Starting phenix.real_space_refine
on Tue Aug 26 09:44:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c97_16504/08_2025/8c97_16504.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c97_16504/08_2025/8c97_16504.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c97_16504/08_2025/8c97_16504.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c97_16504/08_2025/8c97_16504.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c97_16504/08_2025/8c97_16504.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c97_16504/08_2025/8c97_16504.map"
  }
  resolution = 4.07
  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=   0.017 sd=   0.096
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    1292      5.49       5
     S      25      5.16       5
     C   17639      2.51       5
     N    6738      2.21       5
     O   10469      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  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: 36163
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "0"
      Number of atoms: 263
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 263
          Classifications: {'peptide': 33}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 32}
    Chain: "2"
      Number of atoms: 262
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 262
          Classifications: {'peptide': 32}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 31}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 27767
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1292, 27767
          Classifications: {'RNA': 1292}
          Modifications used: {'rna2p_pur': 119, 'rna2p_pyr': 70, 'rna3p_pur': 641, 'rna3p_pyr': 462}
          Link IDs: {'rna2p': 189, 'rna3p': 1102}
          Chain breaks: 6
    Chain: "D"
      Number of atoms: 1200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1200
          Classifications: {'peptide': 161}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 156}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1129
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 143}
          Chain breaks: 1
    Chain: "K"
      Number of atoms: 938
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 938
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 5, 'TRANS': 116}
    Chain: "N"
      Number of atoms: 960
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 960
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 4, 'TRANS': 115}
    Chain: "P"
      Number of atoms: 917
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 917
          Classifications: {'peptide': 114}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 110}
    Chain: "S"
      Number of atoms: 717
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 717
          Classifications: {'peptide': 93}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 91}
          Chain breaks: 1
    Chain: "T"
      Number of atoms: 722
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 722
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 1, 'TRANS': 89}
    Chain: "U"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 779
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 3, 'TRANS': 98}
    Chain: "Y"
      Number of atoms: 509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 509
          Classifications: {'peptide': 63}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 62}
  Time building chain proxies: 6.18, per 1000 atoms: 0.17
  Number of scatterers: 36163
  At special positions: 0
  Unit cell: (150, 175, 203.75, 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      25     16.00
     P    1292     15.00
     O   10469      8.00
     N    6738      7.00
     C   17639      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: 2.07
  Conformation dependent library (CDL) restraints added in 631.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2006

