Starting phenix.real_space_refine
on Wed Aug  5 03:56:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9muo_48639/08_2026/9muo_48639.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9muo_48639/08_2026/9muo_48639.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9muo_48639/08_2026/9muo_48639.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9muo_48639/08_2026/9muo_48639.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9muo_48639/08_2026/9muo_48639.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9muo_48639/08_2026/9muo_48639.cif"
  }
  resolution = 3.3
  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=   0.002 sd=   0.013
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      10      5.49       5
     S      20      5.16       5
     C    5426      2.51       5
     N    1426      2.21       5
     O    1528      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8410
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2022
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 2022
          Classifications: {'peptide': 249}
          Link IDs: {'PTRANS': 12, 'TRANS': 236}
          Chain breaks: 1
    Chain: "a"
      Number of atoms: 88
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 88
          Classifications: {'RNA': 4}
          Modifications used: {'rna2p_pur': 4}
          Link IDs: {'rna2p': 3}
    Chain: "b"
      Number of atoms: 88
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 88
          Classifications: {'RNA': 4}
          Modifications used: {'rna2p_pur': 4}
          Link IDs: {'rna2p': 3}
    Chain: "B"
      Number of atoms: 2073
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 2073
          Classifications: {'peptide': 257}
          Link IDs: {'PTRANS': 13, 'TRANS': 243}
    Chain: "C"
      Number of atoms: 2022
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 2022
          Classifications: {'peptide': 249}
          Link IDs: {'PTRANS': 12, 'TRANS': 236}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2073
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 2073
          Classifications: {'peptide': 257}
          Link IDs: {'PTRANS': 13, 'TRANS': 243}
    Chain: "B"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'DQV': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.06, per 1000 atoms: 0.24
  Number of scatterers: 8410
  At special positions: 0
  Unit cell: (82.65, 131.225, 83.375, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      20     16.00
     P      10     15.00
     O    1528      8.00
     N    1426      7.00
     C    5426      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.71
  Conformation dependent library (CDL) restraints added in 342.7 milliseconds
  

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1932

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 8 sheets defined
      39.9% alpha, 15.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 11
      No H-bonds generated for 'chain 'A' and resid 9 through 11'
    Processing helix  chain 'A' and resid 12 through 25
      removed outlier: 3.743A  pdb=" N   LEU A  17 " --> pdb=" O   LYS A  13 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   GLU A  18 " --> pdb=" O   LYS A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 67
    Processing helix  chain 'A' and resid 68 through 81
      removed outlier: 4.764A  pdb=" N   GLU A  74 " --> pdb=" O   TRP A  70 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LEU A  75 " --> pdb=" O   CYS A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 85
    Processing helix  chain 'A' and resid 96 through 100
    Processing helix  chain 'A' and resid 106 through 119
    Processing helix  chain 'A' and resid 129 through 144
      removed outlier: 4.631A  pdb=" N   ASN A 144 " --> pdb=" O   ALA A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 182
      removed outlier: 3.985A  pdb=" N   HIS A 181 " --> pdb=" O   ASP A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 190
      removed outlier: 3.657A  pdb=" N   ASP A 188 " --> pdb=" O   LYS A 185 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ILE A 190 " --> pdb=" O   GLU A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 222
    Processing helix  chain 'A' and resid 223 through 225
      No H-bonds generated for 'chain 'A' and resid 223 through 225'
    Processing helix  chain 'B' and resid 9 through 11
      No H-bonds generated for 'chain 'B' and resid 9 through 11'
    Processing helix  chain 'B' and resid 12 through 25
      removed outlier: 3.743A  pdb=" N   LEU B  17 " --> pdb=" O   LYS B  13 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   GLU B  18 " --> pdb=" O   LYS B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 67
    Processing helix  chain 'B' and resid 68 through 81
      removed outlier: 4.591A  pdb=" N   GLU B  74 " --> pdb=" O   TRP B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 85
    Processing helix  chain 'B' and resid 96 through 100
    Processing helix  chain 'B' and resid 106 through 119
    Processing helix  chain 'B' and resid 129 through 144
      removed outlier: 4.631A  pdb=" N   ASN B 144 " --> pdb=" O   ALA B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 182
      removed outlier: 3.984A  pdb=" N   HIS B 181 " --> pdb=" O   ASP B 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 190
      removed outlier: 3.657A  pdb=" N   ASP B 188 " --> pdb=" O   LYS B 185 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ILE B 190 " --> pdb=" O   GLU B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 222
    Processing helix  chain 'B' and resid 223 through 225
      No H-bonds generated for 'chain 'B' and resid 223 through 225'
    Processing helix  chain 'C' and resid 9 through 11
      No H-bonds generated for 'chain 'C' and resid 9 through 11'
    Processing helix  chain 'C' and resid 12 through 25
      removed outlier: 3.743A  pdb=" N   LEU C  17 " --> pdb=" O   LYS C  13 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   GLU C  18 " --> pdb=" O   LYS C  14 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 67
    Processing helix  chain 'C' and resid 68 through 81
      removed outlier: 4.763A  pdb=" N   GLU C  74 " --> pdb=" O   TRP C  70 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LEU C  75 " --> pdb=" O   CYS C  71 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 82 through 85
    Processing helix  chain 'C' and resid 96 through 100
    Processing helix  chain 'C' and resid 106 through 119
    Processing helix  chain 'C' and resid 129 through 144
      removed outlier: 4.631A  pdb=" N   ASN C 144 " --> pdb=" O   ALA C 140 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 177 through 182
      removed outlier: 3.985A  pdb=" N   HIS C 181 " --> pdb=" O   ASP C 177 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 185 through 190
      removed outlier: 3.657A  pdb=" N   ASP C 188 " --> pdb=" O   LYS C 185 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ILE C 190 " --> pdb=" O   GLU C 187 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 213 through 222
    Processing helix  chain 'C' and resid 223 through 225
      No H-bonds generated for 'chain 'C' and resid 223 through 225'
    Processing helix  chain 'D' and resid 9 through 11
      No H-bonds generated for 'chain 'D' and resid 9 through 11'
    Processing helix  chain 'D' and resid 12 through 25
      removed outlier: 3.742A  pdb=" N   LEU D  17 " --> pdb=" O   LYS D  13 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   GLU D  18 " --> pdb=" O   LYS D  14 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 67
