Starting phenix.real_space_refine
on Wed Sep 17 11:49:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9muo_48639/09_2025/9muo_48639.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9muo_48639/09_2025/9muo_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9muo_48639/09_2025/9muo_48639.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9muo_48639/09_2025/9muo_48639.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9muo_48639/09_2025/9muo_48639.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9muo_48639/09_2025/9muo_48639.map"
  }
  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-2.0-5805/lib/python3.9/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: 2.53, per 1000 atoms: 0.30
  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: 0.84
  Conformation dependent library (CDL) restraints added in 452.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.25
  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: 1.39

  Time building geometry restraints manager: 1.10 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: 1036
       0.051 -    0.103: 202
       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:             12.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.080
  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:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
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= 0.216
  Angle     :  0.814  15.087  11783  Z= 0.432
  Chirality :  0.046   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 aren 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
  covalent geometry    : bond        0.00456 ( 8648)
  covalent geometry    : angle       0.81399 (11783)
  hydrogen bonds       : bond        0.30607 (  261)
  hydrogen bonds       : angle       8.36780 (  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  : 0.364 
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: 0.1073
  time to fit residues: 37.6086
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  : 0.333 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    4.9990
   overall best weight:    1.4190

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

Flipped N/Q/H residues before XYZ refinement:
B  46 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.097533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.070106 restraints weight = 19024.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 3.65
r_work: 0.2982 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.2474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8648  Z= 0.142
  Angle     :  0.655   7.715  11783  Z= 0.331
  Chirality :  0.047   0.209   1312
  Planarity :  0.005   0.052   1459
  Dihedral  :  9.941  80.209   1226
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 28.84 %
    Favored  : 67.71 %
  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 aren not related in a simple way.
  whole:  0.19 (0.28), residues: 1000
  helix:  0.38 (0.31), residues: 324
  sheet: -0.06 (0.37), residues: 224
  loop :  0.25 (0.32), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 148 
 TYR   0.026   0.002   TYR A  79 
 PHE   0.010   0.001   PHE A 112 
 TRP   0.016   0.001   TRP C  70 
 HIS   0.004   0.001   HIS C  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 8648)
  covalent geometry    : angle       0.65490 (11783)
  hydrogen bonds       : bond        0.05341 (  261)
  hydrogen bonds       : angle       5.31446 (  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
  234 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 203
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.9054 (tp30) cc_final: 0.8777 (tp30)
REVERT: A   57 PHE cc_start: 0.8896 (t80) cc_final: 0.8432 (t80)
REVERT: A   83 GLN cc_start: 0.9186 (mm110) cc_final: 0.8979 (mm110)
REVERT: A  143 GLN cc_start: 0.8909 (tm-30) cc_final: 0.8634 (tm-30)
REVERT: A  185 LYS cc_start: 0.9214 (ptpp) cc_final: 0.8793 (ptmt)
REVERT: B  119 ARG cc_start: 0.8852 (ttp-110) cc_final: 0.8639 (ptp-110)
REVERT: C   11 LYS cc_start: 0.9457 (mmtm) cc_final: 0.9080 (mttp)
