97 "
            pdb=" C   ILE N  97 "
            pdb=" CB  ILE N  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CA  VAL N  60 "
            pdb=" N   VAL N  60 "
            pdb=" C   VAL N  60 "
            pdb=" CB  VAL N  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.19 2.00e-01 2.50e+01 9.45e-01
  ... (remaining 7905 not shown)

  Planarity restraints: 2755
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C A 269 "   -0.005 2.00e-02 2.50e+03   1.95e-02 8.54e+00
        pdb=" N1    C A 269 "    0.005 2.00e-02 2.50e+03
        pdb=" C2    C A 269 "   -0.045 2.00e-02 2.50e+03
        pdb=" O2    C A 269 "    0.029 2.00e-02 2.50e+03
        pdb=" N3    C A 269 "    0.008 2.00e-02 2.50e+03
        pdb=" C4    C A 269 "   -0.015 2.00e-02 2.50e+03
        pdb=" N4    C A 269 "    0.006 2.00e-02 2.50e+03
        pdb=" C5    C A 269 "    0.007 2.00e-02 2.50e+03
        pdb=" C6    C A 269 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A 424 "   -0.003 2.00e-02 2.50e+03   1.29e-02 5.03e+00
        pdb=" N9    G A 424 "    0.001 2.00e-02 2.50e+03
        pdb=" C8    G A 424 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    G A 424 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    G A 424 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    G A 424 "    0.013 2.00e-02 2.50e+03
        pdb=" O6    G A 424 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1    G A 424 "   -0.006 2.00e-02 2.50e+03
        pdb=" C2    G A 424 "    0.035 2.00e-02 2.50e+03
        pdb=" N2    G A 424 "   -0.023 2.00e-02 2.50e+03
        pdb=" N3    G A 424 "   -0.000 2.00e-02 2.50e+03
        pdb=" C4    G A 424 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A 175 "   -0.007 2.00e-02 2.50e+03   1.26e-02 4.74e+00
        pdb=" N9    G A 175 "    0.009 2.00e-02 2.50e+03
        pdb=" C8    G A 175 "    0.004 2.00e-02 2.50e+03
        pdb=" N7    G A 175 "    0.000 2.00e-02 2.50e+03
        pdb=" C5    G A 175 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    G A 175 "   -0.033 2.00e-02 2.50e+03
        pdb=" O6    G A 175 "    0.019 2.00e-02 2.50e+03
        pdb=" N1    G A 175 "    0.005 2.00e-02 2.50e+03
        pdb=" C2    G A 175 "   -0.013 2.00e-02 2.50e+03
        pdb=" N2    G A 175 "    0.009 2.00e-02 2.50e+03
        pdb=" N3    G A 175 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    G A 175 "    0.005 2.00e-02 2.50e+03
  ... (remaining 2752 not shown)

  Histogram of nonbonded interaction distances:
        1.89 -     2.49: 286
        2.49 -     3.09: 25042
        3.09 -     3.70: 71695
        3.70 -     4.30: 99931
        4.30 -     4.90: 134574
  Nonbonded interactions: 331528
  Sorted by model distance:
  nonbonded pdb=" OP2   G A 636 "
            pdb=" OG1 THR L 128 "
     model   vdw
     1.888 3.040
  nonbonded pdb=" O2'   G A 370 "
            pdb=" O4'   G A 424 "
     model   vdw
     1.930 3.040
  nonbonded pdb=" OP2   C A1007 "
            pdb=" O2'   A A1008 "
     model   vdw
     1.954 3.040
  nonbonded pdb=" O2'   A A 981 "
            pdb=" O2'   C A2036 "
     model   vdw
     1.956 3.040
  nonbonded pdb=" O2'   G A 214 "
            pdb=" O4'   G A 215 "
     model   vdw
     1.969 3.040
  ... (remaining 331523 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.550
  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:             0.020
  Extract box with map and model:          0.490
  Check model and map are aligned:         0.110
  Set scattering table:                    0.090
  Process input model:                     34.400
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7206
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      :  0.002   0.033  40250  Z= 0.154
  Angle     :  0.403   6.152  60980  Z= 0.223
  Chirality :  0.027   0.216   7908
  Planarity :  0.003   0.031   2755
  Dihedral  : 22.665 177.539  23786
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.94 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  4.29 %
    Favored  : 95.35 %
  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 aren not related in a simple way.
  whole:  0.26 (0.27), residues: 1033
  helix:  2.27 (0.30), residues: 314
  sheet: -0.51 (0.42), residues: 160
  loop : -0.86 (0.27), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG N  64 
 TYR   0.007   0.001   TYR N 112 
 PHE   0.007   0.001   PHE R  53 
 TRP   0.004   0.001   TRP R  92 
 HIS   0.004   0.001   HIS N   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (40250)
  covalent geometry    : angle       0.40256 (60980)
  hydrogen bonds       : bond        0.08780 ( 1412)
  hydrogen bonds       : angle       3.45262 ( 2626)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 259
  time to evaluate  : 0.606 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   14 ASP cc_start: 0.7736 (p0) cc_final: 0.6730 (p0)
REVERT: J   16 TYR cc_start: 0.8740 (m-10) cc_final: 0.8427 (m-10)
REVERT: J   93 ILE cc_start: 0.7463 (pt) cc_final: 0.7150 (pt)
REVERT: J  122 LEU cc_start: 0.9356 (tp) cc_final: 0.8702 (pp)
REVERT: J  132 HIS cc_start: 0.8317 (m170) cc_final: 0.7903 (m-70)
REVERT: Q   23 TYR cc_start: 0.9223 (m-80) cc_final: 0.8499 (m-80)
REVERT: Q   59 LEU cc_start: 0.9445 (mt) cc_final: 0.9208 (mm)
REVERT: R   39 LEU cc_start: 0.9022 (mm) cc_final: 0.8679 (mp)
REVERT: R   48 LYS cc_start: 0.8079 (mmtm) cc_final: 0.7469 (mmtp)
REVERT: R   81 LYS cc_start: 0.5306 (ttmt) cc_final: 0.3775 (tptt)
REVERT: R   95 ASP cc_start: 0.8578 (m-30) cc_final: 0.7396 (m-30)
REVERT: D   96 ILE cc_start: 0.7350 (mt) cc_final: 0.7127 (tp)
REVERT: D  100 LEU cc_start: 0.8988 (tt) cc_final: 0.8767 (tp)
REVERT: D  165 MET cc_start: 0.4932 (pmm) cc_final: 0.3766 (mpp)
REVERT: D  185 ASN cc_start: 0.7141 (m-40) cc_final: 0.6888 (m110)
REVERT: D  187 LEU cc_start: 0.7584 (tp) cc_final: 0.6826 (pp)
REVERT: E   23 PHE cc_start: 0.8513 (t80) cc_final: 0.8128 (t80)
REVERT: E  101 TYR cc_start: 0.8980 (t80) cc_final: 0.8411 (t80)
REVERT: E  119 ILE cc_start: 0.9492 (mp) cc_final: 0.9250 (mp)
REVERT: E  129 PRO cc_start: 0.7797 (Cg_endo) cc_final: 0.7573 (Cg_exo)
REVERT: E  138 LEU cc_start: 0.9252 (tt) cc_final: 0.9003 (mm)
REVERT: E  188 MET cc_start: 0.9243 (ptp) cc_final: 0.8953 (ptm)
REVERT: L  125 LEU cc_start: 0.5831 (mt) cc_final: 0.5464 (mp)
REVERT: U   45 GLN cc_start: 0.3231 (OUTLIER) cc_final: 0.2790 (pm20)
  outliers start: 3
  outliers final: 0
  residues processed: 260
  average time/residue: 0.2452
  time to fit residues: 99.3314
Evaluate side-chains
  143 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 216 optimal weight:   30.0000
   chunk 98 optimal weight:   10.0000
   chunk 194 optimal weight:    7.9990
   chunk 227 optimal weight:    4.9990
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:   30.0000
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:   30.0000
   chunk 103 optimal weight:   20.0000
   chunk 200 optimal weight:   50.0000
   overall best weight:    8.5996