    Processing helix  chain 'D' and resid 68 through 81
      removed outlier: 4.763A  pdb=" N   GLU D  74 " --> pdb=" O   TRP D  70 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   LEU D  75 " --> pdb=" O   CYS D  71 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 82 through 85
    Processing helix  chain 'D' and resid 96 through 100
    Processing helix  chain 'D' and resid 106 through 119
    Processing helix  chain 'D' and resid 129 through 144
      removed outlier: 4.631A  pdb=" N   ASN D 144 " --> pdb=" O   ALA D 140 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 177 through 182
      removed outlier: 3.984A  pdb=" N   HIS D 181 " --> pdb=" O   ASP D 177 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 185 through 190
      removed outlier: 3.656A  pdb=" N   ASP D 188 " --> pdb=" O   LYS D 185 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ILE D 190 " --> pdb=" O   GLU D 187 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 213 through 222
    Processing helix  chain 'D' and resid 223 through 225
      No H-bonds generated for 'chain 'D' and resid 223 through 225'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 31
      removed outlier: 6.207A  pdb=" N   ALA A   4 " --> pdb=" O   TRP A  31 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   GLN A   3 " --> pdb=" O   TYR A  56 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   LEU A  58 " --> pdb=" O   GLN A   3 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   PHE A   5 " --> pdb=" O   LEU A  58 " (cutoff:3.500A)
      removed outlier: 7.303A  pdb=" N   PHE A  60 " --> pdb=" O   PHE A   5 " (cutoff:3.500A)
      removed outlier: 7.313A  pdb=" N   SER A   7 " --> pdb=" O   PHE A  60 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   GLN A  55 " --> pdb=" O   LYS A  88 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   ILE A  90 " --> pdb=" O   GLN A  55 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   PHE A  57 " --> pdb=" O   ILE A  90 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ILE A  92 " --> pdb=" O   PHE A  57 " (cutoff:3.500A)
      removed outlier: 6.032A  pdb=" N   ALA A  59 " --> pdb=" O   ILE A  92 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 153 through 157
      removed outlier: 6.532A  pdb=" N   VAL A 206 " --> pdb=" O   PHE A 231 " (cutoff:3.500A)
      removed outlier: 8.031A  pdb=" N   PHE A 233 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 7.420A  pdb=" N   LEU A 208 " --> pdb=" O   PHE A 233 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLU A 239 " --> pdb=" O   ASN A 234 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   TYR A 240 " --> pdb=" O   LEU A 256 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 30 through 31
      removed outlier: 6.380A  pdb=" N   ALA B   4 " --> pdb=" O   TRP B  31 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   GLN B   3 " --> pdb=" O   TYR B  56 " (cutoff:3.500A)
      removed outlier: 7.882A  pdb=" N   LEU B  58 " --> pdb=" O   GLN B   3 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   PHE B   5 " --> pdb=" O   LEU B  58 " (cutoff:3.500A)
      removed outlier: 7.303A  pdb=" N   PHE B  60 " --> pdb=" O   PHE B   5 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   SER B   7 " --> pdb=" O   PHE B  60 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   GLN B  55 " --> pdb=" O   LYS B  88 " (cutoff:3.500A)
      removed outlier: 7.603A  pdb=" N   ILE B  90 " --> pdb=" O   GLN B  55 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   PHE B  57 " --> pdb=" O   ILE B  90 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ILE B  92 " --> pdb=" O   PHE B  57 " (cutoff:3.500A)
      removed outlier: 6.032A  pdb=" N   ALA B  59 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 153 through 157
      removed outlier: 6.532A  pdb=" N   VAL B 206 " --> pdb=" O   PHE B 231 " (cutoff:3.500A)
      removed outlier: 8.030A  pdb=" N   PHE B 233 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)
      removed outlier: 7.421A  pdb=" N   LEU B 208 " --> pdb=" O   PHE B 233 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLU B 239 " --> pdb=" O   ASN B 234 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   TYR B 240 " --> pdb=" O   LEU B 256 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 31
      removed outlier: 6.208A  pdb=" N   ALA C   4 " --> pdb=" O   TRP C  31 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   GLN C   3 " --> pdb=" O   TYR C  56 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   LEU C  58 " --> pdb=" O   GLN C   3 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   PHE C   5 " --> pdb=" O   LEU C  58 " (cutoff:3.500A)
      removed outlier: 7.303A  pdb=" N   PHE C  60 " --> pdb=" O   PHE C   5 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   SER C   7 " --> pdb=" O   PHE C  60 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   GLN C  55 " --> pdb=" O   LYS C  88 " (cutoff:3.500A)
      removed outlier: 7.603A  pdb=" N   ILE C  90 " --> pdb=" O   GLN C  55 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   PHE C  57 " --> pdb=" O   ILE C  90 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ILE C  92 " --> pdb=" O   PHE C  57 " (cutoff:3.500A)
      removed outlier: 6.032A  pdb=" N   ALA C  59 " --> pdb=" O   ILE C  92 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 153 through 157
      removed outlier: 6.532A  pdb=" N   VAL C 206 " --> pdb=" O   PHE C 231 " (cutoff:3.500A)
      removed outlier: 8.032A  pdb=" N   PHE C 233 " --> pdb=" O   VAL C 206 " (cutoff:3.500A)
      removed outlier: 7.421A  pdb=" N   LEU C 208 " --> pdb=" O   PHE C 233 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLU C 239 " --> pdb=" O   ASN C 234 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   TYR C 240 " --> pdb=" O   LEU C 256 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 30 through 31
      removed outlier: 6.208A  pdb=" N   ALA D   4 " --> pdb=" O   TRP D  31 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   GLN D   3 " --> pdb=" O   TYR D  56 " (cutoff:3.500A)
      removed outlier: 7.882A  pdb=" N   LEU D  58 " --> pdb=" O   GLN D   3 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   PHE D   5 " --> pdb=" O   LEU D  58 " (cutoff:3.500A)
      removed outlier: 7.304A  pdb=" N   PHE D  60 " --> pdb=" O   PHE D   5 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   SER D   7 " --> pdb=" O   PHE D  60 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   GLN D  55 " --> pdb=" O   LYS D  88 " (cutoff:3.500A)
      removed outlier: 7.603A  pdb=" N   ILE D  90 " --> pdb=" O   GLN D  55 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   PHE D  57 " --> pdb=" O   ILE D  90 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ILE D  92 " --> pdb=" O   PHE D  57 " (cutoff:3.500A)
      removed outlier: 6.031A  pdb=" N   ALA D  59 " --> pdb=" O   ILE D  92 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 153 through 157
      removed outlier: 6.532A  pdb=" N   VAL D 206 " --> pdb=" O   PHE D 231 " (cutoff:3.500A)
      removed outlier: 8.030A  pdb=" N   PHE D 233 " --> pdb=" O   VAL D 206 " (cutoff:3.500A)
      removed outlier: 7.420A  pdb=" N   LEU D 208 " --> pdb=" O   PHE D 233 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLU D 239 " --> pdb=" O   ASN D 234 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   TYR D 240 " --> pdb=" O   LEU D 256 " (cutoff:3.500A)

    261 hydrogen bonds defined for protein.