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 15 sheets defined
      31.6% alpha, 21.4% beta
      404 base pairs and 629 stacking pairs defined.
    Time for finding SS restraints: 4.47
  Creating SS restraints...
    Processing helix  chain '2' and resid 11 through 16
    Processing helix  chain '2' and resid 17 through 24
    Processing helix  chain '2' and resid 24 through 36
    Processing helix  chain 'D' and resid 39 through 44
    Processing helix  chain 'D' and resid 61 through 72
      removed outlier: 3.774A  pdb=" N   LYS D  70 " --> pdb=" O   GLY D  66 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   ALA D  71 " --> pdb=" O   HIS D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 97 through 103
      removed outlier: 4.326A  pdb=" N   ASP D 103 " --> pdb=" O   LEU D 100 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 15 through 20
    Processing helix  chain 'E' and resid 24 through 39
    Processing helix  chain 'E' and resid 97 through 115
    Processing helix  chain 'E' and resid 130 through 142
      removed outlier: 3.513A  pdb=" N   LEU E 134 " --> pdb=" O   LYS E 130 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 154 through 160
      removed outlier: 3.541A  pdb=" N   PHE E 158 " --> pdb=" O   ASP E 154 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 176 through 183
      removed outlier: 3.680A  pdb=" N   PHE E 183 " --> pdb=" O   SER E 179 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 191 through 201
      removed outlier: 4.122A  pdb=" N   GLN E 195 " --> pdb=" O   ASP E 191 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 109 through 113
      removed outlier: 3.800A  pdb=" N   MET K 113 " --> pdb=" O   GLU K 110 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 13 through 32
      removed outlier: 3.542A  pdb=" N   GLN N  18 " --> pdb=" O   SER N  14 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 37 through 56
      removed outlier: 3.712A  pdb=" N   ARG N  46 " --> pdb=" O   LYS N  42 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL N  47 " --> pdb=" O   GLU N  43 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   GLU N  49 " --> pdb=" O   ARG N  45 " (cutoff:3.500A)
      Proline residue:  N  50  - end of helix
    Processing helix  chain 'N' and resid 59 through 68
    Processing helix  chain 'N' and resid 72 through 79
    Processing helix  chain 'N' and resid 82 through 88
    Processing helix  chain 'P' and resid 2 through 10
    Processing helix  chain 'P' and resid 52 through 55
    Processing helix  chain 'P' and resid 96 through 101
    Processing helix  chain 'P' and resid 103 through 108
    Processing helix  chain 'S' and resid 15 through 23
    Processing helix  chain 'S' and resid 28 through 39
    Processing helix  chain 'S' and resid 42 through 62
      removed outlier: 3.981A  pdb=" N   LEU S  46 " --> pdb=" O   LYS S  42 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 17 through 28
    Processing helix  chain 'T' and resid 39 through 52
    Processing helix  chain 'U' and resid 65 through 67
      No H-bonds generated for 'chain 'U' and resid 65 through 67'
    Processing helix  chain 'Y' and resid 2 through 7
    Processing helix  chain 'Y' and resid 9 through 33
      removed outlier: 4.069A  pdb=" N   GLN Y  25 " --> pdb=" O   LEU Y  21 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   PHE Y  26 " --> pdb=" O   LEU Y  22 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   GLN Y  31 " --> pdb=" O   ASN Y  27 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 46 through 56
    Processing sheet with id=AA1, first strand: chain '0' and resid 28 through 29
    Processing sheet with id=AA2, first strand: chain '0' and resid 47 through 48
    Processing sheet with id=AA3, first strand: chain 'D' and resid 170 through 176
      removed outlier: 5.059A  pdb=" N   THR D 171 " --> pdb=" O   GLY D 111 " (cutoff:3.500A)
      removed outlier: 7.255A  pdb=" N   GLY D 111 " --> pdb=" O   THR D 171 " (cutoff:3.500A)
      removed outlier: 5.344A  pdb=" N   GLN D 173 " --> pdb=" O   VAL D 109 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   VAL D 109 " --> pdb=" O   GLN D 173 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ILE D  27 " --> pdb=" O   LEU D 187 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU D 187 " --> pdb=" O   ILE D  27 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 12 through 15
    Processing sheet with id=AA5, first strand: chain 'D' and resid 34 through 38
      removed outlier: 5.653A  pdb=" N   VAL D  34 " --> pdb=" O   THR D  51 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   THR D  51 " --> pdb=" O   VAL D  34 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 121
      removed outlier: 3.707A  pdb=" N   ASP E 168 " --> pdb=" O   VAL E 146 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'K' and resid 6 through 10
      removed outlier: 3.704A  pdb=" N   VAL K  10 " --> pdb=" O   ARG K  17 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ARG K  17 " --> pdb=" O   VAL K  10 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   ALA K  16 " --> pdb=" O   ALA K  46 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ALA K  46 " --> pdb=" O   ALA K  16 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   ARG K  18 " --> pdb=" O   LYS K  44 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   LYS K  40 " --> pdb=" O   ILE K  22 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   VAL K  24 " --> pdb=" O   ILE K  38 " (cutoff:3.500A)
      removed outlier: 8.166A  pdb=" N   ILE K  38 " --> pdb=" O   VAL K  24 " (cutoff:3.500A)
      removed outlier: 5.389A  pdb=" N   VAL K  62 " --> pdb=" O   VAL K  85 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   VAL K  85 " --> pdb=" O   VAL K  62 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   CYS K  84 " --> pdb=" O   MET K   7 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   ASN K   9 " --> pdb=" O   CYS K  84 " (cutoff:3.500A)
      removed outlier: 7.238A  pdb=" N   LEU K  86 " --> pdb=" O   ASN K   9 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'K' and resid 69 through 70
      removed outlier: 3.907A  pdb=" N   VAL K  69 " --> pdb=" O   ILE K  77 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ILE K  77 " --> pdb=" O   VAL K  69 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   VAL K  76 " --> pdb=" O   VAL P  72 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ALA P  48 " --> pdb=" O   THR P  59 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   ARG P  61 " --> pdb=" O   VAL P  46 " (cutoff:3.500A)
      removed outlier: 5.469A  pdb=" N   VAL P  46 " --> pdb=" O   ARG P  61 " (cutoff:3.500A)
      removed outlier: 8.324A  pdb=" N   ILE P  63 " --> pdb=" O   GLY P  44 " (cutoff:3.500A)
      removed outlier: 8.460A  pdb=" N   GLY P  44 " --> pdb=" O   ILE P  63 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   VAL P  46 " --> pdb=" O   ASP P  23 " (cutoff:3.500A)
      removed outlier: 5.181A  pdb=" N   ASP P  23 " --> pdb=" O   VAL P  46 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   GLU P  26 " --> pdb=" O   VAL P  85 " (cutoff:3.500A)
      removed outlier: 5.261A  pdb=" N   VAL P  85 " --> pdb=" O   GLU P  26 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   LYS P  28 " --> pdb=" O   ILE P  83 " (cutoff:3.500A)
      removed outlier: 5.502A  pdb=" N   ILE P  83 " --> pdb=" O   LYS P  28 " (cutoff:3.500A)
      removed outlier: 7.559A  pdb=" N   TRP P  30 " --> pdb=" O   ASP P  81 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   ASP P  81 " --> pdb=" O   TRP P  30 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 33 through 36
      removed outlier: 6.649A  pdb=" N   MET N 110 " --> pdb=" O   CYS N 100 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 2 through 10
      removed outlier: 5.176A  pdb=" N   ILE S   4 " --> pdb=" O   VAL S 107 " (cutoff:3.500A)
      removed outlier: 7.135A  pdb=" N   VAL S 107 " --> pdb=" O   ILE S   4 " (cutoff:3.500A)
      removed outlier: 5.321A  pdb=" N   LYS S   6 " --> pdb=" O   VAL S 105 " (cutoff:3.500A)
      removed outlier: 7.338A  pdb=" N   VAL S 105 " --> pdb=" O   LYS S   6 " (cutoff:3.500A)
      removed outlier: 5.427A  pdb=" N   ARG S   8 " --> pdb=" O   ILE S 103 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   ILE S 103 " --> pdb=" O   ARG S   8 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   HIS S 102 " --> pdb=" O   VAL S  76 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   VAL S  76 " --> pdb=" O   HIS S 102 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   THR S 104 " --> pdb=" O   ILE S  74 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   ILE S  74 " --> pdb=" O   THR S 104 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   VAL S 106 " --> pdb=" O   THR S  72 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'T' and resid 13 through 14
      removed outlier: 3.811A  pdb=" N   LYS T  81 " --> pdb=" O   VAL T  34 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   TRP T  80 " --> pdb=" O   VAL T  62 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   VAL T  62 " --> pdb=" O   TRP T  80 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   LYS T  82 " --> pdb=" O   THR T  60 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   THR T  60 " --> pdb=" O   LYS T  82 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   TYR T  84 " --> pdb=" O   VAL T  58 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   VAL T  58 " --> pdb=" O   TYR T  84 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   THR T  86 " --> pdb=" O   GLU T  56 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'T' and resid 67 through 68
    Processing sheet with id=AB4, first strand: chain 'U' and resid 33 through 35
      removed outlier: 3.827A  pdb=" N   ASN U  26 " --> pdb=" O   ILE U  34 " (cutoff:3.500A)
      removed outlier: 5.918A  pdb=" N   GLU U   9 " --> pdb=" O   PHE U  72 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   PHE U  72 " --> pdb=" O   GLU U   9 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   ASN U  73 " --> pdb=" O   LYS U  78 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   LYS U  78 " --> pdb=" O   ASN U  73 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'U' and resid 40 through 41
      removed outlier: 3.520A  pdb=" N   LYS U  60 " --> pdb=" O   VAL U  41 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'U' and resid 82 through 86