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

Flipped N/Q/H residues before XYZ refinement:
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J  58 ASN
** J  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  16 HIS
Q  51 GLN
** Q  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  49 GLN
L   4 ASN
U  26 ASN
** U  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.053260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.039161 restraints weight = 513624.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.039960 restraints weight = 241179.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.040439 restraints weight = 158483.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.040741 restraints weight = 130935.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.040932 restraints weight = 118974.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.5461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.161  40250  Z= 0.359
  Angle     :  0.910  14.745  60980  Z= 0.443
  Chirality :  0.042   0.299   7908
  Planarity :  0.007   0.128   2755
  Dihedral  : 24.779 179.747  21798
  Min Nonbonded Distance : 1.866

Molprobity Statistics.
  All-atom Clashscore : 35.70
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.81 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  6.56 %
    Favored  : 92.85 %
  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 aren not related in a simple way.
  whole: -1.39 (0.24), residues: 1033
  helix:  0.01 (0.27), residues: 320
  sheet: -1.07 (0.39), residues: 171
  loop : -1.44 (0.25), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.028   0.002   ARG D  46 
 TYR   0.046   0.006   TYR J  74 
 PHE   0.019   0.003   PHE R  93 
 TRP   0.023   0.005   TRP R  92 
 HIS   0.017   0.003   HIS J  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00656 (40250)
  covalent geometry    : angle       0.91007 (60980)
  hydrogen bonds       : bond        0.15057 ( 1412)
  hydrogen bonds       : angle       4.20469 ( 2626)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 172
  time to evaluate  : 0.673 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   49 ASP cc_start: 0.8468 (p0) cc_final: 0.8247 (p0)
REVERT: J   67 ASN cc_start: 0.8907 (m-40) cc_final: 0.8284 (t0)
REVERT: J   71 ASP cc_start: 0.9012 (m-30) cc_final: 0.7732 (m-30)
REVERT: J   93 ILE cc_start: 0.8394 (pt) cc_final: 0.7742 (pt)
REVERT: J  103 ILE cc_start: 0.9445 (mm) cc_final: 0.9224 (pt)
REVERT: J  108 MET cc_start: 0.8250 (tpt) cc_final: 0.7527 (mmm)
REVERT: J  109 LEU cc_start: 0.9613 (tp) cc_final: 0.9221 (tt)
REVERT: J  122 LEU cc_start: 0.9751 (tp) cc_final: 0.9375 (pp)
REVERT: J  141 ASP cc_start: 0.8854 (p0) cc_final: 0.8518 (p0)
REVERT: Q   23 TYR cc_start: 0.9711 (m-80) cc_final: 0.9250 (m-80)
REVERT: Q   51 GLN cc_start: 0.8981 (pt0) cc_final: 0.8748 (pt0)
REVERT: Q   58 GLN cc_start: 0.9529 (tp-100) cc_final: 0.9222 (tp-100)
REVERT: Q  105 PHE cc_start: 0.8764 (t80) cc_final: 0.8519 (t80)
REVERT: Q  116 LEU cc_start: 0.9147 (tt) cc_final: 0.8898 (pp)
REVERT: R   13 ARG cc_start: 0.9206 (tmt170) cc_final: 0.8680 (tmt-80)
REVERT: R   31 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7915 (tm-30)
REVERT: R   39 LEU cc_start: 0.9567 (mm) cc_final: 0.9071 (mp)
REVERT: R   59 ILE cc_start: 0.9488 (mp) cc_final: 0.9269 (mp)
REVERT: R   73 LYS cc_start: 0.9560 (mppt) cc_final: 0.9285 (mmtm)
REVERT: R   81 LYS cc_start: 0.6895 (ttmt) cc_final: 0.5737 (tptt)
REVERT: R   95 ASP cc_start: 0.9296 (m-30) cc_final: 0.8425 (m-30)
REVERT: E   88 ARG cc_start: 0.8877 (mmp80) cc_final: 0.8675 (mmp-170)
REVERT: E  124 PHE cc_start: 0.8262 (m-80) cc_final: 0.7280 (m-80)
REVERT: E  188 MET cc_start: 0.9656 (ptp) cc_final: 0.9189 (ptp)
REVERT: E  199 MET cc_start: 0.8670 (tpt) cc_final: 0.8387 (tpt)
REVERT: L   81 ASP cc_start: 0.8257 (t0) cc_final: 0.7786 (m-30)
REVERT: U   34 ILE cc_start: 0.9129 (mp) cc_final: 0.8510 (mp)
REVERT: U   65 GLN cc_start: 0.9347 (mt0) cc_final: 0.9118 (mt0)
  outliers start: 5
  outliers final: 2
  residues processed: 175
  average time/residue: 0.2628
  time to fit residues: 71.7622
Evaluate side-chains
  126 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 124
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 58 optimal weight:   20.0000
   chunk 65 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   chunk 64 optimal weight:   20.0000
   chunk 75 optimal weight:   10.0000
   chunk 88 optimal weight:   20.0000
   chunk 218 optimal weight:    6.9990
   chunk 122 optimal weight:   40.0000
   chunk 206 optimal weight:    3.9990
   chunk 181 optimal weight:    9.9990
   chunk 106 optimal weight:   10.0000
   overall best weight:    8.1994