    699 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.22

  Time building geometry restraints manager: 0.94 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2546
        1.34 -     1.45: 1373
        1.45 -     1.57: 4675
        1.57 -     1.69: 22
        1.69 -     1.81: 32
  Bond restraints: 8648
  Sorted by residual:
  bond pdb=" N   GLN B  35 "
       pdb=" CA  GLN B  35 "
    ideal  model  delta    sigma   weight residual
    1.452  1.487 -0.035 1.25e-02 6.40e+03 7.74e+00
  bond pdb=" N   ILE B  32 "
       pdb=" CA  ILE B  32 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.25e-02 6.40e+03 6.91e+00
  bond pdb=" N   ASP B  33 "
       pdb=" CA  ASP B  33 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.032 1.25e-02 6.40e+03 6.73e+00
  bond pdb=" N   ILE B  37 "
       pdb=" CA  ILE B  37 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.031 1.23e-02 6.61e+03 6.54e+00
  bond pdb=" N   ILE B  44 "
       pdb=" CA  ILE B  44 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.25e-02 6.40e+03 6.39e+00
  ... (remaining 8643 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.02: 11633
        3.02 -     6.04: 127
        6.04 -     9.05: 18
        9.05 -    12.07: 4
       12.07 -    15.09: 1
  Bond angle restraints: 11783
  Sorted by residual:
  angle pdb=" CA  PRO C 170 "
        pdb=" N   PRO C 170 "
        pdb=" CD  PRO C 170 "
      ideal   model   delta    sigma   weight residual
     112.00  104.37    7.63 1.40e+00 5.10e-01 2.97e+01
  angle pdb=" CA  PRO D 170 "
        pdb=" N   PRO D 170 "
        pdb=" CD  PRO D 170 "
      ideal   model   delta    sigma   weight residual
     112.00  104.39    7.61 1.40e+00 5.10e-01 2.96e+01
  angle pdb=" CA  PRO A 170 "
        pdb=" N   PRO A 170 "
        pdb=" CD  PRO A 170 "
      ideal   model   delta    sigma   weight residual
     112.00  104.39    7.61 1.40e+00 5.10e-01 2.96e+01
  angle pdb=" CA  PRO B 170 "
        pdb=" N   PRO B 170 "
        pdb=" CD  PRO B 170 "
      ideal   model   delta    sigma   weight residual
     112.00  104.42    7.58 1.40e+00 5.10e-01 2.93e+01
  angle pdb=" P   DQV B 301 "
        pdb=" O5  DQV B 301 "
        pdb=" P1  DQV B 301 "
      ideal   model   delta    sigma   weight residual
     124.76  139.85  -15.09 3.00e+00 1.11e-01 2.53e+01
  ... (remaining 11778 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 4336
       17.98 -    35.96: 629
       35.96 -    53.94: 153
       53.94 -    71.91: 21
       71.91 -    89.89: 12
  Dihedral angle restraints: 5151
    sinusoidal: 2181
      harmonic: 2970
  Sorted by residual:
  dihedral pdb=" CD  ARG D 119 "
           pdb=" NE  ARG D 119 "
           pdb=" CZ  ARG D 119 "
           pdb=" NH1 ARG D 119 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   50.44  -50.44     1      1.00e+01 1.00e-02 3.49e+01
  dihedral pdb=" CA  ASP D  33 "
           pdb=" C   ASP D  33 "
           pdb=" N   GLN D  34 "
           pdb=" CA  GLN D  34 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.01   22.99     0      5.00e+00 4.00e-02 2.11e+01
  dihedral pdb=" CA  SER C 238 "
           pdb=" C   SER C 238 "
           pdb=" N   GLU C 239 "
           pdb=" CA  GLU C 239 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.44   20.56     0      5.00e+00 4.00e-02 1.69e+01
  ... (remaining 5148 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1028
       0.051 -    0.103: 210
       0.103 -    0.154: 70
       0.154 -    0.205: 3
       0.205 -    0.256: 1
  Chirality restraints: 1312
  Sorted by residual:
  chirality pdb=" C20 DQV B 301 "
            pdb=" C21 DQV B 301 "
            pdb=" C8  DQV B 301 "
            pdb=" O12 DQV B 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.55   -2.81    0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" C21 DQV B 301 "
            pdb=" C20 DQV B 301 "
            pdb=" C7  DQV B 301 "
            pdb=" O13 DQV B 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.73    2.54    0.19 2.00e-01 2.50e+01 9.23e-01
  chirality pdb=" CA  ILE B  32 "
            pdb=" N   ILE B  32 "
            pdb=" C   ILE B  32 "
            pdb=" CB  ILE B  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 8.10e-01
  ... (remaining 1309 not shown)

  Planarity restraints: 1459
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 119 "   -0.839 9.50e-02 1.11e+02   3.76e-01 8.60e+01
        pdb=" NE  ARG D 119 "    0.050 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 119 "    0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 119 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 119 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D 169 "   -0.068 5.00e-02 4.00e+02   9.81e-02 1.54e+01
        pdb=" N   PRO D 170 "    0.169 5.00e-02 4.00e+02
        pdb=" CA  PRO D 170 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO D 170 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 169 "   -0.068 5.00e-02 4.00e+02   9.80e-02 1.54e+01
        pdb=" N   PRO B 170 "    0.169 5.00e-02 4.00e+02
        pdb=" CA  PRO B 170 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO B 170 "   -0.053 5.00e-02 4.00e+02
  ... (remaining 1456 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1038
        2.75 -     3.29: 8577
        3.29 -     3.83: 14337
        3.83 -     4.36: 17326
        4.36 -     4.90: 28583
  Nonbonded interactions: 69861
  Sorted by model distance:
  nonbonded pdb=" N   GLN B  99 "
            pdb=" OE1 GLN B  99 "
     model   vdw
     2.216 3.120
  nonbonded pdb=" N   GLN C  99 "
            pdb=" OE1 GLN C  99 "
     model   vdw
     2.216 3.120
  nonbonded pdb=" N   GLN A  99 "
            pdb=" OE1 GLN A  99 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" N   GLN D  99 "
            pdb=" OE1 GLN D  99 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" OH  TYR C  56 "
            pdb=" OE1 GLU C 145 "
     model   vdw
     2.266 3.040
  ... (remaining 69856 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 2 through 33 or resid 42 through 258))
  selection = chain 'C'
  selection = (chain 'D' and (resid 2 through 33 or resid 42 through 258))
}
ncs_group {
  reference = chain 'a'
  selection = chain 'b'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             11.180
  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:          0.240
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.690
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.109   8648  Z= 0.217
  Angle     :  0.818  15.087  11783  Z= 0.440
  Chirality :  0.047   0.256   1312
  Planarity :  0.012   0.376   1459
  Dihedral  : 17.637  89.893   3219
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 14.57
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  5.30 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 31.74 %
    Favored  : 66.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.28), residues: 1000
  helix: -0.12 (0.31), residues: 312
  sheet: -0.37 (0.40), residues: 192
  loop :  0.03 (0.30), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 148 
 TYR   0.015   0.001   TYR D 122 
 PHE   0.015   0.001   PHE C   6 
 TRP   0.012   0.001   TRP C  31 
 HIS   0.001   0.000   HIS C   8 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00456 /  0.22 ( 8648)
  covalent geometry    : angle       0.81758 /  0.44 (11783)
  hydrogen bonds       : bond        0.30607 / 20.04 (  261)
  hydrogen bonds       : angle       8.36780 /  5.92 (  699)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 258
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 GLN cc_start: 0.8268 (pm20) cc_final: 0.7988 (pm20)
REVERT: B   68 SER cc_start: 0.8876 (OUTLIER) cc_final: 0.8462 (t)
REVERT: B  101 ASP cc_start: 0.8619 (t0) cc_final: 0.8415 (t0)
REVERT: C    3 GLN cc_start: 0.7851 (mp10) cc_final: 0.7506 (mp10)
REVERT: C   11 LYS cc_start: 0.9337 (mmtm) cc_final: 0.9119 (mttp)
REVERT: C  129 ASN cc_start: 0.8386 (t0) cc_final: 0.7979 (t0)