REVERT: C   70 TRP cc_start: 0.8184 (OUTLIER) cc_final: 0.7897 (p-90)
REVERT: C  112 PHE cc_start: 0.9236 (t80) cc_final: 0.8941 (t80)
REVERT: C  122 TYR cc_start: 0.8731 (p90) cc_final: 0.8504 (p90)
REVERT: C  129 ASN cc_start: 0.8381 (t0) cc_final: 0.7747 (t0)
REVERT: C  142 TRP cc_start: 0.9074 (m100) cc_final: 0.8291 (m100)
REVERT: C  143 GLN cc_start: 0.9175 (tt0) cc_final: 0.8439 (tm-30)
REVERT: C  144 ASN cc_start: 0.8720 (p0) cc_final: 0.8374 (p0)
REVERT: C  195 ASN cc_start: 0.9407 (m-40) cc_final: 0.9058 (p0)
REVERT: C  209 TYR cc_start: 0.8770 (t80) cc_final: 0.7983 (t80)
REVERT: D   24 ARG cc_start: 0.8633 (ttp80) cc_final: 0.8203 (ttp80)
REVERT: D  101 ASP cc_start: 0.8814 (t0) cc_final: 0.7953 (p0)
REVERT: D  119 ARG cc_start: 0.9419 (ptp90) cc_final: 0.8959 (ptp90)
REVERT: D  132 ARG cc_start: 0.8960 (tmt170) cc_final: 0.8594 (tmm-80)
REVERT: D  139 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8473 (tm-30)
REVERT: D  154 MET cc_start: 0.9125 (mtp) cc_final: 0.8522 (mtp)
REVERT: D  161 GLU cc_start: 0.8705 (tp30) cc_final: 0.8196 (tp30)
REVERT: D  185 LYS cc_start: 0.9034 (ptpp) cc_final: 0.8801 (pttm)
  outliers start: 31
  outliers final: 19
  residues processed: 222
  average time/residue: 0.1073
  time to fit residues: 31.5728
Evaluate side-chains
  204 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 184
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
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  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  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   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  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  174 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 46 optimal weight:    7.9990
   chunk 30 optimal weight:    8.9990
   chunk 3 optimal weight:    5.9990
   chunk 10 optimal weight:   20.0000
   chunk 71 optimal weight:    3.9990
   chunk 13 optimal weight:    8.9990
   chunk 84 optimal weight:    0.7980
   chunk 39 optimal weight:    4.9990
   chunk 54 optimal weight:   10.0000
   chunk 49 optimal weight:    9.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    3.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 226 ASN
A 234 ASN
B   8 HIS
B 234 ASN
C 234 ASN
D   8 HIS
D 234 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.091735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.064148 restraints weight = 19148.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 3.51
r_work: 0.2837 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          0.3371

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= 0.217
  Angle     :  0.660   7.354  11783  Z= 0.330
  Chirality :  0.047   0.169   1312
  Planarity :  0.005   0.053   1459
  Dihedral  :  9.478  79.890   1221
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 14.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 26.73 %
    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 aren not related in a simple way.
  whole:  0.14 (0.28), residues: 1000
  helix:  0.53 (0.30), residues: 326
  sheet: -0.36 (0.36), residues: 228
  loop :  0.22 (0.32), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 148 
 TYR   0.023   0.002   TYR C 244 
 PHE   0.012   0.001   PHE D  60 
 TRP   0.019   0.001   TRP B  31 
 HIS   0.003   0.001   HIS D   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00513 ( 8648)
  covalent geometry    : angle       0.65996 (11783)
  hydrogen bonds       : bond        0.04461 (  261)
  hydrogen bonds       : angle       4.93369 (  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
  222 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 179
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 PHE cc_start: 0.8952 (t80) cc_final: 0.8342 (t80)
REVERT: A  119 ARG cc_start: 0.9193 (ttp-110) cc_final: 0.8477 (ptp90)
REVERT: A  166 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8334 (tp30)
REVERT: A  185 LYS cc_start: 0.9241 (ptpp) cc_final: 0.8824 (ptmt)
REVERT: B  166 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8562 (tp30)
REVERT: C    9 ASN cc_start: 0.8880 (t0) cc_final: 0.8077 (m-40)