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

Flipped N/Q/H residues before XYZ refinement:
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J  58 ASN
J  77 HIS
** Q  51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  36 GLN
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.046689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.030883 restraints weight = 418354.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.031907 restraints weight = 194533.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.032458 restraints weight = 129154.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.032725 restraints weight = 104865.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.032851 restraints weight = 94912.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.7242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.081  40250  Z= 0.293
  Angle     :  0.734   8.918  60980  Z= 0.369
  Chirality :  0.038   0.219   7908
  Planarity :  0.006   0.094   2755
  Dihedral  : 25.118 178.333  21798
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 31.12
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.52 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  7.39 %
    Favored  : 92.13 %
  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 aren not related in a simple way.
  whole: -1.67 (0.24), residues: 1033
  helix: -0.12 (0.27), residues: 328
  sheet: -1.48 (0.39), residues: 159
  loop : -1.60 (0.25), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.002   ARG R  90 
 TYR   0.024   0.004   TYR J  74 
 PHE   0.020   0.002   PHE R  53 
 TRP   0.027   0.005   TRP D  80 
 HIS   0.014   0.003   HIS R  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00547 (40250)
  covalent geometry    : angle       0.73362 (60980)
  hydrogen bonds       : bond        0.09944 ( 1412)
  hydrogen bonds       : angle       3.85357 ( 2626)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 149
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   49 ASP cc_start: 0.8359 (p0) cc_final: 0.7863 (p0)
REVERT: J   67 ASN cc_start: 0.9380 (m-40) cc_final: 0.8937 (t0)
REVERT: J   71 ASP cc_start: 0.9042 (m-30) cc_final: 0.7893 (m-30)
REVERT: J  141 ASP cc_start: 0.9252 (p0) cc_final: 0.8956 (p0)
REVERT: Q   10 ARG cc_start: 0.8890 (tpp80) cc_final: 0.8566 (ttt180)
REVERT: Q   19 GLN cc_start: 0.9475 (mp10) cc_final: 0.9197 (mp10)
REVERT: Q   23 TYR cc_start: 0.9656 (m-80) cc_final: 0.8906 (m-80)
REVERT: Q   61 ILE cc_start: 0.9433 (mt) cc_final: 0.9197 (tt)
REVERT: Q  116 LEU cc_start: 0.9335 (tt) cc_final: 0.8990 (pp)
REVERT: R   13 ARG cc_start: 0.9295 (tmt170) cc_final: 0.8473 (ttp80)
REVERT: R   37 GLU cc_start: 0.8004 (pm20) cc_final: 0.7727 (pm20)
REVERT: R   39 LEU cc_start: 0.9660 (mm) cc_final: 0.9070 (mt)
REVERT: R   53 PHE cc_start: 0.9073 (p90) cc_final: 0.8782 (p90)
REVERT: R   81 LYS cc_start: 0.6951 (ttmt) cc_final: 0.6047 (tptt)
REVERT: R   95 ASP cc_start: 0.8735 (m-30) cc_final: 0.8412 (m-30)
REVERT: E  100 MET cc_start: 0.9382 (mmp) cc_final: 0.8998 (mmm)
REVERT: E  124 PHE cc_start: 0.8617 (m-80) cc_final: 0.7708 (m-80)
REVERT: E  188 MET cc_start: 0.9638 (ptp) cc_final: 0.9261 (ptm)
REVERT: L   81 ASP cc_start: 0.8512 (t0) cc_final: 0.8073 (m-30)
REVERT: U   64 ILE cc_start: 0.9802 (pt) cc_final: 0.9555 (mm)
REVERT: U   65 GLN cc_start: 0.9312 (mt0) cc_final: 0.8902 (mt0)
REVERT: U   90 LYS cc_start: 0.8439 (mmmt) cc_final: 0.8135 (mttt)
  outliers start: 4
  outliers final: 2
  residues processed: 152
  average time/residue: 0.2293
  time to fit residues: 55.3480
Evaluate side-chains
  127 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 125
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 27 optimal weight:    4.9990
   chunk 89 optimal weight:   20.0000
   chunk 143 optimal weight:   10.0000
   chunk 189 optimal weight:    0.9990
   chunk 73 optimal weight:   10.0000
   chunk 111 optimal weight:   30.0000
   chunk 202 optimal weight:    0.0870
   chunk 31 optimal weight:    8.9990
   chunk 43 optimal weight:    6.9990
   chunk 115 optimal weight:   10.0000
   overall best weight:    4.4166