REVERT: C  142 TRP cc_start: 0.9061 (m100) cc_final: 0.8761 (m100)
REVERT: C  143 GLN cc_start: 0.8997 (tt0) cc_final: 0.8324 (tm-30)
REVERT: C  144 ASN cc_start: 0.8734 (p0) cc_final: 0.8468 (p0)
REVERT: C  183 ASP cc_start: 0.8462 (p0) cc_final: 0.8037 (p0)
REVERT: C  195 ASN cc_start: 0.9141 (m-40) cc_final: 0.8833 (p0)
REVERT: C  209 TYR cc_start: 0.8651 (t80) cc_final: 0.8030 (t80)
REVERT: D   24 ARG cc_start: 0.8428 (ttp80) cc_final: 0.7814 (ttp80)
REVERT: D   34 GLN cc_start: 0.4719 (OUTLIER) cc_final: 0.1972 (pp30)
REVERT: D  101 ASP cc_start: 0.8694 (t0) cc_final: 0.7914 (p0)
REVERT: D  114 GLU cc_start: 0.9280 (tp30) cc_final: 0.9077 (mm-30)
REVERT: D  122 TYR cc_start: 0.8456 (p90) cc_final: 0.8017 (p90)
REVERT: D  132 ARG cc_start: 0.8717 (tmt170) cc_final: 0.8397 (tmm-80)
REVERT: D  166 GLU cc_start: 0.8943 (tp30) cc_final: 0.8703 (tp30)
REVERT: D  185 LYS cc_start: 0.8981 (ptpp) cc_final: 0.8687 (pttm)
  outliers start: 13
  outliers final: 2
  residues processed: 264
  average time/residue: 0.0965
  time to fit residues: 34.3482
Evaluate side-chains
  186 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 182
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   68 SER
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain D residue   34 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    0.0010
   chunk 65 optimal weight:    0.1980
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.0770
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   overall best weight:    1.2346

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  46 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.098692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.071346 restraints weight = 19017.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 3.68
r_work: 0.3005 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
moved from start:          0.2127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   8648  Z= 0.159
  Angle     :  0.702   7.909  11783  Z= 0.360
  Chirality :  0.049   0.200   1312
  Planarity :  0.006   0.056   1459
  Dihedral  : 10.505  77.775   1226
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 29.06 %
    Favored  : 67.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.09 (0.28), residues: 1000
  helix:  0.03 (0.29), residues: 324
  sheet: -0.31 (0.35), residues: 224
  loop :  0.24 (0.32), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 148 
 TYR   0.022   0.002   TYR A  79 
 PHE   0.011   0.001   PHE C  60 
 TRP   0.020   0.001   TRP B  31 
 HIS   0.002   0.001   HIS A   8 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00352 /  0.16 ( 8648)
  covalent geometry    : angle       0.70184 /  0.36 (11783)
  hydrogen bonds       : bond        0.06867 /  4.40 (  261)
  hydrogen bonds       : angle       5.79267 /  4.08 (  699)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 196
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.8922 (pm20) cc_final: 0.8706 (pm20)
REVERT: A   79 TYR cc_start: 0.9514 (t80) cc_final: 0.9233 (t80)
REVERT: A  101 ASP cc_start: 0.8988 (t0) cc_final: 0.8781 (t0)
REVERT: A  143 GLN cc_start: 0.8963 (tm-30) cc_final: 0.8675 (tm-30)
REVERT: A  166 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8074 (tp30)
REVERT: A  185 LYS cc_start: 0.9225 (ptpp) cc_final: 0.8822 (ptmt)
REVERT: B  119 ARG cc_start: 0.8757 (ttp-110) cc_final: 0.8541 (ptp-110)
REVERT: C   11 LYS cc_start: 0.9441 (mmtm) cc_final: 0.9065 (mttp)
REVERT: C  129 ASN cc_start: 0.8513 (t0) cc_final: 0.7989 (t0)
REVERT: C  142 TRP cc_start: 0.9015 (m100) cc_final: 0.8803 (m100)
REVERT: C  143 GLN cc_start: 0.9187 (tt0) cc_final: 0.8461 (tm-30)
REVERT: C  144 ASN cc_start: 0.8833 (p0) cc_final: 0.8519 (p0)
REVERT: C  195 ASN cc_start: 0.9380 (m-40) cc_final: 0.9021 (p0)
REVERT: C  209 TYR cc_start: 0.8747 (t80) cc_final: 0.7970 (t80)
REVERT: D   97 ARG cc_start: 0.8723 (tpt-90) cc_final: 0.8424 (ttt180)
REVERT: D  101 ASP cc_start: 0.8755 (t0) cc_final: 0.7959 (p0)
REVERT: D  119 ARG cc_start: 0.9381 (ptp90) cc_final: 0.9176 (ptp90)
REVERT: D  132 ARG cc_start: 0.8980 (tmt170) cc_final: 0.8614 (tmm-80)
REVERT: D  154 MET cc_start: 0.9081 (mtp) cc_final: 0.8489 (mtp)
REVERT: D  161 GLU cc_start: 0.8780 (tp30) cc_final: 0.8287 (tp30)
  outliers start: 33
  outliers final: 22
  residues processed: 218
  average time/residue: 0.0924
  time to fit residues: 27.3569
Evaluate side-chains
  197 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 174
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  193 SER
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain C residue   15 ILE
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  176 VAL
Chi-restraints excluded: chain D residue  124 GLU
Chi-restraints excluded: chain D residue  144 ASN
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  188 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 30 optimal weight:    8.9990
   chunk 3 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 71 optimal weight:    0.8980
   chunk 13 optimal weight:   10.0000
   chunk 84 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   chunk 54 optimal weight:    0.7980
   chunk 49 optimal weight:   10.0000
   chunk 37 optimal weight:    5.9990
   overall best weight:    2.5384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 234 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.095608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.068494 restraints weight = 19205.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 3.57
r_work: 0.2929 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.2692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8648  Z= 0.172
  Angle     :  0.652   7.723  11783  Z= 0.329
  Chirality :  0.047   0.177   1312
  Planarity :  0.005   0.052   1459
  Dihedral  :  9.960  78.214   1221
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 26.95 %
    Favored  : 68.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.28), residues: 1000
  helix:  0.09 (0.29), residues: 324
  sheet: -0.29 (0.36), residues: 224
  loop :  0.23 (0.32), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D 148 
 TYR   0.019   0.002   TYR C 244 
 PHE   0.020   0.001   PHE C 112 
 TRP   0.013   0.001   TRP B  31 
 HIS   0.006   0.001   HIS D  22 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00399 /  0.17 ( 8648)
  covalent geometry    : angle       0.65169 /  0.33 (11783)
  hydrogen bonds       : bond        0.05209 /  3.38 (  261)
  hydrogen bonds       : angle       5.28358 /  3.73 (  699)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 182
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 ASP cc_start: 0.8983 (t0) cc_final: 0.8654 (t0)
REVERT: A  119 ARG cc_start: 0.9186 (ttp-110) cc_final: 0.8499 (ptp90)
REVERT: A  166 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8134 (tp30)
REVERT: A  185 LYS cc_start: 0.9231 (ptpp) cc_final: 0.8820 (ptmt)
REVERT: B  119 ARG cc_start: 0.8867 (ttp-110) cc_final: 0.8658 (ptp-110)
REVERT: B  166 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8470 (tp30)
REVERT: C   11 LYS cc_start: 0.9464 (mmtm) cc_final: 0.9067 (mttp)
REVERT: C   70 TRP cc_start: 0.8216 (OUTLIER) cc_final: 0.7838 (p-90)
REVERT: C   71 CYS cc_start: 0.7544 (m) cc_final: 0.6920 (m)
REVERT: C  122 TYR cc_start: 0.8807 (p90) cc_final: 0.8552 (p90)
REVERT: C  129 ASN cc_start: 0.8436 (t0) cc_final: 0.7855 (t0)
REVERT: C  130 MET cc_start: 0.8628 (tpt) cc_final: 0.8274 (tpp)
REVERT: C  143 GLN cc_start: 0.9214 (tt0) cc_final: 0.8474 (tm-30)
REVERT: C  144 ASN cc_start: 0.8803 (p0) cc_final: 0.8403 (p0)
REVERT: C  183 ASP cc_start: 0.8912 (p0) cc_final: 0.8517 (p0)
REVERT: C  195 ASN cc_start: 0.9430 (m-40) cc_final: 0.9088 (p0)
REVERT: D   97 ARG cc_start: 0.8721 (tpt-90) cc_final: 0.8479 (ttt180)
REVERT: D  101 ASP cc_start: 0.8813 (t0) cc_final: 0.7939 (p0)
REVERT: D  119 ARG cc_start: 0.9418 (ptp90) cc_final: 0.9113 (ptp90)