REVERT: C   11 LYS cc_start: 0.9468 (mmtm) cc_final: 0.9048 (mtmt)
REVERT: C   56 TYR cc_start: 0.8133 (m-80) cc_final: 0.7815 (m-80)
REVERT: C   65 TYR cc_start: 0.8748 (t80) cc_final: 0.7795 (t80)
REVERT: C   70 TRP cc_start: 0.8154 (OUTLIER) cc_final: 0.7440 (p-90)
REVERT: C   71 CYS cc_start: 0.7665 (m) cc_final: 0.6857 (m)
REVERT: C  112 PHE cc_start: 0.9261 (t80) cc_final: 0.9061 (t80)
REVERT: C  122 TYR cc_start: 0.8776 (p90) cc_final: 0.8559 (p90)
REVERT: C  129 ASN cc_start: 0.8370 (t0) cc_final: 0.7900 (t0)
REVERT: C  130 MET cc_start: 0.8602 (tpt) cc_final: 0.8256 (tpp)
REVERT: C  166 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8403 (tp30)
REVERT: C  183 ASP cc_start: 0.8980 (p0) cc_final: 0.8717 (p0)
REVERT: C  195 ASN cc_start: 0.9452 (m-40) cc_final: 0.9096 (p0)
REVERT: C  209 TYR cc_start: 0.8892 (t80) cc_final: 0.7927 (t80)
REVERT: C  257 LYS cc_start: 0.6318 (tptt) cc_final: 0.6069 (tmtt)
REVERT: D   24 ARG cc_start: 0.8791 (ttp80) cc_final: 0.8234 (ttp80)
REVERT: D   31 TRP cc_start: 0.9163 (m100) cc_final: 0.8690 (m100)
REVERT: D  101 ASP cc_start: 0.8856 (t0) cc_final: 0.8058 (p0)
REVERT: D  132 ARG cc_start: 0.8965 (tmt170) cc_final: 0.8611 (tmm-80)
REVERT: D  139 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8311 (tm-30)
REVERT: D  154 MET cc_start: 0.9243 (mtp) cc_final: 0.8649 (mtp)
REVERT: D  161 GLU cc_start: 0.8650 (tp30) cc_final: 0.8223 (tp30)
REVERT: D  185 LYS cc_start: 0.9052 (ptpp) cc_final: 0.8651 (ptpp)
  outliers start: 43
  outliers final: 27
  residues processed: 210
  average time/residue: 0.1152
  time to fit residues: 31.5953
Evaluate side-chains
  190 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 159
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   81 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  166 GLU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  221 THR
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  166 GLU
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   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  164 VAL
Chi-restraints excluded: chain D residue  166 GLU
Chi-restraints excluded: chain D residue  174 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 89 optimal weight:    4.9990
   chunk 97 optimal weight:    9.9990
   chunk 80 optimal weight:    6.9990
   chunk 54 optimal weight:    5.9990
   chunk 2 optimal weight:   10.0000
   chunk 50 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9990
   chunk 8 optimal weight:   10.0000
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3516 r_free = 0.3516 target = 0.091739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.064651 restraints weight = 19373.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 3.49
r_work: 0.2853 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.3749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8648  Z= 0.147
  Angle     :  0.609   7.223  11783  Z= 0.305
  Chirality :  0.045   0.147   1312
  Planarity :  0.005   0.042   1459
  Dihedral  :  9.224  84.641   1221
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 26.84 %
    Favored  : 68.82 %
  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 aren not related in a simple way.
  whole:  0.23 (0.29), residues: 1000
  helix:  0.67 (0.31), residues: 328
  sheet: -0.62 (0.36), residues: 236
  loop :  0.43 (0.32), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 148 
 TYR   0.019   0.002   TYR A  79 
 PHE   0.017   0.001   PHE C  57 
 TRP   0.017   0.001   TRP C  70 
 HIS   0.003   0.001   HIS B  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 8648)
  covalent geometry    : angle       0.60907 (11783)
  hydrogen bonds       : bond        0.03642 (  261)
  hydrogen bonds       : angle       4.77838 (  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
  218 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 179
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 PHE cc_start: 0.8923 (t80) cc_final: 0.8299 (t80)
REVERT: A  101 ASP cc_start: 0.8900 (t0) cc_final: 0.8650 (t0)