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

Flipped N/Q/H residues before XYZ refinement:
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J  67 ASN
J  76 HIS
Q  51 GLN
R  82 HIS
** R  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  32 ASN
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  94 GLN
** U  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
U  45 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.047363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.031494 restraints weight = 412912.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.032511 restraints weight = 192324.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.033040 restraints weight = 128528.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 69)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.033299 restraints weight = 105130.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.033408 restraints weight = 95416.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.7570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  40250  Z= 0.183
  Angle     :  0.580   9.786  60980  Z= 0.293
  Chirality :  0.031   0.221   7908
  Planarity :  0.004   0.047   2755
  Dihedral  : 24.781 179.994  21798
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 23.51
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.03 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  4.53 %
    Favored  : 95.35 %
  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 aren not related in a simple way.
  whole: -1.49 (0.25), residues: 1033
  helix:  0.12 (0.28), residues: 328
  sheet: -1.69 (0.41), residues: 144
  loop : -1.47 (0.24), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG R  68 
 TYR   0.012   0.002   TYR J  75 
 PHE   0.016   0.002   PHE R  93 
 TRP   0.028   0.003   TRP E  78 
 HIS   0.007   0.002   HIS R  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (40250)
  covalent geometry    : angle       0.57988 (60980)
  hydrogen bonds       : bond        0.08141 ( 1412)
  hydrogen bonds       : angle       3.50458 ( 2626)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 162
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   49 ASP cc_start: 0.8298 (p0) cc_final: 0.7798 (p0)
REVERT: J   67 ASN cc_start: 0.9299 (m110) cc_final: 0.8893 (t0)
REVERT: J  122 LEU cc_start: 0.9680 (tp) cc_final: 0.9239 (pp)
REVERT: J  141 ASP cc_start: 0.9199 (p0) cc_final: 0.8917 (p0)
REVERT: N   42 LYS cc_start: 0.9250 (pttm) cc_final: 0.8725 (tptt)
REVERT: Q   19 GLN cc_start: 0.9547 (mp10) cc_final: 0.9133 (mp10)
REVERT: Q   23 TYR cc_start: 0.9628 (m-80) cc_final: 0.8546 (m-80)
REVERT: Q   89 ILE cc_start: 0.9619 (mm) cc_final: 0.9402 (mm)
REVERT: Q  116 LEU cc_start: 0.9352 (tt) cc_final: 0.9018 (pp)
REVERT: R   13 ARG cc_start: 0.9063 (tmt170) cc_final: 0.8200 (tmm160)
REVERT: R   31 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7781 (tm-30)
REVERT: R   37 GLU cc_start: 0.7859 (pm20) cc_final: 0.7378 (pm20)
REVERT: R   39 LEU cc_start: 0.9715 (mm) cc_final: 0.8974 (mt)
REVERT: R   81 LYS cc_start: 0.7907 (ttmt) cc_final: 0.7111 (tptt)
REVERT: D  187 LEU cc_start: 0.7859 (tp) cc_final: 0.6542 (pp)
REVERT: E  100 MET cc_start: 0.9348 (mmp) cc_final: 0.8996 (mmm)
REVERT: L   81 ASP cc_start: 0.8522 (t0) cc_final: 0.8132 (m-30)
REVERT: U   61 GLU cc_start: 0.7547 (pp20) cc_final: 0.7235 (pp20)
REVERT: U   65 GLN cc_start: 0.9389 (mt0) cc_final: 0.9122 (mt0)
  outliers start: 1
  outliers final: 0
  residues processed: 163
  average time/residue: 0.2293
  time to fit residues: 59.3244
Evaluate side-chains
  125 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 216 optimal weight:    0.5980
   chunk 212 optimal weight:    5.9990
   chunk 127 optimal weight:   20.0000
   chunk 148 optimal weight:   20.0000
   chunk 211 optimal weight:    0.4980
   chunk 231 optimal weight:    9.9990
   chunk 130 optimal weight:   10.0000
   chunk 165 optimal weight:   20.0000
   chunk 7 optimal weight:   20.0000
   chunk 154 optimal weight:   10.0000
   chunk 30 optimal weight:    6.9990
   overall best weight:    4.8186

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

Flipped N/Q/H residues before XYZ refinement:
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J  77 HIS
** R  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  94 GLN
** U  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  45 GLN ** 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 = 0.3215 r_free = 0.3215 target = 0.046216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.030505 restraints weight = 422250.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.031497 restraints weight = 195338.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.032008 restraints weight = 130675.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.032271 restraints weight = 106918.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.032399 restraints weight = 97152.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.8308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073  40250  Z= 0.199
  Angle     :  0.598  10.435  60980  Z= 0.301
  Chirality :  0.032   0.244   7908
  Planarity :  0.005   0.065   2755
  Dihedral  : 24.865 179.371  21798
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 25.04
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.62 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  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 aren not related in a simple way.
  whole: -1.63 (0.25), residues: 1033
  helix:  0.04 (0.28), residues: 328
  sheet: -1.66 (0.38), residues: 166
  loop : -1.59 (0.26), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG J  34 
 TYR   0.024   0.003   TYR Q  44 
 PHE   0.024   0.002   PHE R  53 
 TRP   0.009   0.002   TRP D  80 
 HIS   0.007   0.002   HIS R  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (40250)
  covalent geometry    : angle       0.59819 (60980)
  hydrogen bonds       : bond        0.08273 ( 1412)
  hydrogen bonds       : angle       3.59734 ( 2626)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   49 ASP cc_start: 0.8362 (p0) cc_final: 0.7861 (p0)
REVERT: J   71 ASP cc_start: 0.9218 (p0) cc_final: 0.8778 (p0)
REVERT: J   74 TYR cc_start: 0.8628 (m-10) cc_final: 0.8288 (m-10)
REVERT: J  108 MET cc_start: 0.8654 (mmm) cc_final: 0.8030 (mmm)
REVERT: J  122 LEU cc_start: 0.9661 (tp) cc_final: 0.9386 (pp)
REVERT: J  141 ASP cc_start: 0.9285 (p0) cc_final: 0.8970 (p0)
REVERT: N   42 LYS cc_start: 0.9262 (pttm) cc_final: 0.8755 (tptt)
REVERT: Q   19 GLN cc_start: 0.9470 (mp10) cc_final: 0.9065 (mp10)
REVERT: Q   23 TYR cc_start: 0.9624 (m-80) cc_final: 0.8530 (m-80)
REVERT: Q   44 TYR cc_start: 0.9279 (m-80) cc_final: 0.8285 (m-10)
REVERT: Q  116 LEU cc_start: 0.9378 (tt) cc_final: 0.9021 (pp)
REVERT: R   13 ARG cc_start: 0.9233 (tmt170) cc_final: 0.8470 (tmm160)
REVERT: R   31 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7997 (tm-30)
REVERT: R   35 PHE cc_start: 0.9056 (m-80) cc_final: 0.8698 (m-80)
REVERT: R   37 GLU cc_start: 0.8055 (pm20) cc_final: 0.7500 (pm20)
REVERT: R   39 LEU cc_start: 0.9753 (mm) cc_final: 0.9026 (mt)
REVERT: R   81 LYS cc_start: 0.7563 (ttmt) cc_final: 0.6997 (tptt)
REVERT: E  100 MET cc_start: 0.9373 (mmp) cc_final: 0.8930 (mmm)
REVERT: E  199 MET cc_start: 0.8746 (tpt) cc_final: 0.8531 (tpt)
REVERT: L   81 ASP cc_start: 0.8592 (t0) cc_final: 0.8216 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.2222
  time to fit residues: 55.9911
Evaluate side-chains
  126 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 217 optimal weight:    0.0670
   chunk 48 optimal weight:   10.0000
   chunk 153 optimal weight:   20.0000
   chunk 86 optimal weight:   30.0000
   chunk 136 optimal weight:   10.0000
   chunk 193 optimal weight:    2.9990
   chunk 119 optimal weight:   20.0000
   chunk 188 optimal weight:   10.0000
   chunk 127 optimal weight:   20.0000
   chunk 155 optimal weight:   20.0000
   chunk 106 optimal weight:   10.0000
   overall best weight:    6.6132