REVERT: D  132 ARG cc_start: 0.8962 (tmt170) cc_final: 0.8741 (ttp-170)
REVERT: D  154 MET cc_start: 0.9160 (mtp) cc_final: 0.8517 (mtp)
REVERT: D  161 GLU cc_start: 0.8698 (tp30) cc_final: 0.8167 (tp30)
REVERT: D  166 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8510 (tp30)
  outliers start: 39
  outliers final: 22
  residues processed: 208
  average time/residue: 0.0929
  time to fit residues: 25.9357
Evaluate side-chains
  194 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 168
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  193 SER
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  166 GLU
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain C residue   15 ILE
Chi-restraints excluded: chain C residue   70 TRP
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  176 VAL
Chi-restraints excluded: chain D residue   12 ASP
Chi-restraints excluded: chain D residue   71 CYS
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  124 GLU
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  166 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 89 optimal weight:    3.9990
   chunk 97 optimal weight:    8.9990
   chunk 80 optimal weight:   10.0000
   chunk 54 optimal weight:    3.9990
   chunk 2 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9980
   chunk 39 optimal weight:    8.9990
   chunk 64 optimal weight:    9.9990
   chunk 12 optimal weight:    9.9990
   chunk 84 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    3.7988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 234 ASN
** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 234 ASN
D   8 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.092689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.065866 restraints weight = 19466.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 3.47
r_work: 0.2866 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8724
moved from start:          0.3142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   8648  Z= 0.220
  Angle     :  0.666   9.134  11783  Z= 0.334
  Chirality :  0.047   0.203   1312
  Planarity :  0.005   0.045   1459
  Dihedral  :  9.784  78.665   1221
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 14.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 27.62 %
    Favored  : 68.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.28), residues: 1000
  helix:  0.24 (0.30), residues: 328
  sheet: -0.58 (0.36), residues: 232
  loop :  0.28 (0.32), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 148 
 TYR   0.023   0.002   TYR A  79 
 PHE   0.021   0.001   PHE C  57 
 TRP   0.012   0.001   TRP C  70 
 HIS   0.005   0.001   HIS A  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00522 /  0.22 ( 8648)
  covalent geometry    : angle       0.66566 /  0.33 (11783)
  hydrogen bonds       : bond        0.04552 /  2.96 (  261)
  hydrogen bonds       : angle       5.13419 /  3.60 (  699)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 163
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 LYS cc_start: 0.9127 (mmtt) cc_final: 0.8904 (mmtm)
REVERT: A   79 TYR cc_start: 0.9455 (t80) cc_final: 0.8965 (t80)
REVERT: A   83 GLN cc_start: 0.9163 (mm110) cc_final: 0.8845 (mp10)
REVERT: A  114 GLU cc_start: 0.9511 (tp30) cc_final: 0.9091 (mt-10)
REVERT: A  119 ARG cc_start: 0.9152 (ttp-110) cc_final: 0.8451 (ptp90)
REVERT: A  166 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8201 (tp30)
REVERT: A  185 LYS cc_start: 0.9246 (ptpp) cc_final: 0.8844 (ptmt)
REVERT: B  119 ARG cc_start: 0.8946 (ttp-110) cc_final: 0.8631 (ptp-110)
REVERT: B  166 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8526 (tp30)
REVERT: C    9 ASN cc_start: 0.8861 (t0) cc_final: 0.8004 (m-40)
REVERT: C   11 LYS cc_start: 0.9474 (mmtm) cc_final: 0.9069 (mtmt)
REVERT: C   56 TYR cc_start: 0.8257 (m-80) cc_final: 0.7753 (m-10)
REVERT: C   70 TRP cc_start: 0.8182 (OUTLIER) cc_final: 0.7604 (p-90)
REVERT: C   71 CYS cc_start: 0.7585 (m) cc_final: 0.6745 (m)
REVERT: C  119 ARG cc_start: 0.9148 (ptp90) cc_final: 0.8798 (ptp90)
REVERT: C  129 ASN cc_start: 0.8414 (t0) cc_final: 0.7938 (t0)
REVERT: C  130 MET cc_start: 0.8596 (tpt) cc_final: 0.8244 (tpp)
REVERT: C  195 ASN cc_start: 0.9449 (m-40) cc_final: 0.9103 (p0)
REVERT: C  209 TYR cc_start: 0.8696 (t80) cc_final: 0.7829 (t80)
REVERT: D   97 ARG cc_start: 0.8778 (tpt-90) cc_final: 0.8512 (ttt180)
REVERT: D  101 ASP cc_start: 0.8855 (t0) cc_final: 0.7972 (p0)
REVERT: D  154 MET cc_start: 0.9226 (mtp) cc_final: 0.8548 (mtp)
REVERT: D  161 GLU cc_start: 0.8655 (tp30) cc_final: 0.8121 (tp30)
REVERT: D  166 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8554 (tp30)
  outliers start: 38
  outliers final: 25
  residues processed: 189
  average time/residue: 0.0852
  time to fit residues: 22.0893
Evaluate side-chains
  179 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 150
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  166 GLU
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain C residue   12 ASP
Chi-restraints excluded: chain C residue   15 ILE
Chi-restraints excluded: chain C residue   70 TRP
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  174 LEU
Chi-restraints excluded: chain C residue  221 THR
Chi-restraints excluded: chain C residue  229 THR
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  124 GLU
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  166 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 54 optimal weight:    6.9990
   chunk 43 optimal weight:    3.9990
   chunk 51 optimal weight:    0.4980
   chunk 25 optimal weight:    6.9990
   chunk 87 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 76 optimal weight:    0.0670
   chunk 31 optimal weight:    5.9990
   chunk 95 optimal weight:    2.9990
   overall best weight:    1.4922

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  25 GLN
** C 163 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 = 0.3544 r_free = 0.3544 target = 0.093746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.066559 restraints weight = 19301.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3021 rms_B_bonded: 3.53
r_work: 0.2889 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8697
moved from start:          0.3360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   8648  Z= 0.139
  Angle     :  0.631   7.662  11783  Z= 0.317
  Chirality :  0.046   0.267   1312
  Planarity :  0.005   0.057   1459
  Dihedral  :  9.638  79.331   1221
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 13.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 26.73 %
    Favored  : 68.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.28), residues: 1000
  helix:  0.40 (0.31), residues: 328
  sheet: -0.49 (0.36), residues: 228
  loop :  0.31 (0.32), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 148 
 TYR   0.015   0.002   TYR A 122 
 PHE   0.015   0.001   PHE C 112 
 TRP   0.016   0.001   TRP C  72 
 HIS   0.004   0.001   HIS A  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.14 ( 8648)
  covalent geometry    : angle       0.63080 /  0.32 (11783)
  hydrogen bonds       : bond        0.04201 /  2.73 (  261)
  hydrogen bonds       : angle       5.00690 /  3.51 (  699)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 170
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.8396 (pp20) cc_final: 0.8167 (pp20)
REVERT: A   79 TYR cc_start: 0.9444 (t80) cc_final: 0.9211 (t80)
REVERT: A  114 GLU cc_start: 0.9512 (tp30) cc_final: 0.9088 (mt-10)
REVERT: A  119 ARG cc_start: 0.9116 (ttp-110) cc_final: 0.8399 (ptp90)
REVERT: A  166 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8163 (tp30)
REVERT: A  185 LYS cc_start: 0.9246 (ptpp) cc_final: 0.8836 (ptmt)
REVERT: B  166 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8408 (tp30)
REVERT: C   11 LYS cc_start: 0.9448 (mmtm) cc_final: 0.9044 (mttp)
REVERT: C   70 TRP cc_start: 0.8136 (OUTLIER) cc_final: 0.7464 (p-90)