REVERT: A  119 ARG cc_start: 0.9150 (ttp-110) cc_final: 0.8449 (ptp90)
REVERT: A  166 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8270 (tp30)
REVERT: A  185 LYS cc_start: 0.9253 (ptpp) cc_final: 0.8820 (ptmt)
REVERT: B   97 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7061 (tpt-90)
REVERT: B  166 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8412 (tp30)
REVERT: C    9 ASN cc_start: 0.8861 (t0) cc_final: 0.8043 (m110)
REVERT: C   11 LYS cc_start: 0.9491 (mmtm) cc_final: 0.9082 (mtmt)
REVERT: C   65 TYR cc_start: 0.8714 (t80) cc_final: 0.7774 (t80)
REVERT: C   70 TRP cc_start: 0.8116 (OUTLIER) cc_final: 0.7212 (p-90)
REVERT: C   71 CYS cc_start: 0.7651 (m) cc_final: 0.6840 (m)
REVERT: C  112 PHE cc_start: 0.9250 (t80) cc_final: 0.8906 (t80)
REVERT: C  129 ASN cc_start: 0.8481 (t0) cc_final: 0.7856 (t0)
REVERT: C  130 MET cc_start: 0.8638 (tpt) cc_final: 0.8384 (tpp)
REVERT: C  166 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8397 (tp30)
REVERT: C  183 ASP cc_start: 0.9107 (p0) cc_final: 0.8609 (p0)
REVERT: C  188 ASP cc_start: 0.9215 (m-30) cc_final: 0.8776 (t0)
REVERT: C  195 ASN cc_start: 0.9439 (m-40) cc_final: 0.9074 (p0)
REVERT: C  209 TYR cc_start: 0.8784 (t80) cc_final: 0.8021 (t80)
REVERT: D   24 ARG cc_start: 0.8867 (ttp80) cc_final: 0.8627 (ttp80)
REVERT: D   31 TRP cc_start: 0.9192 (m100) cc_final: 0.8624 (m100)
REVERT: D  101 ASP cc_start: 0.8854 (t0) cc_final: 0.8038 (p0)
REVERT: D  130 MET cc_start: 0.8867 (tpp) cc_final: 0.8621 (tpp)
REVERT: D  132 ARG cc_start: 0.8959 (tmt170) cc_final: 0.8613 (tmm-80)
REVERT: D  139 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8275 (tm-30)
REVERT: D  185 LYS cc_start: 0.8939 (ptpp) cc_final: 0.8612 (ptpp)
  outliers start: 39
  outliers final: 25
  residues processed: 204
  average time/residue: 0.1133
  time to fit residues: 30.5113
Evaluate side-chains
  180 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 150
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 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   72 TRP
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue   97 ARG
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  131 THR
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   70 TRP
Chi-restraints excluded: chain C residue  166 GLU
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  124 GLU
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  174 LEU
Chi-restraints excluded: chain D residue  188 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 54 optimal weight:    8.9990
   chunk 43 optimal weight:    5.9990
   chunk 51 optimal weight:    9.9990
   chunk 25 optimal weight:    7.9990
   chunk 87 optimal weight:    0.9980
   chunk 38 optimal weight:    7.9990
   chunk 30 optimal weight:    5.9990
   chunk 76 optimal weight:    0.0980
   chunk 31 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** B  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 234 ASN
D 234 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.093716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.067806 restraints weight = 19095.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 3.42
r_work: 0.2900 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8605
moved from start:          0.3901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8648  Z= 0.111
  Angle     :  0.601   8.823  11783  Z= 0.299
  Chirality :  0.044   0.142   1312
  Planarity :  0.004   0.044   1459
  Dihedral  :  9.099  88.693   1221
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 26.50 %
    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 aren not related in a simple way.
  whole:  0.37 (0.29), residues: 1000
  helix:  0.81 (0.31), residues: 326
  sheet: -0.63 (0.36), residues: 236
  loop :  0.57 (0.33), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 148 
 TYR   0.022   0.002   TYR A  79 
 PHE   0.011   0.001   PHE C  57 
 TRP   0.017   0.001   TRP C  70 
 HIS   0.004   0.000   HIS A  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 8648)
  covalent geometry    : angle       0.60106 (11783)
  hydrogen bonds       : bond        0.03290 (  261)