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

Flipped N/Q/H residues before XYZ refinement:
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J  58 ASN
** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  51 GLN
** Q  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  94 GLN
** U  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  68 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.043986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.028834 restraints weight = 431912.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2758 r_free = 0.2758 target = 0.029769 restraints weight = 197535.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.030223 restraints weight = 131915.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.030456 restraints weight = 108866.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.030549 restraints weight = 99243.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.9699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  40250  Z= 0.261
  Angle     :  0.702  10.941  60980  Z= 0.351
  Chirality :  0.036   0.276   7908
  Planarity :  0.005   0.061   2755
  Dihedral  : 25.270 178.369  21798
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 32.82
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.29 %
    Favored  : 90.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  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 aren not related in a simple way.
  whole: -2.08 (0.24), residues: 1033
  helix: -0.28 (0.28), residues: 328
  sheet: -1.99 (0.39), residues: 153
  loop : -1.91 (0.24), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG Q  49 
 TYR   0.022   0.003   TYR R   2 
 PHE   0.028   0.003   PHE D  90 
 TRP   0.010   0.002   TRP D  80 
 HIS   0.044   0.004   HIS U  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 (40250)
  covalent geometry    : angle       0.70193 (60980)
  hydrogen bonds       : bond        0.10889 ( 1412)
  hydrogen bonds       : angle       3.85302 ( 2626)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   36 LEU cc_start: 0.9675 (pp) cc_final: 0.9123 (tp)
REVERT: J   49 ASP cc_start: 0.8557 (p0) cc_final: 0.8169 (p0)
REVERT: J   67 ASN cc_start: 0.9028 (t0) cc_final: 0.8542 (t0)
REVERT: J   71 ASP cc_start: 0.9048 (p0) cc_final: 0.8817 (p0)
REVERT: J   74 TYR cc_start: 0.8592 (m-10) cc_final: 0.8170 (m-80)
REVERT: J  108 MET cc_start: 0.8918 (mmm) cc_final: 0.8096 (mmm)
REVERT: J  118 MET cc_start: 0.9287 (ptt) cc_final: 0.8603 (mtt)
REVERT: J  122 LEU cc_start: 0.9699 (tp) cc_final: 0.9391 (pp)
REVERT: J  141 ASP cc_start: 0.9201 (p0) cc_final: 0.8805 (p0)
REVERT: N   42 LYS cc_start: 0.9431 (pttm) cc_final: 0.9010 (tptt)
REVERT: Q   19 GLN cc_start: 0.9491 (mp10) cc_final: 0.9109 (mp10)
REVERT: Q   23 TYR cc_start: 0.9634 (m-80) cc_final: 0.8527 (m-80)
REVERT: Q   44 TYR cc_start: 0.9545 (m-80) cc_final: 0.8897 (m-10)
REVERT: Q   48 ASP cc_start: 0.8712 (t70) cc_final: 0.7104 (t0)
REVERT: Q   88 GLU cc_start: 0.7914 (mp0) cc_final: 0.7110 (mp0)
REVERT: R    6 GLN cc_start: 0.9211 (pm20) cc_final: 0.8645 (pm20)
REVERT: R   13 ARG cc_start: 0.9220 (tmt170) cc_final: 0.8630 (tmm160)
REVERT: R   31 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8362 (tm-30)
REVERT: R   39 LEU cc_start: 0.9812 (mm) cc_final: 0.8868 (mm)
REVERT: R   48 LYS cc_start: 0.9680 (tptt) cc_final: 0.9295 (tppt)
REVERT: R   81 LYS cc_start: 0.7106 (ttmt) cc_final: 0.6298 (tptt)
REVERT: E  100 MET cc_start: 0.9124 (mmp) cc_final: 0.8582 (mmm)
REVERT: E  124 PHE cc_start: 0.9282 (t80) cc_final: 0.8939 (t80)
REVERT: E  188 MET cc_start: 0.9351 (ptm) cc_final: 0.9036 (pmm)
REVERT: U   65 GLN cc_start: 0.9738 (mt0) cc_final: 0.9299 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.2293
  time to fit residues: 58.2086
Evaluate side-chains
  120 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 107 optimal weight:   10.0000
   chunk 133 optimal weight:   20.0000
   chunk 121 optimal weight:   30.0000
   chunk 177 optimal weight:   40.0000
   chunk 126 optimal weight:   20.0000
   chunk 212 optimal weight:    3.9990
   chunk 79 optimal weight:   10.0000
   chunk 116 optimal weight:   20.0000
   chunk 64 optimal weight:   10.0000
   chunk 185 optimal weight:   10.0000
   chunk 192 optimal weight:    7.9990
   overall best weight:    8.3996