    311 hydrogen bonds defined for protein.
    858 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      1029 hydrogen bonds
      1648 hydrogen bond angles
      0 basepair planarities
      404 basepair parallelities
      629 stacking parallelities
  Total time for adding SS restraints: 12.28

  Time building geometry restraints manager: 3.00 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 5958
        1.33 -     1.45: 16665
        1.45 -     1.57: 14330
        1.57 -     1.69: 2578
        1.69 -     1.81: 47
  Bond restraints: 39578
  Sorted by residual:
  bond pdb=" C1'   U A 138 "
       pdb=" N1    U A 138 "
    ideal  model  delta    sigma   weight residual
    1.480  1.573 -0.093 1.50e-02 4.44e+03 3.83e+01
  bond pdb=" O5'   A A2733 "
       pdb=" C5'   A A2733 "
    ideal  model  delta    sigma   weight residual
    1.420  1.457 -0.037 1.50e-02 4.44e+03 5.93e+00
  bond pdb=" N   GLU T   4 "
       pdb=" CA  GLU T   4 "
    ideal  model  delta    sigma   weight residual
    1.453  1.484 -0.031 1.37e-02 5.33e+03 4.97e+00
  bond pdb=" N   GLU T   5 "
       pdb=" CA  GLU T   5 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.029 1.29e-02 6.01e+03 4.92e+00
  bond pdb=" O5'   A A2734 "
       pdb=" C5'   A A2734 "
    ideal  model  delta    sigma   weight residual
    1.420  1.448 -0.028 1.50e-02 4.44e+03 3.49e+00
  ... (remaining 39573 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.83: 59769
        2.83 -     5.66: 87
        5.66 -     8.49: 10
        8.49 -    11.32: 0
       11.32 -    14.15: 1
  Bond angle restraints: 59867
  Sorted by residual:
  angle pdb=" C3'   A A2733 "
        pdb=" O3'   A A2733 "
        pdb=" P     A A2734 "
      ideal   model   delta    sigma   weight residual
     120.20  106.05   14.15 1.50e+00 4.44e-01 8.89e+01
  angle pdb=" N   GLU T   4 "
        pdb=" CA  GLU T   4 "
        pdb=" C   GLU T   4 "
      ideal   model   delta    sigma   weight residual
     110.41  104.28    6.13 1.23e+00 6.61e-01 2.48e+01
  angle pdb=" C3'   G A2732 "
        pdb=" O3'   G A2732 "
        pdb=" P     A A2733 "
      ideal   model   delta    sigma   weight residual
     120.20  112.76    7.44 1.50e+00 4.44e-01 2.46e+01
  angle pdb=" CA  GLU T   4 "
        pdb=" C   GLU T   4 "
        pdb=" O   GLU T   4 "
      ideal   model   delta    sigma   weight residual
     121.99  116.68    5.31 1.14e+00 7.69e-01 2.17e+01
  angle pdb=" O2'   A A2733 "
        pdb=" C2'   A A2733 "
        pdb=" C1'   A A2733 "
      ideal   model   delta    sigma   weight residual
     108.40  114.33   -5.93 1.50e+00 4.44e-01 1.57e+01
  ... (remaining 59862 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.91: 22201
       35.91 -    71.82: 2787
       71.82 -   107.73: 346
      107.73 -   143.64: 14
      143.64 -   179.54: 4
  Dihedral angle restraints: 25352
    sinusoidal: 22272
      harmonic: 3080
  Sorted by residual:
  dihedral pdb=" O4'   U A1340 "
           pdb=" C1'   U A1340 "
           pdb=" N1    U A1340 "
           pdb=" C2    U A1340 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   42.32 -170.32     1      1.70e+01 3.46e-03 6.60e+01
  dihedral pdb=" O4'   U A1313 "
           pdb=" C1'   U A1313 "
           pdb=" N1    U A1313 "
           pdb=" C2    U A1313 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   95.41  104.59     1      1.50e+01 4.44e-03 5.34e+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  -18.41 -109.59     1      1.70e+01 3.46e-03 4.44e+01
  ... (remaining 25349 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 7660
       0.092 -    0.184: 126
       0.184 -    0.276: 1
       0.276 -    0.368: 1
       0.368 -    0.460: 2
  Chirality restraints: 7790
  Sorted by residual:
  chirality pdb=" P     G A2732 "
            pdb=" OP1   G A2732 "
            pdb=" OP2   G A2732 "
            pdb=" O5'   G A2732 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.87   -0.46 2.00e-01 2.50e+01 5.29e+00
  chirality pdb=" P     A A2733 "
            pdb=" OP1   A A2733 "
            pdb=" OP2   A A2733 "
            pdb=" O5'   A A2733 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.87   -0.46 2.00e-01 2.50e+01 5.18e+00
  chirality pdb=" P     A A2734 "
            pdb=" OP1   A A2734 "
            pdb=" OP2   A A2734 "
            pdb=" O5'   A A2734 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.75   -0.34 2.00e-01 2.50e+01 2.92e+00
  ... (remaining 7787 not shown)