  hydrogen bonds       : angle       4.65288 (  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
  218 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 175
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 PHE cc_start: 0.8917 (t80) cc_final: 0.8303 (t80)
REVERT: A   79 TYR cc_start: 0.9438 (t80) cc_final: 0.9139 (t80)
REVERT: A  119 ARG cc_start: 0.9176 (ttp-110) cc_final: 0.8488 (ptp90)
REVERT: A  166 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8255 (tp30)
REVERT: A  185 LYS cc_start: 0.9195 (ptpp) cc_final: 0.8774 (ptmt)
REVERT: A  239 GLU cc_start: 0.8528 (mp0) cc_final: 0.7925 (mp0)
REVERT: C   11 LYS cc_start: 0.9498 (mmtm) cc_final: 0.9127 (mttp)
REVERT: C   18 GLU cc_start: 0.9463 (tt0) cc_final: 0.9232 (tp30)
REVERT: C   45 GLN cc_start: 0.8910 (pm20) cc_final: 0.8497 (pm20)
REVERT: C   70 TRP cc_start: 0.8107 (OUTLIER) cc_final: 0.7113 (p-90)
REVERT: C   71 CYS cc_start: 0.7631 (m) cc_final: 0.6960 (m)
REVERT: C   97 ARG cc_start: 0.9251 (ttt180) cc_final: 0.8919 (ttt180)
REVERT: C  112 PHE cc_start: 0.9163 (t80) cc_final: 0.8942 (t80)
REVERT: C  119 ARG cc_start: 0.9032 (ptp90) cc_final: 0.8819 (ptp90)
REVERT: C  122 TYR cc_start: 0.8933 (p90) cc_final: 0.8355 (p90)
REVERT: C  129 ASN cc_start: 0.8491 (t0) cc_final: 0.7923 (t0)
REVERT: C  130 MET cc_start: 0.8626 (tpt) cc_final: 0.8418 (tpp)
REVERT: C  142 TRP cc_start: 0.9100 (m100) cc_final: 0.8124 (m100)
REVERT: C  183 ASP cc_start: 0.9072 (p0) cc_final: 0.8534 (p0)
REVERT: C  188 ASP cc_start: 0.9197 (m-30) cc_final: 0.8771 (t0)
REVERT: C  195 ASN cc_start: 0.9431 (m-40) cc_final: 0.9072 (p0)
REVERT: C  209 TYR cc_start: 0.8641 (t80) cc_final: 0.8122 (t80)
REVERT: D   24 ARG cc_start: 0.8870 (ttp80) cc_final: 0.8603 (ttp80)
REVERT: D   31 TRP cc_start: 0.9176 (m100) cc_final: 0.8596 (m100)
REVERT: D  101 ASP cc_start: 0.8848 (t0) cc_final: 0.8055 (p0)
REVERT: D  130 MET cc_start: 0.8884 (tpp) cc_final: 0.8637 (tpp)
REVERT: D  132 ARG cc_start: 0.8953 (tmt170) cc_final: 0.8600 (tmm-80)
REVERT: D  139 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8314 (tm-30)
REVERT: D  185 LYS cc_start: 0.8872 (ptpp) cc_final: 0.8576 (ptpp)
  outliers start: 43
  outliers final: 27
  residues processed: 201
  average time/residue: 0.1054
  time to fit residues: 28.1206
Evaluate side-chains
  193 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 164
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ILE
Chi-restraints excluded: chain A residue   81 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   72 TRP
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain B residue  107 ASP
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 B residue  254 MET
Chi-restraints excluded: chain C residue   12 ASP
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue   70 TRP
Chi-restraints excluded: chain C residue  106 THR
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 D residue   12 ASP
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  206 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 57 optimal weight:    8.9990
   chunk 61 optimal weight:    5.9990
   chunk 55 optimal weight:    9.9990
   chunk 23 optimal weight:    5.9990
   chunk 39 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 87 optimal weight:    5.9990
   chunk 52 optimal weight:    4.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A  25 GLN
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.091744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.065286 restraints weight = 19091.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.2998 rms_B_bonded: 3.47
r_work: 0.2865 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.4116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8648  Z= 0.139
  Angle     :  0.599   7.245  11783  Z= 0.296
  Chirality :  0.045   0.144   1312
  Planarity :  0.004   0.046   1459
  Dihedral  :  9.023  85.109   1221
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 27.39 %
    Favored  : 67.82 %
  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 aren not related in a simple way.