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

Flipped N/Q/H residues before XYZ refinement:
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J  58 ASN
** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  58 ASN
D  94 GLN
E   9 GLN
** U  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.042692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2692 r_free = 0.2692 target = 0.027932 restraints weight = 434746.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.028834 restraints weight = 197870.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.029266 restraints weight = 131635.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.029486 restraints weight = 108286.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.029588 restraints weight = 98758.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          1.0690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  40250  Z= 0.300
  Angle     :  0.743  10.039  60980  Z= 0.371
  Chirality :  0.039   0.210   7908
  Planarity :  0.006   0.087   2755
  Dihedral  : 25.542 177.190  21798
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 36.26
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.20 %
    Favored  : 90.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  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 aren not related in a simple way.
  whole: -2.23 (0.24), residues: 1033
  helix: -0.26 (0.28), residues: 319
  sheet: -2.13 (0.39), residues: 155
  loop : -2.05 (0.24), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG J  34 
 TYR   0.021   0.003   TYR R   2 
 PHE   0.031   0.003   PHE E  19 
 TRP   0.011   0.003   TRP E  78 
 HIS   0.012   0.002   HIS R  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00549 (40250)
  covalent geometry    : angle       0.74291 (60980)
  hydrogen bonds       : bond        0.11062 ( 1412)
  hydrogen bonds       : angle       3.99511 ( 2626)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   36 LEU cc_start: 0.9655 (pp) cc_final: 0.9225 (tp)
REVERT: J   49 ASP cc_start: 0.8600 (p0) cc_final: 0.8308 (p0)
REVERT: J   67 ASN cc_start: 0.9327 (t0) cc_final: 0.8862 (t0)
REVERT: J   71 ASP cc_start: 0.8636 (p0) cc_final: 0.8305 (p0)
REVERT: J   74 TYR cc_start: 0.8525 (m-10) cc_final: 0.8118 (m-10)
REVERT: J   93 ILE cc_start: 0.8829 (pt) cc_final: 0.8588 (pt)
REVERT: J  108 MET cc_start: 0.9248 (mmm) cc_final: 0.8353 (mmm)
REVERT: J  118 MET cc_start: 0.9090 (ptt) cc_final: 0.8689 (mtt)
REVERT: J  141 ASP cc_start: 0.9254 (p0) cc_final: 0.8918 (p0)
REVERT: N   42 LYS cc_start: 0.9444 (pttm) cc_final: 0.9004 (tptt)
REVERT: Q   19 GLN cc_start: 0.9537 (mp10) cc_final: 0.9175 (mp10)
REVERT: Q   23 TYR cc_start: 0.9629 (m-80) cc_final: 0.8543 (m-80)
REVERT: Q   44 TYR cc_start: 0.9586 (m-80) cc_final: 0.8648 (m-10)
REVERT: Q  116 LEU cc_start: 0.9389 (tp) cc_final: 0.9107 (mt)
REVERT: R   13 ARG cc_start: 0.9241 (tmt170) cc_final: 0.8935 (tmm-80)
REVERT: R   25 LEU cc_start: 0.9258 (mt) cc_final: 0.8987 (mt)
REVERT: R   41 ILE cc_start: 0.9513 (mp) cc_final: 0.9238 (mm)
REVERT: R   48 LYS cc_start: 0.9737 (tptt) cc_final: 0.9229 (tppt)
REVERT: R   53 PHE cc_start: 0.9544 (p90) cc_final: 0.9185 (p90)
REVERT: R   73 LYS cc_start: 0.9586 (mppt) cc_final: 0.9353 (mmtm)
REVERT: R   81 LYS cc_start: 0.6924 (ttmt) cc_final: 0.6267 (tptt)
REVERT: E  100 MET cc_start: 0.9077 (mmp) cc_final: 0.8519 (mmm)
REVERT: L   17 LYS cc_start: 0.9133 (mppt) cc_final: 0.8813 (mppt)
REVERT: U   61 GLU cc_start: 0.7678 (pp20) cc_final: 0.7432 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 0.2449
  time to fit residues: 58.7089
Evaluate side-chains
  118 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 62 optimal weight:   20.0000
   chunk 207 optimal weight:    0.3980
   chunk 176 optimal weight:   40.0000
   chunk 224 optimal weight:   20.0000
   chunk 189 optimal weight:    9.9990
   chunk 143 optimal weight:   10.0000
   chunk 77 optimal weight:   10.0000
   chunk 231 optimal weight:   10.0000
   chunk 126 optimal weight:   20.0000
   chunk 61 optimal weight:   20.0000
   chunk 164 optimal weight:   20.0000
   overall best weight:    8.0794