REVERT: C   71 CYS cc_start: 0.7533 (m) cc_final: 0.6876 (m)
REVERT: C  122 TYR cc_start: 0.8820 (p90) cc_final: 0.8601 (p90)
REVERT: C  129 ASN cc_start: 0.8462 (t0) cc_final: 0.7856 (t0)
REVERT: C  130 MET cc_start: 0.8607 (tpt) cc_final: 0.8293 (tpp)
REVERT: C  183 ASP cc_start: 0.8936 (p0) cc_final: 0.8609 (p0)
REVERT: C  195 ASN cc_start: 0.9445 (m-40) cc_final: 0.9089 (p0)
REVERT: C  209 TYR cc_start: 0.8640 (t80) cc_final: 0.7828 (t80)
REVERT: D   97 ARG cc_start: 0.8766 (tpt-90) cc_final: 0.8497 (ttt180)
REVERT: D  101 ASP cc_start: 0.8875 (t0) cc_final: 0.7997 (p0)
REVERT: D  121 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7800 (tttt)
REVERT: D  154 MET cc_start: 0.9215 (mtp) cc_final: 0.8599 (mtp)
REVERT: D  161 GLU cc_start: 0.8604 (tp30) cc_final: 0.8133 (tp30)
REVERT: D  166 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8522 (tp30)
  outliers start: 45
  outliers final: 29
  residues processed: 200
  average time/residue: 0.0814
  time to fit residues: 21.9814
Evaluate side-chains
  189 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 155
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  121 LYS
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  166 GLU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain C residue   12 ASP
Chi-restraints excluded: chain C residue   15 ILE
Chi-restraints excluded: chain C residue   70 TRP
Chi-restraints excluded: chain C residue   77 GLN
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  174 LEU
Chi-restraints excluded: chain C residue  176 VAL
Chi-restraints excluded: chain C residue  229 THR
Chi-restraints excluded: chain D residue   71 CYS
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  121 LYS
Chi-restraints excluded: chain D residue  124 GLU
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  166 GLU
Chi-restraints excluded: chain D residue  188 ASP
Chi-restraints excluded: chain D residue  206 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 15 optimal weight:    4.9990
   chunk 9 optimal weight:   10.0000
   chunk 57 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 55 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 87 optimal weight:    4.9990
   chunk 52 optimal weight:    0.4980
   overall best weight:    1.6986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 163 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.092929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.066320 restraints weight = 19060.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 3.43
r_work: 0.2886 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8720
moved from start:          0.3525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.080   8648  Z= 0.144
  Angle     :  0.633   7.817  11783  Z= 0.317
  Chirality :  0.046   0.155   1312
  Planarity :  0.004   0.043   1459
  Dihedral  :  9.482  80.528   1221
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 13.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 26.61 %
    Favored  : 68.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.09 (0.28), residues: 1000
  helix:  0.45 (0.31), residues: 328
  sheet: -0.69 (0.36), residues: 232
  loop :  0.43 (0.32), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 148 
 TYR   0.017   0.002   TYR A 122 
 PHE   0.013   0.001   PHE C 112 
 TRP   0.012   0.001   TRP C  70 
 HIS   0.003   0.001   HIS B  22 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.14 ( 8648)
  covalent geometry    : angle       0.63333 /  0.32 (11783)
  hydrogen bonds       : bond        0.04013 /  2.61 (  261)
  hydrogen bonds       : angle       4.93092 /  3.47 (  699)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 169
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 LYS cc_start: 0.9141 (mmtt) cc_final: 0.8844 (mptt)
REVERT: A  119 ARG cc_start: 0.9089 (ttp-110) cc_final: 0.8360 (ptp90)
REVERT: A  166 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8118 (tp30)
REVERT: A  185 LYS cc_start: 0.9221 (ptpp) cc_final: 0.8793 (ptmt)
REVERT: C   11 LYS cc_start: 0.9457 (mmtm) cc_final: 0.9029 (mttp)
REVERT: C   70 TRP cc_start: 0.8175 (OUTLIER) cc_final: 0.7607 (p-90)
REVERT: C  122 TYR cc_start: 0.8869 (p90) cc_final: 0.8649 (p90)
REVERT: C  129 ASN cc_start: 0.8461 (t0) cc_final: 0.7959 (t0)
REVERT: C  130 MET cc_start: 0.8636 (tpt) cc_final: 0.8343 (tpp)
REVERT: C  195 ASN cc_start: 0.9443 (m-40) cc_final: 0.9091 (p0)
REVERT: C  209 TYR cc_start: 0.8616 (t80) cc_final: 0.7843 (t80)
REVERT: D   97 ARG cc_start: 0.8766 (tpt-90) cc_final: 0.8481 (ttt180)
REVERT: D  101 ASP cc_start: 0.8876 (t0) cc_final: 0.7993 (p0)
REVERT: D  121 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7830 (tttt)
REVERT: D  132 ARG cc_start: 0.8871 (ttp-170) cc_final: 0.8666 (ttp80)
REVERT: D  154 MET cc_start: 0.9211 (mtp) cc_final: 0.8590 (mtp)
REVERT: D  161 GLU cc_start: 0.8610 (tp30) cc_final: 0.8141 (tp30)
REVERT: D  166 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8528 (tp30)
  outliers start: 40
  outliers final: 28
  residues processed: 197
  average time/residue: 0.0876
  time to fit residues: 23.3467
Evaluate side-chains
  189 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 157
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  121 LYS
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain C residue   12 ASP
Chi-restraints excluded: chain C residue   15 ILE
Chi-restraints excluded: chain C residue   70 TRP
Chi-restraints excluded: chain C residue   77 GLN
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  176 VAL
Chi-restraints excluded: chain C residue  229 THR
Chi-restraints excluded: chain D residue   71 CYS
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  121 LYS
Chi-restraints excluded: chain D residue  124 GLU
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  166 GLU
Chi-restraints excluded: chain D residue  206 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 12 optimal weight:   20.0000
   chunk 30 optimal weight:    0.9990
   chunk 42 optimal weight:    6.9990
   chunk 32 optimal weight:    8.9990
   chunk 22 optimal weight:    0.5980
   chunk 89 optimal weight:    0.9990
   chunk 58 optimal weight:   20.0000
   chunk 29 optimal weight:    4.9990
   chunk 62 optimal weight:    7.9990
   chunk 71 optimal weight:    0.9980
   chunk 8 optimal weight:    9.9990
   overall best weight:    1.7186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 226 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.092904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.066226 restraints weight = 19357.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3014 rms_B_bonded: 3.46
r_work: 0.2882 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8722
moved from start:          0.3682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8648  Z= 0.142
  Angle     :  0.646   8.327  11783  Z= 0.325
  Chirality :  0.046   0.177   1312
  Planarity :  0.005   0.043   1459
  Dihedral  :  9.383  82.270   1221
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 27.17 %
    Favored  : 68.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.29), residues: 1000
  helix:  0.50 (0.31), residues: 328
  sheet: -0.80 (0.36), residues: 236
  loop :  0.55 (0.32), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  97 
 TYR   0.047   0.002   TYR A  79 
 PHE   0.014   0.001   PHE C 112 
 TRP   0.012   0.001   TRP C  70 
 HIS   0.004   0.001   HIS A  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.14 ( 8648)
  covalent geometry    : angle       0.64603 /  0.32 (11783)
  hydrogen bonds       : bond        0.03845 /  2.47 (  261)
  hydrogen bonds       : angle       4.90964 /  3.46 (  699)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 162
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 GLN cc_start: 0.9158 (mm110) cc_final: 0.8878 (mp-120)
REVERT: A   97 ARG cc_start: 0.8166 (ttp-170) cc_final: 0.7922 (ttp-170)
REVERT: A  166 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8125 (tp30)