  whole:  0.46 (0.29), residues: 1000
  helix:  0.96 (0.32), residues: 320
  sheet: -0.75 (0.36), residues: 240
  loop :  0.69 (0.33), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 148 
 TYR   0.017   0.002   TYR C  56 
 PHE   0.010   0.001   PHE C  57 
 TRP   0.016   0.001   TRP C  70 
 HIS   0.002   0.001   HIS A  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 8648)
  covalent geometry    : angle       0.59906 (11783)
  hydrogen bonds       : bond        0.03361 (  261)
  hydrogen bonds       : angle       4.60550 (  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
  208 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 165
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 PHE cc_start: 0.8940 (t80) cc_final: 0.8321 (t80)
REVERT: A  109 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8196 (mmm160)
REVERT: A  119 ARG cc_start: 0.9167 (ttp-110) cc_final: 0.8434 (ptp90)
REVERT: A  166 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8210 (tp30)
REVERT: A  185 LYS cc_start: 0.9196 (ptpp) cc_final: 0.8766 (ptmt)
REVERT: B   97 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.6974 (tpt-90)
REVERT: C   11 LYS cc_start: 0.9528 (mmtm) cc_final: 0.9164 (mttp)
REVERT: C   45 GLN cc_start: 0.8902 (pm20) cc_final: 0.8453 (pm20)
REVERT: C   70 TRP cc_start: 0.8131 (OUTLIER) cc_final: 0.7271 (p-90)
REVERT: C   71 CYS cc_start: 0.7712 (m) cc_final: 0.7403 (m)
REVERT: C   72 TRP cc_start: 0.8377 (m100) cc_final: 0.8172 (m100)
REVERT: C   97 ARG cc_start: 0.9233 (ttt180) cc_final: 0.8900 (ttt180)
REVERT: C  112 PHE cc_start: 0.9189 (t80) cc_final: 0.8923 (t80)
REVERT: C  122 TYR cc_start: 0.8974 (p90) cc_final: 0.8352 (p90)
REVERT: C  129 ASN cc_start: 0.8503 (t0) cc_final: 0.7906 (t0)
REVERT: C  142 TRP cc_start: 0.9075 (m100) cc_final: 0.8129 (m100)
REVERT: C  161 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8328 (tp30)
REVERT: C  183 ASP cc_start: 0.9047 (p0) cc_final: 0.8505 (p0)
REVERT: C  185 LYS cc_start: 0.9064 (mmtm) cc_final: 0.8848 (mmtm)
REVERT: C  188 ASP cc_start: 0.9207 (m-30) cc_final: 0.8784 (t0)
REVERT: C  195 ASN cc_start: 0.9431 (m-40) cc_final: 0.9071 (p0)
REVERT: C  209 TYR cc_start: 0.8693 (t80) cc_final: 0.7772 (t80)
REVERT: D   18 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8265 (tm-30)
REVERT: D   24 ARG cc_start: 0.8885 (ttp80) cc_final: 0.8569 (ttp80)
REVERT: D   31 TRP cc_start: 0.9116 (m100) cc_final: 0.8570 (m100)
REVERT: D  101 ASP cc_start: 0.8839 (t0) cc_final: 0.8023 (p0)
REVERT: D  132 ARG cc_start: 0.8949 (tmt170) cc_final: 0.8596 (tmm-80)
REVERT: D  139 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8323 (tm-30)
REVERT: D  185 LYS cc_start: 0.8896 (ptpp) cc_final: 0.8510 (ptpp)
  outliers start: 43
  outliers final: 34
  residues processed: 196
  average time/residue: 0.1107
  time to fit residues: 28.7352
Evaluate side-chains
  198 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 160
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ILE
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  109 ARG
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 A residue  229 THR
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue   97 ARG
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 B residue  254 MET
Chi-restraints excluded: chain C residue   12 ASP
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue   70 TRP
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  174 LEU
Chi-restraints excluded: chain C residue  229 THR
Chi-restraints excluded: chain D residue   12 ASP
Chi-restraints excluded: chain D residue   27 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  164 VAL
Chi-restraints excluded: chain D residue  174 LEU
Chi-restraints excluded: chain D residue  188 ASP
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:    5.9990
   chunk 30 optimal weight:    9.9990
   chunk 42 optimal weight:    0.0770
   chunk 32 optimal weight:   10.0000
   chunk 22 optimal weight:    0.8980
   chunk 89 optimal weight:    2.9990
   chunk 58 optimal weight:   20.0000
   chunk 29 optimal weight:    8.9990
   chunk 62 optimal weight:   20.0000
   chunk 71 optimal weight:   10.0000
   chunk 8 optimal weight:   20.0000
   overall best weight:    3.7944

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

Flipped N/Q/H residues before XYZ refinement:
** B  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 226 ASN
** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  22 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.089256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.062510 restraints weight = 19556.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 3.41
r_work: 0.2847 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8774
moved from start:          0.4533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   8648  Z= 0.216
  Angle     :  0.654  11.012  11783  Z= 0.327
  Chirality :  0.046   0.161   1312
  Planarity :  0.004   0.044   1459
  Dihedral  :  9.138  75.962   1221
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 26.95 %
    Favored  : 67.82 %
  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 aren not related in a simple way.