  Planarity restraints: 2745
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C A1575 "    0.003 2.00e-02 2.50e+03   1.94e-02 8.44e+00
        pdb=" N1    C A1575 "   -0.006 2.00e-02 2.50e+03
        pdb=" C2    C A1575 "   -0.047 2.00e-02 2.50e+03
        pdb=" O2    C A1575 "    0.031 2.00e-02 2.50e+03
        pdb=" N3    C A1575 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    C A1575 "   -0.002 2.00e-02 2.50e+03
        pdb=" N4    C A1575 "    0.003 2.00e-02 2.50e+03
        pdb=" C5    C A1575 "    0.007 2.00e-02 2.50e+03
        pdb=" C6    C A1575 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C A 305 "   -0.005 2.00e-02 2.50e+03   1.55e-02 5.42e+00
        pdb=" N1    C A 305 "    0.010 2.00e-02 2.50e+03
        pdb=" C2    C A 305 "   -0.038 2.00e-02 2.50e+03
        pdb=" O2    C A 305 "    0.023 2.00e-02 2.50e+03
        pdb=" N3    C A 305 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    C A 305 "   -0.006 2.00e-02 2.50e+03
        pdb=" N4    C A 305 "    0.004 2.00e-02 2.50e+03
        pdb=" C5    C A 305 "    0.004 2.00e-02 2.50e+03
        pdb=" C6    C A 305 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A 363 "   -0.004 2.00e-02 2.50e+03   1.14e-02 3.92e+00
        pdb=" N9    G A 363 "    0.004 2.00e-02 2.50e+03
        pdb=" C8    G A 363 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    G A 363 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5    G A 363 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    G A 363 "   -0.005 2.00e-02 2.50e+03
        pdb=" O6    G A 363 "    0.001 2.00e-02 2.50e+03
        pdb=" N1    G A 363 "    0.004 2.00e-02 2.50e+03
        pdb=" C2    G A 363 "    0.030 2.00e-02 2.50e+03
        pdb=" N2    G A 363 "   -0.024 2.00e-02 2.50e+03
        pdb=" N3    G A 363 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    G A 363 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 2742 not shown)

  Histogram of nonbonded interaction distances:
        1.90 -     2.50: 256
        2.50 -     3.10: 25207
        3.10 -     3.70: 68095
        3.70 -     4.30: 95019
        4.30 -     4.90: 129330
  Nonbonded interactions: 317907
  Sorted by model distance:
  nonbonded pdb=" O2'   G A1734 "
            pdb=" OP1   A A1735 "
     model   vdw
     1.904 3.040
  nonbonded pdb=" O2'   G A2692 "
            pdb=" O2'   U A2847 "
     model   vdw
     1.926 3.040
  nonbonded pdb=" O2'   C A1351 "
            pdb=" O2'   A A1571 "
     model   vdw
     1.931 3.040
  nonbonded pdb=" O2'   G A2859 "
            pdb=" O4'   A A2860 "
     model   vdw
     1.943 3.040
  nonbonded pdb=" OP2   G A1521 "
            pdb=" O2'   A A1522 "
     model   vdw
     1.976 3.040
  ... (remaining 317902 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:             2.060
  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:             0.010
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     34.020
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  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:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
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   0.093  39578  Z= 0.087
  Angle     :  0.391  14.146  59867  Z= 0.205
  Chirality :  0.027   0.460   7790
  Planarity :  0.002   0.025   2745
  Dihedral  : 23.091 179.544  23346
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.58 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  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:  0.72 (0.28), residues: 1047
  helix:  2.05 (0.34), residues: 301
  sheet:  0.67 (0.36), residues: 233
  loop : -0.57 (0.28), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG U  85 
 TYR   0.004   0.001   TYR N 112 
 PHE   0.008   0.001   PHE U  95 
 TRP   0.003   0.000   TRP T  80 
 HIS   0.002   0.000   HIS S   7 

Details of bonding type rmsd
  covalent geometry    : bond        0.00153 (39578)
  covalent geometry    : angle       0.39119 (59867)
  hydrogen bonds       : bond        0.09439 ( 1340)
  hydrogen bonds       : angle       4.76139 ( 2506)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   11 MET cc_start: 0.7337 (ptm) cc_final: 0.7043 (ppp)
REVERT: E    1 MET cc_start: 0.9193 (tmm) cc_final: 0.8787 (tmm)
REVERT: K    4 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7523 (mp0)
REVERT: K   20 MET cc_start: 0.8023 (ttt) cc_final: 0.7681 (tpp)
REVERT: K  109 SER cc_start: 0.8242 (t) cc_final: 0.7994 (p)
REVERT: K  113 MET cc_start: 0.8764 (mmp) cc_final: 0.8478 (mmm)
REVERT: S   68 ASP cc_start: 0.8803 (t0) cc_final: 0.8233 (t0)
REVERT: S  110 ARG cc_start: 0.8923 (tmm-80) cc_final: 0.8481 (ttp80)
REVERT: U   38 ILE cc_start: 0.9062 (mm) cc_final: 0.8835 (mm)
REVERT: Y   30 MET cc_start: 0.8937 (mmp) cc_final: 0.8426 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.2098
  time to fit residues: 20.8592
Evaluate side-chains
  40 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 98 optimal weight:   30.0000
   chunk 194 optimal weight:   20.0000
   chunk 227 optimal weight:    9.9990
   chunk 107 optimal weight:   30.0000
   chunk 10 optimal weight:   20.0000
   chunk 66 optimal weight:   50.0000
   chunk 130 optimal weight:   20.0000
   chunk 124 optimal weight:   50.0000
   chunk 103 optimal weight:   20.0000
   chunk 200 optimal weight:    9.9990
   overall best weight:   13.9994