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

Flipped N/Q/H residues before XYZ refinement:
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  45 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 = 0.3106 r_free = 0.3106 target = 0.042163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2685 r_free = 0.2685 target = 0.027705 restraints weight = 433491.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.028487 restraints weight = 197351.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.028898 restraints weight = 129546.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.029148 restraints weight = 107210.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 55)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.029248 restraints weight = 97325.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8651
moved from start:          1.1379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  40250  Z= 0.289
  Angle     :  0.732   9.812  60980  Z= 0.367
  Chirality :  0.038   0.252   7908
  Planarity :  0.005   0.053   2755
  Dihedral  : 25.580 177.028  21798
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 35.17
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.97 %
    Favored  : 89.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  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 aren not related in a simple way.
  whole: -2.41 (0.24), residues: 1033
  helix: -0.40 (0.27), residues: 320
  sheet: -2.37 (0.40), residues: 147
  loop : -2.14 (0.23), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG J  99 
 TYR   0.021   0.003   TYR R   2 
 PHE   0.018   0.002   PHE N  87 
 TRP   0.012   0.002   TRP E  78 
 HIS   0.008   0.002   HIS R  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 (40250)
  covalent geometry    : angle       0.73219 (60980)
  hydrogen bonds       : bond        0.10955 ( 1412)
  hydrogen bonds       : angle       3.95472 ( 2626)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.614 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   36 LEU cc_start: 0.9780 (pp) cc_final: 0.9326 (pp)
REVERT: J   49 ASP cc_start: 0.8486 (p0) cc_final: 0.8243 (p0)
REVERT: J   67 ASN cc_start: 0.9387 (t0) cc_final: 0.8914 (t0)
REVERT: J   71 ASP cc_start: 0.8471 (p0) cc_final: 0.7920 (p0)
REVERT: J   74 TYR cc_start: 0.8420 (m-10) cc_final: 0.8041 (m-10)
REVERT: J  108 MET cc_start: 0.9266 (mmm) cc_final: 0.9013 (tpp)
REVERT: J  118 MET cc_start: 0.9293 (ptt) cc_final: 0.8670 (ttm)
REVERT: J  122 LEU cc_start: 0.9713 (tp) cc_final: 0.9491 (pp)
REVERT: J  130 HIS cc_start: 0.8890 (p-80) cc_final: 0.8375 (p-80)
REVERT: J  141 ASP cc_start: 0.9210 (p0) cc_final: 0.8889 (p0)
REVERT: N   42 LYS cc_start: 0.9390 (pttm) cc_final: 0.8896 (tptt)
REVERT: Q   19 GLN cc_start: 0.9534 (mp10) cc_final: 0.9168 (mp10)
REVERT: Q   23 TYR cc_start: 0.9630 (m-80) cc_final: 0.8565 (m-80)
REVERT: Q   44 TYR cc_start: 0.9543 (m-80) cc_final: 0.8623 (m-10)
REVERT: Q  110 GLU cc_start: 0.8876 (mp0) cc_final: 0.8664 (pm20)
REVERT: R   13 ARG cc_start: 0.9211 (tmt170) cc_final: 0.9011 (tmm-80)
REVERT: R   25 LEU cc_start: 0.9016 (mt) cc_final: 0.8753 (mt)
REVERT: R   35 PHE cc_start: 0.9245 (m-80) cc_final: 0.8600 (m-80)
REVERT: R   37 GLU cc_start: 0.9026 (pm20) cc_final: 0.8556 (pm20)
REVERT: R   48 LYS cc_start: 0.9389 (tptt) cc_final: 0.9164 (tppt)
REVERT: R   53 PHE cc_start: 0.9460 (p90) cc_final: 0.9259 (p90)
REVERT: R   81 LYS cc_start: 0.6901 (ttmt) cc_final: 0.6331 (tptt)
REVERT: E  100 MET cc_start: 0.9150 (mmp) cc_final: 0.8714 (mmm)
REVERT: L   13 LYS cc_start: 0.9548 (mmpt) cc_final: 0.9250 (mmmt)
REVERT: L   17 LYS cc_start: 0.9143 (mppt) cc_final: 0.8765 (mppt)
REVERT: U   61 GLU cc_start: 0.7739 (pp20) cc_final: 0.7507 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.2551
  time to fit residues: 62.5968
Evaluate side-chains
  121 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 165 optimal weight:   20.0000
   chunk 227 optimal weight:    5.9990
   chunk 87 optimal weight:   20.0000
   chunk 110 optimal weight:   30.0000
   chunk 160 optimal weight:   50.0000
   chunk 0 optimal weight:   10.0000
   chunk 176 optimal weight:   30.0000
   chunk 229 optimal weight:    0.0970
   chunk 14 optimal weight:   40.0000
   chunk 145 optimal weight:   10.0000
   chunk 3 optimal weight:    5.9990
   overall best weight:    6.4190

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

Flipped N/Q/H residues before XYZ refinement:
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
U  45 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.042544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.028041 restraints weight = 434925.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.028853 restraints weight = 196172.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2738 r_free = 0.2738 target = 0.029291 restraints weight = 127162.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.029539 restraints weight = 104562.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.029621 restraints weight = 94709.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          1.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  40250  Z= 0.240
  Angle     :  0.667   9.234  60980  Z= 0.336
  Chirality :  0.036   0.234   7908
  Planarity :  0.005   0.066   2755
  Dihedral  : 25.490 177.764  21798
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 31.33
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.10 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.43 %
    Favored  : 98.45 %
  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 aren not related in a simple way.
  whole: -2.42 (0.24), residues: 1033
  helix: -0.35 (0.28), residues: 321
  sheet: -2.32 (0.38), residues: 156
  loop : -2.19 (0.24), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 179 
 TYR   0.016   0.002   TYR R   2 
 PHE   0.017   0.002   PHE N  87 
 TRP   0.060   0.004   TRP E  78 
 HIS   0.009   0.002   HIS R  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 (40250)
  covalent geometry    : angle       0.66708 (60980)
  hydrogen bonds       : bond        0.09556 ( 1412)
  hydrogen bonds       : angle       3.83590 ( 2626)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 156
  time to evaluate  : 0.596 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J    1 MET cc_start: 0.9191 (tmm) cc_final: 0.8931 (tmm)
REVERT: J   49 ASP cc_start: 0.8443 (p0) cc_final: 0.8170 (p0)
REVERT: J   67 ASN cc_start: 0.9351 (t0) cc_final: 0.8718 (t0)
REVERT: J   71 ASP cc_start: 0.8447 (p0) cc_final: 0.7983 (p0)
REVERT: J   74 TYR cc_start: 0.8375 (m-10) cc_final: 0.8011 (m-10)
REVERT: J   93 ILE cc_start: 0.8945 (pt) cc_final: 0.8667 (pt)
REVERT: J  130 HIS cc_start: 0.8911 (p-80) cc_final: 0.8496 (p-80)
REVERT: J  141 ASP cc_start: 0.9358 (p0) cc_final: 0.9090 (p0)
REVERT: N   42 LYS cc_start: 0.9384 (pttm) cc_final: 0.8891 (tptt)
REVERT: Q   44 TYR cc_start: 0.9509 (m-80) cc_final: 0.8576 (m-10)
REVERT: Q   59 LEU cc_start: 0.9792 (tp) cc_final: 0.9587 (tp)
REVERT: R   13 ARG cc_start: 0.9079 (tmt170) cc_final: 0.8615 (tmm160)
REVERT: R   25 LEU cc_start: 0.8814 (mt) cc_final: 0.8529 (mt)
REVERT: R   35 PHE cc_start: 0.9266 (m-80) cc_final: 0.9045 (m-80)
REVERT: R   48 LYS cc_start: 0.9495 (tptt) cc_final: 0.9168 (tppt)
REVERT: R   53 PHE cc_start: 0.9517 (p90) cc_final: 0.8953 (p90)
REVERT: R   81 LYS cc_start: 0.6844 (ttmt) cc_final: 0.5856 (tptt)
REVERT: D   43 ASP cc_start: 0.9127 (m-30) cc_final: 0.8438 (t70)
REVERT: E  100 MET cc_start: 0.8906 (mmp) cc_final: 0.8320 (mmm)
REVERT: L   17 LYS cc_start: 0.9167 (mppt) cc_final: 0.8767 (mppt)
REVERT: U   61 GLU cc_start: 0.7714 (pp20) cc_final: 0.7445 (pp20)
  outliers start: 1
  outliers final: 1
  residues processed: 157
  average time/residue: 0.2409
  time to fit residues: 59.5271
Evaluate side-chains
  124 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 129 optimal weight:   10.0000
   chunk 178 optimal weight:   30.0000
   chunk 10 optimal weight:    5.9990
   chunk 37 optimal weight:    9.9990
   chunk 173 optimal weight:   40.0000
   chunk 20 optimal weight:   20.0000
   chunk 85 optimal weight:   30.0000
   chunk 59 optimal weight:   20.0000
   chunk 153 optimal weight:   20.0000
   chunk 157 optimal weight:   30.0000
   chunk 44 optimal weight:    6.9990
   overall best weight:   10.5994