  whole:  0.34 (0.29), residues: 1000
  helix:  0.89 (0.32), residues: 322
  sheet: -0.79 (0.36), residues: 232
  loop :  0.54 (0.32), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 148 
 TYR   0.022   0.002   TYR C 244 
 PHE   0.014   0.001   PHE B  60 
 TRP   0.016   0.001   TRP C  70 
 HIS   0.004   0.001   HIS A  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 ( 8648)
  covalent geometry    : angle       0.65418 (11783)
  hydrogen bonds       : bond        0.03622 (  261)
  hydrogen bonds       : angle       4.70107 (  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
  195 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 148
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 LYS cc_start: 0.9235 (mmtt) cc_final: 0.8991 (mptt)
REVERT: A   57 PHE cc_start: 0.9060 (t80) cc_final: 0.8524 (t80)
REVERT: A  109 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8104 (mmm160)
REVERT: A  166 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8273 (tp30)
REVERT: A  185 LYS cc_start: 0.9219 (ptpp) cc_final: 0.8892 (ptmt)
REVERT: B   33 ASP cc_start: 0.6763 (OUTLIER) cc_final: 0.6324 (p0)
REVERT: B   97 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7066 (tpt-90)
REVERT: B  130 MET cc_start: 0.8564 (tpp) cc_final: 0.8180 (tpp)
REVERT: C   11 LYS cc_start: 0.9516 (mmtm) cc_final: 0.9195 (mttp)
REVERT: C   45 GLN cc_start: 0.8934 (pm20) cc_final: 0.8505 (pm20)
REVERT: C   70 TRP cc_start: 0.8114 (OUTLIER) cc_final: 0.7057 (p-90)
REVERT: C   71 CYS cc_start: 0.7789 (m) cc_final: 0.7021 (m)
REVERT: C   97 ARG cc_start: 0.9253 (ttt180) cc_final: 0.8975 (ttt180)
REVERT: C  112 PHE cc_start: 0.9242 (t80) cc_final: 0.8852 (t80)
REVERT: C  129 ASN cc_start: 0.8533 (t0) cc_final: 0.8077 (t0)
REVERT: C  161 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8389 (tp30)
REVERT: C  183 ASP cc_start: 0.8994 (p0) cc_final: 0.8543 (p0)
REVERT: C  185 LYS cc_start: 0.9176 (mmtm) cc_final: 0.8916 (mmtm)
REVERT: C  188 ASP cc_start: 0.9148 (m-30) cc_final: 0.8754 (t0)
REVERT: C  195 ASN cc_start: 0.9365 (m-40) cc_final: 0.9061 (p0)
REVERT: C  209 TYR cc_start: 0.8655 (t80) cc_final: 0.8124 (t80)
REVERT: D   24 ARG cc_start: 0.8995 (ttp80) cc_final: 0.8752 (ttp80)
REVERT: D   31 TRP cc_start: 0.9182 (m100) cc_final: 0.8853 (m100)
REVERT: D  101 ASP cc_start: 0.8854 (t0) cc_final: 0.8018 (p0)
REVERT: D  132 ARG cc_start: 0.8896 (tmt170) cc_final: 0.8622 (tmm-80)
REVERT: D  139 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8324 (tm-30)
REVERT: D  154 MET cc_start: 0.9219 (mtp) cc_final: 0.8915 (mtp)
REVERT: D  185 LYS cc_start: 0.8916 (ptpp) cc_final: 0.8560 (ptpp)
  outliers start: 47
  outliers final: 33
  residues processed: 187
  average time/residue: 0.1155
  time to fit residues: 28.2589
Evaluate side-chains
  179 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 141
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ILE
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  109 ARG
Chi-restraints excluded: chain A residue  143 GLN
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 A residue  229 THR
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   33 ASP
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain B residue   97 ARG
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  206 VAL
Chi-restraints excluded: chain B residue  254 MET
Chi-restraints excluded: chain C residue   12 ASP
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue   70 TRP
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  174 LEU
Chi-restraints excluded: chain C residue  229 THR
Chi-restraints excluded: chain D residue   12 ASP
Chi-restraints excluded: chain D residue   27 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  164 VAL
Chi-restraints excluded: chain D residue  174 LEU
Chi-restraints excluded: chain D residue  206 VAL
Chi-restraints excluded: chain D residue  254 MET
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:    7.9990
   chunk 80 optimal weight:    6.9990
   chunk 79 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0970
   chunk 8 optimal weight:    9.9990