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

Flipped N/Q/H residues before XYZ refinement:
0  41 HIS
D  36 GLN
E 115 GLN
N  62 ASN
S  31 GLN
S  61 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.044720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.031992 restraints weight = 477586.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.031830 restraints weight = 219790.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.032071 restraints weight = 151051.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.032201 restraints weight = 129058.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.032217 restraints weight = 121764.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.3911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.099  39578  Z= 0.408
  Angle     :  0.872  10.821  59867  Z= 0.429
  Chirality :  0.043   0.269   7790
  Planarity :  0.006   0.060   2745
  Dihedral  : 24.473 179.951  21228
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 24.18
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.55 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  4.55 %
    Favored  : 95.12 %
  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: -0.91 (0.25), residues: 1047
  helix: -0.13 (0.29), residues: 318
  sheet: -0.32 (0.33), residues: 244
  loop : -0.98 (0.28), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG 2  14 
 TYR   0.012   0.002   TYR N 112 
 PHE   0.035   0.003   PHE N  87 
 TRP   0.014   0.003   TRP P  30 
 HIS   0.030   0.003   HIS K  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00775 (39578)
  covalent geometry    : angle       0.87211 (59867)
  hydrogen bonds       : bond        0.12453 ( 1340)
  hydrogen bonds       : angle       4.49814 ( 2506)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    1 MET cc_start: 0.9065 (tmm) cc_final: 0.8704 (tmm)
REVERT: K   20 MET cc_start: 0.8143 (ttt) cc_final: 0.7521 (tpp)
REVERT: K  109 SER cc_start: 0.7863 (t) cc_final: 0.7545 (t)
REVERT: N    1 MET cc_start: 0.2679 (ttt) cc_final: 0.2263 (ttp)
REVERT: P   12 MET cc_start: 0.7504 (mmt) cc_final: 0.6964 (mmt)
REVERT: Y   30 MET cc_start: 0.9008 (mmp) cc_final: 0.8425 (mmp)
  outliers start: 3
  outliers final: 3
  residues processed: 43
  average time/residue: 0.2033
  time to fit residues: 14.8304
Evaluate side-chains
  36 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 105 optimal weight:   30.0000
   chunk 184 optimal weight:    4.9990
   chunk 60 optimal weight:   50.0000
   chunk 34 optimal weight:   20.0000
   chunk 133 optimal weight:   10.0000
   chunk 192 optimal weight:    8.9990
   chunk 96 optimal weight:   30.0000
   chunk 111 optimal weight:   30.0000
   chunk 81 optimal weight:   30.0000
   chunk 119 optimal weight:   10.0000
   chunk 126 optimal weight:   10.0000
   overall best weight:    8.7996

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

Flipped N/Q/H residues before XYZ refinement:
2  29 GLN
** K  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 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 = 0.3499 r_free = 0.3499 target = 0.044596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.032319 restraints weight = 478308.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.032989 restraints weight = 224923.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.032482 restraints weight = 149161.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.032569 restraints weight = 150623.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.032589 restraints weight = 135712.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.4407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  39578  Z= 0.261
  Angle     :  0.640   9.048  59867  Z= 0.322
  Chirality :  0.035   0.244   7790
  Planarity :  0.005   0.037   2745
  Dihedral  : 24.486 178.052  21228
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 16.79
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  6.69 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  4.11 %
    Favored  : 95.78 %
  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: -0.97 (0.25), residues: 1047
  helix: -0.04 (0.29), residues: 314
  sheet: -0.40 (0.33), residues: 232
  loop : -1.08 (0.27), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG 2  34 
 TYR   0.011   0.002   TYR S  38 
 PHE   0.012   0.002   PHE N  87 
 TRP   0.007   0.001   TRP D  80 
 HIS   0.006   0.002   HIS 0  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 (39578)
  covalent geometry    : angle       0.64005 (59867)
  hydrogen bonds       : bond        0.08881 ( 1340)
  hydrogen bonds       : angle       4.12449 ( 2506)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 37
  time to evaluate  : 0.608 
Fit side-chains
REVERT: E    1 MET cc_start: 0.8894 (tmm) cc_final: 0.8542 (tmm)
REVERT: E  141 MET cc_start: 0.8116 (tpt) cc_final: 0.7900 (tpp)
REVERT: K   20 MET cc_start: 0.8365 (ttt) cc_final: 0.7527 (tpp)
REVERT: K  113 MET cc_start: 0.8722 (mmp) cc_final: 0.8476 (mmm)
REVERT: Y   30 MET cc_start: 0.8983 (mmp) cc_final: 0.8323 (mmp)
  outliers start: 1
  outliers final: 0
  residues processed: 37
  average time/residue: 0.2021
  time to fit residues: 13.1594
Evaluate side-chains
  32 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 151 optimal weight:   40.0000
   chunk 47 optimal weight:   50.0000
   chunk 31 optimal weight:   40.0000
   chunk 158 optimal weight:    8.9990
   chunk 138 optimal weight:    2.9990
   chunk 171 optimal weight:   50.0000
   chunk 40 optimal weight:   10.0000
   chunk 225 optimal weight:    9.9990
   chunk 96 optimal weight:   30.0000
   chunk 163 optimal weight:    8.9990
   chunk 75 optimal weight:   30.0000
   overall best weight:    8.1992

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

Flipped N/Q/H residues before XYZ refinement:
2  29 GLN
K  29 HIS
P  40 GLN
** U  53 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 = 0.3486 r_free = 0.3486 target = 0.044319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.031775 restraints weight = 479722.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.031573 restraints weight = 216391.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.031832 restraints weight = 148775.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.031975 restraints weight = 126218.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.032006 restraints weight = 118283.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.5303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  39578  Z= 0.264
  Angle     :  0.667   9.129  59867  Z= 0.335
  Chirality :  0.036   0.254   7790
  Planarity :  0.005   0.054   2745
  Dihedral  : 24.617 178.654  21228
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 20.09
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  7.83 %
    Favored  : 91.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  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: -1.48 (0.25), residues: 1047
  helix: -0.55 (0.28), residues: 326
  sheet: -0.90 (0.33), residues: 234
  loop : -1.22 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG 2  34 
 TYR   0.013   0.002   TYR N 112 
 PHE   0.021   0.002   PHE Y  26 
 TRP   0.008   0.001   TRP D  80 
 HIS   0.006   0.002   HIS 2  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 (39578)
  covalent geometry    : angle       0.66698 (59867)
  hydrogen bonds       : bond        0.09788 ( 1340)
  hydrogen bonds       : angle       4.16163 ( 2506)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
REVERT: E    1 MET cc_start: 0.9112 (tmm) cc_final: 0.8674 (tmm)
REVERT: K   20 MET cc_start: 0.8161 (ttt) cc_final: 0.7592 (tpp)
REVERT: N    1 MET cc_start: 0.2330 (ttt) cc_final: 0.1935 (ttp)
REVERT: Y   30 MET cc_start: 0.8954 (mmp) cc_final: 0.8332 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.2041
  time to fit residues: 12.0799
Evaluate side-chains
  31 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 78 optimal weight:   10.0000
   chunk 224 optimal weight:    5.9990
   chunk 214 optimal weight:    7.9990
   chunk 20 optimal weight:   30.0000
   chunk 103 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   chunk 233 optimal weight:   10.0000
   chunk 187 optimal weight:    7.9990
   chunk 49 optimal weight:   20.0000
   chunk 89 optimal weight:   30.0000
   chunk 223 optimal weight:    9.9990
   overall best weight:    8.3992