REVERT: A  185 LYS cc_start: 0.9196 (ptpp) cc_final: 0.8783 (ptmt)
REVERT: C   11 LYS cc_start: 0.9457 (mmtm) cc_final: 0.9037 (mttp)
REVERT: C   70 TRP cc_start: 0.8132 (OUTLIER) cc_final: 0.7496 (p-90)
REVERT: C  119 ARG cc_start: 0.9066 (ptp90) cc_final: 0.8863 (ptp90)
REVERT: C  122 TYR cc_start: 0.8883 (p90) cc_final: 0.8630 (p90)
REVERT: C  129 ASN cc_start: 0.8524 (t0) cc_final: 0.7923 (t0)
REVERT: C  130 MET cc_start: 0.8637 (tpt) cc_final: 0.8365 (tpp)
REVERT: C  195 ASN cc_start: 0.9463 (m-40) cc_final: 0.9103 (p0)
REVERT: C  209 TYR cc_start: 0.8598 (t80) cc_final: 0.7845 (t80)
REVERT: D   97 ARG cc_start: 0.8775 (tpt-90) cc_final: 0.8467 (ttt180)
REVERT: D  101 ASP cc_start: 0.8873 (t0) cc_final: 0.7978 (p0)
REVERT: D  121 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7861 (tttt)
REVERT: D  132 ARG cc_start: 0.8882 (ttp-170) cc_final: 0.8672 (ttp80)
REVERT: D  154 MET cc_start: 0.9217 (mtp) cc_final: 0.8585 (mtp)
REVERT: D  161 GLU cc_start: 0.8617 (tp30) cc_final: 0.8127 (tp30)
REVERT: D  166 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8538 (tp30)
  outliers start: 39
  outliers final: 30
  residues processed: 189
  average time/residue: 0.0850
  time to fit residues: 21.8496
Evaluate side-chains
  193 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 159
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain B residue   31 TRP
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  121 LYS
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain C residue   15 ILE
Chi-restraints excluded: chain C residue   70 TRP
Chi-restraints excluded: chain C residue   77 GLN
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  174 LEU
Chi-restraints excluded: chain C residue  176 VAL
Chi-restraints excluded: chain C residue  229 THR
Chi-restraints excluded: chain D residue   71 CYS
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  121 LYS
Chi-restraints excluded: chain D residue  124 GLU
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  166 GLU
Chi-restraints excluded: chain D residue  206 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 85 optimal weight:    6.9990
   chunk 80 optimal weight:    0.9990
   chunk 79 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0060
   chunk 8 optimal weight:    3.9990
   chunk 21 optimal weight:    0.4980
   chunk 40 optimal weight:    0.6980
   chunk 60 optimal weight:    8.9990
   chunk 74 optimal weight:    0.4980
   overall best weight:    0.5398

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  22 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.094367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.067911 restraints weight = 18952.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 3.44
r_work: 0.2912 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8700
moved from start:          0.3800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8648  Z= 0.122
  Angle     :  0.659   9.506  11783  Z= 0.330
  Chirality :  0.047   0.317   1312
  Planarity :  0.005   0.059   1459
  Dihedral  :  9.308  84.322   1221
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 28.84 %
    Favored  : 67.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.29), residues: 1000
  helix:  0.58 (0.31), residues: 328
  sheet: -0.68 (0.36), residues: 228
  loop :  0.49 (0.32), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 148 
 TYR   0.020   0.002   TYR C  79 
 PHE   0.012   0.001   PHE C 112 
 TRP   0.011   0.001   TRP C  70 
 HIS   0.003   0.000   HIS B  22 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.12 ( 8648)
  covalent geometry    : angle       0.65930 /  0.33 (11783)
  hydrogen bonds       : bond        0.03704 /  2.40 (  261)
  hydrogen bonds       : angle       4.83176 /  3.41 (  699)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 172
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 LYS cc_start: 0.9152 (mmtt) cc_final: 0.8808 (mptt)
REVERT: A   79 TYR cc_start: 0.9499 (t80) cc_final: 0.9199 (t80)
REVERT: A  122 TYR cc_start: 0.8693 (p90) cc_final: 0.8399 (p90)
REVERT: A  166 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8103 (tp30)
REVERT: A  185 LYS cc_start: 0.9181 (ptpp) cc_final: 0.8771 (ptmt)
REVERT: B  217 TYR cc_start: 0.9009 (m-10) cc_final: 0.8806 (m-80)
REVERT: C   11 LYS cc_start: 0.9471 (mmtm) cc_final: 0.9049 (mttp)
REVERT: C   70 TRP cc_start: 0.8088 (OUTLIER) cc_final: 0.7642 (p-90)
REVERT: C  122 TYR cc_start: 0.8884 (p90) cc_final: 0.8626 (p90)
REVERT: C  129 ASN cc_start: 0.8522 (t0) cc_final: 0.7872 (t0)
REVERT: C  130 MET cc_start: 0.8634 (tpt) cc_final: 0.8394 (tpp)
REVERT: C  183 ASP cc_start: 0.8799 (p0) cc_final: 0.8496 (p0)
REVERT: C  195 ASN cc_start: 0.9448 (m-40) cc_final: 0.9084 (p0)
REVERT: C  209 TYR cc_start: 0.8487 (t80) cc_final: 0.7728 (t80)
REVERT: D   31 TRP cc_start: 0.9115 (m100) cc_final: 0.8575 (m100)
REVERT: D   97 ARG cc_start: 0.8756 (tpt-90) cc_final: 0.8533 (ttt180)
REVERT: D  101 ASP cc_start: 0.8870 (t0) cc_final: 0.7989 (p0)
REVERT: D  121 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7875 (tttt)
REVERT: D  238 SER cc_start: 0.9400 (t) cc_final: 0.9200 (p)
  outliers start: 35
  outliers final: 24
  residues processed: 195
  average time/residue: 0.0825
  time to fit residues: 21.8980
Evaluate side-chains
  187 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 160
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain C residue   15 ILE
Chi-restraints excluded: chain C residue   70 TRP
Chi-restraints excluded: chain C residue   77 GLN
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  174 LEU
Chi-restraints excluded: chain C residue  176 VAL
Chi-restraints excluded: chain C residue  229 THR
Chi-restraints excluded: chain D residue   71 CYS
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  121 LYS
Chi-restraints excluded: chain D residue  124 GLU
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  206 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 61 optimal weight:    6.9990
   chunk 8 optimal weight:   10.0000
   chunk 50 optimal weight:    0.2980
   chunk 22 optimal weight:    7.9990
   chunk 35 optimal weight:    5.9990
   chunk 96 optimal weight:    4.9990
   chunk 84 optimal weight:    6.9990
   chunk 4 optimal weight:   20.0000
   chunk 25 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9980
   overall best weight:    2.6586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 226 ASN
** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 129 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.092454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.065816 restraints weight = 19257.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 3.46
r_work: 0.2868 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8741
moved from start:          0.3939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8648  Z= 0.173
  Angle     :  0.682   8.702  11783  Z= 0.341
  Chirality :  0.047   0.176   1312
  Planarity :  0.004   0.045   1459
  Dihedral  :  9.253  86.430   1221
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 29.40 %
    Favored  : 66.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.29), residues: 1000
  helix:  0.50 (0.31), residues: 328
  sheet: -0.78 (0.36), residues: 232
  loop :  0.50 (0.32), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 148 
 TYR   0.030   0.002   TYR C  65 
 PHE   0.011   0.001   PHE C 112 
 TRP   0.015   0.001   TRP B  31 
 HIS   0.002   0.001   HIS A  22 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00418 /  0.17 ( 8648)
  covalent geometry    : angle       0.68207 /  0.34 (11783)
  hydrogen bonds       : bond        0.03680 /  2.35 (  261)
  hydrogen bonds       : angle       4.94184 /  3.48 (  699)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 164
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 LYS cc_start: 0.9139 (mmtt) cc_final: 0.8814 (mptt)