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

Flipped N/Q/H residues before XYZ refinement:
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J  58 ASN
** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.040668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.026541 restraints weight = 448583.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.027314 restraints weight = 203329.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2677 r_free = 0.2677 target = 0.027741 restraints weight = 133247.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2683 r_free = 0.2683 target = 0.027937 restraints weight = 109691.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.028046 restraints weight = 100458.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8669
moved from start:          1.2398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.069  40250  Z= 0.374
  Angle     :  0.850   9.669  60980  Z= 0.422
  Chirality :  0.044   0.247   7908
  Planarity :  0.006   0.066   2755
  Dihedral  : 25.885 175.664  21798
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 45.78
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 11.62 %
    Favored  : 88.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  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 aren not related in a simple way.
  whole: -2.91 (0.23), residues: 1033
  helix: -0.77 (0.27), residues: 327
  sheet: -2.39 (0.39), residues: 143
  loop : -2.59 (0.22), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E  44 
 TYR   0.024   0.003   TYR R   2 
 PHE   0.031   0.003   PHE E 124 
 TRP   0.052   0.004   TRP E  78 
 HIS   0.011   0.003   HIS R  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00685 (40250)
  covalent geometry    : angle       0.84997 (60980)
  hydrogen bonds       : bond        0.13750 ( 1412)
  hydrogen bonds       : angle       4.21711 ( 2626)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.663 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J    1 MET cc_start: 0.9329 (tmm) cc_final: 0.9093 (tmm)
REVERT: J   67 ASN cc_start: 0.9357 (t0) cc_final: 0.8742 (t0)
REVERT: J   71 ASP cc_start: 0.8513 (p0) cc_final: 0.7943 (p0)
REVERT: J   74 TYR cc_start: 0.8380 (m-10) cc_final: 0.8078 (m-10)
REVERT: J  118 MET cc_start: 0.9350 (ptt) cc_final: 0.9064 (ptm)
REVERT: J  141 ASP cc_start: 0.9243 (p0) cc_final: 0.8973 (p0)
REVERT: N   42 LYS cc_start: 0.9402 (pttm) cc_final: 0.8849 (tptt)
REVERT: Q   19 GLN cc_start: 0.9597 (mp10) cc_final: 0.9171 (mp10)
REVERT: Q   23 TYR cc_start: 0.9538 (m-80) cc_final: 0.8606 (m-80)
REVERT: Q   44 TYR cc_start: 0.9566 (m-80) cc_final: 0.8617 (m-10)
REVERT: R   13 ARG cc_start: 0.9264 (tmt170) cc_final: 0.8997 (tmm-80)
REVERT: R   25 LEU cc_start: 0.8892 (mt) cc_final: 0.8556 (mt)
REVERT: R   35 PHE cc_start: 0.9310 (m-80) cc_final: 0.8729 (m-80)
REVERT: R   37 GLU cc_start: 0.8947 (pm20) cc_final: 0.8572 (pm20)
REVERT: R   41 ILE cc_start: 0.9516 (mm) cc_final: 0.9269 (mm)
REVERT: R   48 LYS cc_start: 0.9633 (tptt) cc_final: 0.9349 (tppt)
REVERT: R   81 LYS cc_start: 0.6846 (ttmt) cc_final: 0.6341 (tptt)
REVERT: E    1 MET cc_start: 0.8315 (pmm) cc_final: 0.8076 (pmm)
REVERT: E  100 MET cc_start: 0.8887 (mmp) cc_final: 0.8362 (mmm)
REVERT: L   17 LYS cc_start: 0.9133 (mppt) cc_final: 0.8732 (mppt)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.2430
  time to fit residues: 54.7106
Evaluate side-chains
  112 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 66 optimal weight:   20.0000
   chunk 174 optimal weight:   30.0000
   chunk 69 optimal weight:   20.0000
   chunk 45 optimal weight:    7.9990
   chunk 137 optimal weight:   10.0000
   chunk 211 optimal weight:    8.9990
   chunk 166 optimal weight:   40.0000
   chunk 104 optimal weight:   20.0000
   chunk 77 optimal weight:   10.0000
   chunk 92 optimal weight:   10.0000
   chunk 112 optimal weight:   20.0000
   overall best weight:    9.3996

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

Flipped N/Q/H residues before XYZ refinement:
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  44 HIS ** 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 = 0.3056 r_free = 0.3056 target = 0.040752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2640 r_free = 0.2640 target = 0.026679 restraints weight = 442853.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2671 r_free = 0.2671 target = 0.027522 restraints weight = 197713.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.027948 restraints weight = 130749.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.028158 restraints weight = 107438.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.028256 restraints weight = 97864.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.2645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
moved from start:          1.2835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  40250  Z= 0.323
  Angle     :  0.775  16.520  60980  Z= 0.387
  Chirality :  0.040   0.221   7908
  Planarity :  0.006   0.059   2755
  Dihedral  : 25.883 175.608  21798
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 40.68
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 11.81 %
    Favored  : 88.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  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 aren not related in a simple way.
  whole: -2.90 (0.23), residues: 1033
  helix: -0.75 (0.27), residues: 327
  sheet: -2.44 (0.40), residues: 138
  loop : -2.58 (0.22), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D 184 
 TYR   0.018   0.003   TYR R   2 
 PHE   0.038   0.003   PHE R  53 
 TRP   0.038   0.004   TRP E  78 
 HIS   0.010   0.002   HIS J 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00594 (40250)
  covalent geometry    : angle       0.77527 (60980)
  hydrogen bonds       : bond        0.11657 ( 1412)
  hydrogen bonds       : angle       4.09638 ( 2626)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5767.21 seconds
wall clock time: 101 minutes 30.28 seconds (6090.28 seconds total)