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

Flipped N/Q/H residues before XYZ refinement:
P  11 GLN
** U  53 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 = 0.3487 r_free = 0.3487 target = 0.044096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.031571 restraints weight = 480120.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.031618 restraints weight = 210145.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.031895 restraints weight = 143312.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.032058 restraints weight = 120439.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.032080 restraints weight = 113330.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.5671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  39578  Z= 0.260
  Angle     :  0.648   9.337  59867  Z= 0.325
  Chirality :  0.035   0.246   7790
  Planarity :  0.005   0.044   2745
  Dihedral  : 24.708 178.299  21228
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 19.62
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  7.26 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  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: -1.59 (0.25), residues: 1047
  helix: -0.59 (0.28), residues: 319
  sheet: -1.05 (0.32), residues: 228
  loop : -1.27 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG 2  34 
 TYR   0.013   0.002   TYR N 112 
 PHE   0.016   0.002   PHE U  86 
 TRP   0.007   0.001   TRP D  80 
 HIS   0.006   0.002   HIS S   7 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 (39578)
  covalent geometry    : angle       0.64788 (59867)
  hydrogen bonds       : bond        0.08982 ( 1340)
  hydrogen bonds       : angle       4.13120 ( 2506)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
REVERT: E    1 MET cc_start: 0.9174 (tmm) cc_final: 0.8712 (tmm)
REVERT: K   20 MET cc_start: 0.8160 (ttt) cc_final: 0.7594 (tpp)
REVERT: N    1 MET cc_start: 0.2465 (ttt) cc_final: 0.2007 (ttp)
REVERT: S   68 ASP cc_start: 0.9068 (t70) cc_final: 0.8790 (t0)
REVERT: Y   30 MET cc_start: 0.9019 (mmp) cc_final: 0.8319 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1763
  time to fit residues: 10.9941
Evaluate side-chains
  31 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 142 optimal weight:   20.0000
   chunk 57 optimal weight:   10.0000
   chunk 211 optimal weight:    5.9990
   chunk 205 optimal weight:    4.9990
   chunk 41 optimal weight:   30.0000
   chunk 225 optimal weight:    9.9990
   chunk 104 optimal weight:   20.0000
   chunk 143 optimal weight:    7.9990
   chunk 147 optimal weight:    9.9990
   chunk 196 optimal weight:   10.0000
   chunk 179 optimal weight:    4.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
S  31 GLN
** U  53 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 = 0.3493 r_free = 0.3493 target = 0.044252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.031814 restraints weight = 477613.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.031738 restraints weight = 210361.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.032027 restraints weight = 143192.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.032061 restraints weight = 121640.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.032062 restraints weight = 117384.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.5810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  39578  Z= 0.218
  Angle     :  0.607   9.373  59867  Z= 0.306
  Chirality :  0.033   0.246   7790
  Planarity :  0.004   0.043   2745
  Dihedral  : 24.627 178.261  21228
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 17.38
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  7.55 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -1.51 (0.25), residues: 1047
  helix: -0.43 (0.29), residues: 318
  sheet: -0.99 (0.32), residues: 242
  loop : -1.30 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG T  73 
 TYR   0.011   0.001   TYR N 112 
 PHE   0.012   0.002   PHE Y  26 
 TRP   0.006   0.001   TRP D  80 
 HIS   0.004   0.001   HIS S   7 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (39578)
  covalent geometry    : angle       0.60663 (59867)
  hydrogen bonds       : bond        0.08486 ( 1340)
  hydrogen bonds       : angle       4.00592 ( 2506)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
REVERT: E    1 MET cc_start: 0.9086 (tmm) cc_final: 0.8629 (tmm)
REVERT: K   20 MET cc_start: 0.8119 (ttt) cc_final: 0.7538 (tpp)
REVERT: N    1 MET cc_start: 0.2590 (ttt) cc_final: 0.1967 (ttp)
REVERT: S   68 ASP cc_start: 0.9009 (t70) cc_final: 0.8783 (t0)
REVERT: Y   30 MET cc_start: 0.8964 (mmp) cc_final: 0.8296 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1789
  time to fit residues: 10.9253
Evaluate side-chains
  31 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 70 optimal weight:   20.0000
   chunk 2 optimal weight:    0.0870
   chunk 30 optimal weight:   50.0000
   chunk 43 optimal weight:   50.0000
   chunk 108 optimal weight:   30.0000
   chunk 24 optimal weight:   20.0000
   chunk 9 optimal weight:   20.0000
   chunk 154 optimal weight:    8.9990
   chunk 92 optimal weight:   20.0000
   chunk 190 optimal weight:    6.9990
   chunk 216 optimal weight:    9.9990
   overall best weight:    9.2168