REVERT: A   79 TYR cc_start: 0.9485 (t80) cc_final: 0.9161 (t80)
REVERT: A  122 TYR cc_start: 0.8601 (p90) cc_final: 0.8400 (p90)
REVERT: A  166 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8123 (tp30)
REVERT: A  185 LYS cc_start: 0.9192 (ptpp) cc_final: 0.8788 (ptmt)
REVERT: C   11 LYS cc_start: 0.9487 (mmtm) cc_final: 0.9096 (mttp)
REVERT: C   45 GLN cc_start: 0.8933 (pm20) cc_final: 0.8562 (pm20)
REVERT: C   70 TRP cc_start: 0.8206 (OUTLIER) cc_final: 0.7687 (p-90)
REVERT: C   72 TRP cc_start: 0.8838 (t-100) cc_final: 0.8375 (m-90)
REVERT: C  122 TYR cc_start: 0.8937 (p90) cc_final: 0.8646 (p90)
REVERT: C  129 ASN cc_start: 0.8484 (t0) cc_final: 0.7852 (t0)
REVERT: C  130 MET cc_start: 0.8668 (tpt) cc_final: 0.8445 (tpp)
REVERT: C  188 ASP cc_start: 0.8986 (m-30) cc_final: 0.8526 (t0)
REVERT: C  195 ASN cc_start: 0.9461 (m-40) cc_final: 0.9095 (p0)
REVERT: C  203 ASP cc_start: 0.9295 (t0) cc_final: 0.9079 (t0)
REVERT: C  209 TYR cc_start: 0.8593 (t80) cc_final: 0.7849 (t80)
REVERT: C  257 LYS cc_start: 0.6377 (tptt) cc_final: 0.6164 (tmtt)
REVERT: D   97 ARG cc_start: 0.8811 (tpt-90) cc_final: 0.8578 (ttt180)
REVERT: D  101 ASP cc_start: 0.8889 (t0) cc_final: 0.8005 (p0)
REVERT: D  121 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7857 (tttt)
  outliers start: 33
  outliers final: 25
  residues processed: 188
  average time/residue: 0.0893
  time to fit residues: 22.3887
Evaluate side-chains
  184 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 156
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain B residue   31 TRP
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  121 LYS
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain C residue   15 ILE
Chi-restraints excluded: chain C residue   70 TRP
Chi-restraints excluded: chain C residue   77 GLN
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  174 LEU
Chi-restraints excluded: chain C residue  229 THR
Chi-restraints excluded: chain D residue   71 CYS
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  121 LYS
Chi-restraints excluded: chain D residue  124 GLU
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  206 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 48 optimal weight:    0.0040
   chunk 80 optimal weight:    0.9990
   chunk 11 optimal weight:    5.9990
   chunk 73 optimal weight:   10.0000
   chunk 51 optimal weight:    9.9990
   chunk 26 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 27 optimal weight:    5.9990
   chunk 81 optimal weight:    0.6980
   chunk 33 optimal weight:    0.0000
   chunk 95 optimal weight:    2.9990
   overall best weight:    0.9400

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 234 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.093886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.067115 restraints weight = 19095.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3036 rms_B_bonded: 3.47
r_work: 0.2904 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8714
moved from start:          0.3988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8648  Z= 0.129
  Angle     :  0.674   8.955  11783  Z= 0.339
  Chirality :  0.046   0.197   1312
  Planarity :  0.005   0.045   1459
  Dihedral  :  9.245  88.939   1221
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 13.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 29.40 %
    Favored  : 67.37 %
  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 are not related in a simple way.
  whole:  0.20 (0.29), residues: 1000
  helix:  0.55 (0.32), residues: 326
  sheet: -0.76 (0.36), residues: 232
  loop :  0.58 (0.32), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 148 
 TYR   0.021   0.002   TYR C  56 
 PHE   0.011   0.001   PHE C 112 
 TRP   0.013   0.001   TRP B  31 
 HIS   0.002   0.000   HIS C  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.13 ( 8648)
  covalent geometry    : angle       0.67391 /  0.34 (11783)
  hydrogen bonds       : bond        0.03660 /  2.33 (  261)
  hydrogen bonds       : angle       4.92525 /  3.45 (  699)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 169
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 LYS cc_start: 0.9129 (mmtt) cc_final: 0.8824 (mptt)
REVERT: A   79 TYR cc_start: 0.9459 (t80) cc_final: 0.9185 (t80)
REVERT: A   97 ARG cc_start: 0.8044 (ttp-110) cc_final: 0.7787 (ttp-170)
REVERT: A  166 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8085 (tp30)
REVERT: A  185 LYS cc_start: 0.9179 (ptpp) cc_final: 0.8773 (ptmt)
REVERT: C   11 LYS cc_start: 0.9498 (mmtm) cc_final: 0.9117 (mttp)
REVERT: C   18 GLU cc_start: 0.9482 (tt0) cc_final: 0.9240 (tp30)
REVERT: C   45 GLN cc_start: 0.8949 (pm20) cc_final: 0.8573 (pm20)
REVERT: C   66 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9042 (mt)
REVERT: C   70 TRP cc_start: 0.8210 (OUTLIER) cc_final: 0.7766 (p-90)
REVERT: C   72 TRP cc_start: 0.8802 (t-100) cc_final: 0.8363 (m-90)
REVERT: C  122 TYR cc_start: 0.8947 (p90) cc_final: 0.8620 (p90)
REVERT: C  129 ASN cc_start: 0.8514 (t0) cc_final: 0.7973 (t0)
REVERT: C  130 MET cc_start: 0.8664 (tpt) cc_final: 0.8453 (tpp)
REVERT: C  195 ASN cc_start: 0.9452 (m-40) cc_final: 0.9086 (p0)
REVERT: C  203 ASP cc_start: 0.9262 (t0) cc_final: 0.9059 (t0)
REVERT: C  209 TYR cc_start: 0.8505 (t80) cc_final: 0.7822 (t80)
REVERT: D   31 TRP cc_start: 0.9143 (m100) cc_final: 0.8598 (m100)
REVERT: D   97 ARG cc_start: 0.8794 (tpt-90) cc_final: 0.8514 (ttt180)
REVERT: D  101 ASP cc_start: 0.8895 (t0) cc_final: 0.8031 (p0)
REVERT: D  154 MET cc_start: 0.9241 (mtp) cc_final: 0.8719 (mtp)
  outliers start: 29
  outliers final: 21
  residues processed: 187
  average time/residue: 0.0951
  time to fit residues: 23.7183
Evaluate side-chains
  179 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 155
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   70 TRP
Chi-restraints excluded: chain C residue   77 GLN
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  174 LEU
Chi-restraints excluded: chain C residue  229 THR
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  124 GLU
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  206 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 60 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   chunk 95 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 16 optimal weight:    0.4980
   chunk 45 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0370
   overall best weight:    0.8862

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 163 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 = 0.3559 r_free = 0.3559 target = 0.094240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.067786 restraints weight = 19151.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 3.47
r_work: 0.2920 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8706
moved from start:          0.4066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8648  Z= 0.130
  Angle     :  0.682   8.989  11783  Z= 0.343
  Chirality :  0.046   0.191   1312
  Planarity :  0.005   0.045   1459
  Dihedral  :  9.212  88.451   1221
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 30.18 %
    Favored  : 66.93 %
  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 are not related in a simple way.
  whole:  0.22 (0.29), residues: 1000
  helix:  0.50 (0.31), residues: 326
  sheet: -0.71 (0.37), residues: 230
  loop :  0.62 (0.32), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 148 
 TYR   0.023   0.002   TYR C  56 
 PHE   0.011   0.001   PHE C 112 
 TRP   0.014   0.001   TRP B  31 
 HIS   0.001   0.000   HIS A  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00310 /  0.13 ( 8648)
  covalent geometry    : angle       0.68169 /  0.34 (11783)
  hydrogen bonds       : bond        0.03738 /  2.36 (  261)
  hydrogen bonds       : angle       4.97133 /  3.48 (  699)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1838.76 seconds
wall clock time: 32 minutes 17.31 seconds (1937.31 seconds total)