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

Flipped N/Q/H residues before XYZ refinement:
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
T  72 GLN
** U  53 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 = 0.3480 r_free = 0.3480 target = 0.044162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.031592 restraints weight = 478325.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.031428 restraints weight = 216574.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.031541 restraints weight = 149221.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.031788 restraints weight = 133237.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.031875 restraints weight = 121090.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.6306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  39578  Z= 0.280
  Angle     :  0.685  13.577  59867  Z= 0.342
  Chirality :  0.037   0.257   7790
  Planarity :  0.005   0.044   2745
  Dihedral  : 24.838 178.283  21228
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 21.35
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  8.31 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -1.74 (0.25), residues: 1047
  helix: -0.60 (0.29), residues: 312
  sheet: -1.18 (0.33), residues: 228
  loop : -1.42 (0.26), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG 0  39 
 TYR   0.013   0.002   TYR N 112 
 PHE   0.024   0.002   PHE U  86 
 TRP   0.006   0.001   TRP D  80 
 HIS   0.005   0.001   HIS 2  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00531 (39578)
  covalent geometry    : angle       0.68464 (59867)
  hydrogen bonds       : bond        0.09604 ( 1340)
  hydrogen bonds       : angle       4.18663 ( 2506)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
REVERT: D   11 MET cc_start: 0.7984 (ppp) cc_final: 0.7406 (ppp)
REVERT: E    1 MET cc_start: 0.9021 (tmm) cc_final: 0.8578 (tmm)
REVERT: K   20 MET cc_start: 0.7902 (ttt) cc_final: 0.7401 (tpp)
REVERT: N    1 MET cc_start: 0.2820 (ttt) cc_final: 0.2193 (ttp)
REVERT: N   20 MET cc_start: 0.9479 (tmm) cc_final: 0.9263 (tmm)
REVERT: S   68 ASP cc_start: 0.8943 (t70) cc_final: 0.8684 (t0)
REVERT: Y   30 MET cc_start: 0.8969 (mmp) cc_final: 0.8288 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1784
  time to fit residues: 10.9294
Evaluate side-chains
  32 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 3 optimal weight:   20.0000
   chunk 229 optimal weight:    4.9990
   chunk 165 optimal weight:   50.0000
   chunk 227 optimal weight:   10.0000
   chunk 127 optimal weight:   10.0000
   chunk 230 optimal weight:    3.9990
   chunk 221 optimal weight:    9.9990
   chunk 6 optimal weight:   50.0000
   chunk 199 optimal weight:    9.9990
   chunk 60 optimal weight:   50.0000
   chunk 65 optimal weight:   50.0000
   overall best weight:    7.7992

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

Flipped N/Q/H residues before XYZ refinement:
** U  53 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 = 0.3485 r_free = 0.3485 target = 0.044231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.031378 restraints weight = 478530.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.031478 restraints weight = 222823.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.031752 restraints weight = 152328.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.031829 restraints weight = 128856.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 55)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.031952 restraints weight = 122871.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.6444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  39578  Z= 0.241
  Angle     :  0.632  14.054  59867  Z= 0.317
  Chirality :  0.034   0.245   7790
  Planarity :  0.004   0.039   2745
  Dihedral  : 24.767 178.244  21228
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 18.54
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  8.02 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  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: -1.70 (0.25), residues: 1047
  helix: -0.45 (0.29), residues: 312
  sheet: -1.26 (0.33), residues: 228
  loop : -1.42 (0.27), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG Y  52 
 TYR   0.012   0.002   TYR N 112 
 PHE   0.012   0.002   PHE Y  26 
 TRP   0.005   0.001   TRP D  80 
 HIS   0.005   0.001   HIS S   7 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 (39578)
  covalent geometry    : angle       0.63228 (59867)
  hydrogen bonds       : bond        0.08589 ( 1340)
  hydrogen bonds       : angle       4.06211 ( 2506)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
REVERT: E    1 MET cc_start: 0.9015 (tmm) cc_final: 0.8579 (tmm)
REVERT: K   20 MET cc_start: 0.7880 (ttt) cc_final: 0.7426 (tpp)
REVERT: N    1 MET cc_start: 0.2723 (ttt) cc_final: 0.2146 (ttp)
REVERT: N   20 MET cc_start: 0.9485 (tmm) cc_final: 0.9267 (tmm)
REVERT: T   24 MET cc_start: 0.9266 (tmm) cc_final: 0.8814 (tmm)
REVERT: Y    1 MET cc_start: 0.8967 (ppp) cc_final: 0.8679 (tmm)
REVERT: Y   30 MET cc_start: 0.8978 (mmp) cc_final: 0.8346 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.2072
  time to fit residues: 12.9105
Evaluate side-chains
  31 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 216 optimal weight:    8.9990
   chunk 141 optimal weight:    6.9990
   chunk 32 optimal weight:   30.0000
   chunk 90 optimal weight:   40.0000
   chunk 12 optimal weight:   20.0000
   chunk 122 optimal weight:   40.0000
   chunk 91 optimal weight:   20.0000
   chunk 200 optimal weight:    5.9990
   chunk 83 optimal weight:   20.0000
   chunk 165 optimal weight:   40.0000
   chunk 233 optimal weight:    6.9990
   overall best weight:    9.7992

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

Flipped N/Q/H residues before XYZ refinement:
** U  53 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 = 0.3474 r_free = 0.3474 target = 0.044004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.031337 restraints weight = 479890.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.031331 restraints weight = 221575.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.031610 restraints weight = 153646.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 60)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.031729 restraints weight = 129869.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.031760 restraints weight = 121706.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.6816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  39578  Z= 0.298
  Angle     :  0.704  13.569  59867  Z= 0.351
  Chirality :  0.037   0.269   7790
  Planarity :  0.005   0.042   2745
  Dihedral  : 24.920 178.636  21228
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 22.33
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  8.79 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  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: -1.94 (0.25), residues: 1047
  helix: -0.77 (0.28), residues: 307
  sheet: -1.29 (0.33), residues: 227
  loop : -1.54 (0.26), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG 0  39 
 TYR   0.017   0.002   TYR N 112 
 PHE   0.016   0.002   PHE U  86 
 TRP   0.005   0.001   TRP D  80 
 HIS   0.005   0.001   HIS 2  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00566 (39578)
  covalent geometry    : angle       0.70352 (59867)
  hydrogen bonds       : bond        0.09911 ( 1340)
  hydrogen bonds       : angle       4.23400 ( 2506)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
REVERT: D   11 MET cc_start: 0.7929 (ppp) cc_final: 0.7429 (ppp)
REVERT: D  165 MET cc_start: 0.6655 (tmm) cc_final: 0.6442 (tmm)
REVERT: E    1 MET cc_start: 0.9023 (tmm) cc_final: 0.8497 (tmm)
REVERT: K   20 MET cc_start: 0.7904 (ttt) cc_final: 0.7453 (tpp)
REVERT: K   32 TYR cc_start: 0.5423 (m-10) cc_final: 0.5197 (m-10)
REVERT: N    1 MET cc_start: 0.2862 (ttt) cc_final: 0.2238 (ttp)
REVERT: N   20 MET cc_start: 0.9466 (tmm) cc_final: 0.9220 (tmm)
REVERT: T   24 MET cc_start: 0.9291 (tmm) cc_final: 0.8871 (tmm)
REVERT: Y    1 MET cc_start: 0.8757 (ppp) cc_final: 0.7953 (ppp)
REVERT: Y   30 MET cc_start: 0.8908 (mmp) cc_final: 0.8072 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.2088
  time to fit residues: 12.7920
Evaluate side-chains
  33 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 19 optimal weight:   30.0000
   chunk 30 optimal weight:   50.0000
   chunk 12 optimal weight:   20.0000
   chunk 193 optimal weight:    9.9990
   chunk 107 optimal weight:   30.0000
   chunk 69 optimal weight:   10.0000
   chunk 35 optimal weight:   10.0000
   chunk 52 optimal weight:   20.0000
   chunk 188 optimal weight:    2.9990
   chunk 94 optimal weight:   10.0000
   chunk 145 optimal weight:    4.9990
   overall best weight:    7.5994

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

Flipped N/Q/H residues before XYZ refinement:
** U  53 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 = 0.3482 r_free = 0.3482 target = 0.044149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.031524 restraints weight = 477888.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.031499 restraints weight = 215872.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.031750 restraints weight = 149765.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.031840 restraints weight = 127826.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.031901 restraints weight = 121643.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.6822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  39578  Z= 0.238
  Angle     :  0.639  14.982  59867  Z= 0.320
  Chirality :  0.035   0.243   7790
  Planarity :  0.004   0.037   2745
  Dihedral  : 24.800 178.298  21228
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 18.93
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  8.02 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  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: -1.88 (0.25), residues: 1047
  helix: -0.62 (0.29), residues: 311
  sheet: -1.38 (0.33), residues: 236
  loop : -1.50 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG Y   7 
 TYR   0.010   0.002   TYR S  38 
 PHE   0.009   0.002   PHE U  86 
 TRP   0.006   0.001   TRP D  80 
 HIS   0.005   0.001   HIS S   7 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 (39578)
  covalent geometry    : angle       0.63898 (59867)
  hydrogen bonds       : bond        0.08651 ( 1340)
  hydrogen bonds       : angle       4.08041 ( 2506)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
REVERT: D   11 MET cc_start: 0.7959 (ppp) cc_final: 0.7414 (ppp)
REVERT: E    1 MET cc_start: 0.9102 (tmm) cc_final: 0.8673 (tmm)
REVERT: K   20 MET cc_start: 0.7924 (ttt) cc_final: 0.7460 (tpp)
REVERT: K   32 TYR cc_start: 0.5746 (m-10) cc_final: 0.5444 (m-10)
REVERT: N    1 MET cc_start: 0.2820 (ttt) cc_final: 0.2226 (ttp)
REVERT: N   20 MET cc_start: 0.9502 (tmm) cc_final: 0.9273 (tmm)
REVERT: T   24 MET cc_start: 0.9320 (tmm) cc_final: 0.8897 (tmm)
REVERT: Y    1 MET cc_start: 0.8648 (ppp) cc_final: 0.7570 (ppp)
REVERT: Y   30 MET cc_start: 0.8927 (mmp) cc_final: 0.8244 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.2322
  time to fit residues: 14.2285
Evaluate side-chains
  32 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 145 optimal weight:    4.9990
   chunk 64 optimal weight:   50.0000
   chunk 231 optimal weight:    7.9990
   chunk 116 optimal weight:   10.0000
   chunk 233 optimal weight:    0.9990
   chunk 105 optimal weight:   30.0000
   chunk 222 optimal weight:    7.9990
   chunk 154 optimal weight:    9.9990
   chunk 115 optimal weight:   20.0000
   chunk 182 optimal weight:    0.9990
   chunk 3 optimal weight:   30.0000
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** S  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 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 = 0.3499 r_free = 0.3499 target = 0.044292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.031930 restraints weight = 474187.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.031889 restraints weight = 210230.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.032162 restraints weight = 143265.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.032230 restraints weight = 122644.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.032314 restraints weight = 117538.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.6616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  39578  Z= 0.159
  Angle     :  0.563  15.646  59867  Z= 0.282
  Chirality :  0.031   0.237   7790
  Planarity :  0.004   0.038   2745
  Dihedral  : 24.567 178.086  21228
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 14.60
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  7.55 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  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: -1.59 (0.25), residues: 1047
  helix: -0.24 (0.30), residues: 306
  sheet: -1.24 (0.34), residues: 230
  loop : -1.41 (0.27), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG Y   7 
 TYR   0.010   0.001   TYR S  38 
 PHE   0.006   0.001   PHE N  21 
 TRP   0.005   0.001   TRP D  80 
 HIS   0.005   0.001   HIS S   7 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (39578)
  covalent geometry    : angle       0.56324 (59867)
  hydrogen bonds       : bond        0.07512 ( 1340)
  hydrogen bonds       : angle       3.84489 ( 2506)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5072.91 seconds
wall clock time: 89 minutes 18.00 seconds (5358.00 seconds total)