   chunk 21 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 60 optimal weight:    9.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3459 r_free = 0.3459 target = 0.088912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.062070 restraints weight = 18829.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.2932 rms_B_bonded: 3.64
r_work: 0.2791 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8561
moved from start:          0.4627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8648  Z= 0.138
  Angle     :  0.631   9.569  11783  Z= 0.313
  Chirality :  0.045   0.160   1312
  Planarity :  0.004   0.041   1459
  Dihedral  :  9.133  77.013   1221
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 27.39 %
    Favored  : 67.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.29), residues: 1000
  helix:  0.87 (0.31), residues: 324
  sheet: -0.81 (0.36), residues: 232
  loop :  0.59 (0.32), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 148 
 TYR   0.018   0.002   TYR A  79 
 PHE   0.011   0.001   PHE C  57 
 TRP   0.026   0.001   TRP D  31 
 HIS   0.002   0.000   HIS C   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 8648)
  covalent geometry    : angle       0.63089 (11783)
  hydrogen bonds       : bond        0.03394 (  261)
  hydrogen bonds       : angle       4.64003 (  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
  195 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 149
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 LYS cc_start: 0.9242 (mmtt) cc_final: 0.8987 (mptt)
REVERT: A   57 PHE cc_start: 0.8956 (t80) cc_final: 0.8392 (t80)
REVERT: A  109 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8055 (mmm160)
REVERT: A  185 LYS cc_start: 0.9183 (ptpp) cc_final: 0.8753 (ptmt)
REVERT: A  239 GLU cc_start: 0.8501 (mt-10) cc_final: 0.7843 (mp0)
REVERT: B   33 ASP cc_start: 0.6503 (OUTLIER) cc_final: 0.6034 (p0)
REVERT: B   97 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7053 (tpt-90)
REVERT: B  139 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8400 (tm-30)
REVERT: C   11 LYS cc_start: 0.9521 (mmtm) cc_final: 0.9168 (mttp)
REVERT: C   45 GLN cc_start: 0.8948 (pm20) cc_final: 0.8519 (pm20)
REVERT: C   65 TYR cc_start: 0.8647 (t80) cc_final: 0.8202 (t80)
REVERT: C   70 TRP cc_start: 0.8108 (OUTLIER) cc_final: 0.7018 (p-90)
REVERT: C   71 CYS cc_start: 0.7847 (m) cc_final: 0.7055 (m)
REVERT: C   97 ARG cc_start: 0.9267 (ttt180) cc_final: 0.9015 (ttt180)
REVERT: C  112 PHE cc_start: 0.9189 (t80) cc_final: 0.8781 (t80)
REVERT: C  161 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8420 (tp30)
REVERT: C  183 ASP cc_start: 0.9113 (p0) cc_final: 0.8629 (p0)
REVERT: C  185 LYS cc_start: 0.9050 (mmtm) cc_final: 0.8770 (mmtm)
REVERT: C  188 ASP cc_start: 0.9222 (m-30) cc_final: 0.8771 (t0)
REVERT: C  195 ASN cc_start: 0.9485 (m-40) cc_final: 0.9098 (p0)
REVERT: C  209 TYR cc_start: 0.8682 (t80) cc_final: 0.7961 (t80)
REVERT: D   18 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8156 (tm-30)
REVERT: D   24 ARG cc_start: 0.8815 (ttp80) cc_final: 0.8502 (ttp80)
REVERT: D  101 ASP cc_start: 0.8847 (t0) cc_final: 0.7970 (p0)
REVERT: D  132 ARG cc_start: 0.8934 (tmt170) cc_final: 0.8582 (tmm-80)
REVERT: D  139 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8273 (tm-30)
REVERT: D  185 LYS cc_start: 0.8786 (ptpp) cc_final: 0.8384 (ptpp)
  outliers start: 46
  outliers final: 36
  residues processed: 184
  average time/residue: 0.1078
  time to fit residues: 26.3922
Evaluate side-chains
  185 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 145
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ILE
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  109 ARG
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain B residue   31 TRP
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   33 ASP
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain B residue   97 ARG
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 B residue  206 VAL
Chi-restraints excluded: chain B residue  254 MET
Chi-restraints excluded: chain C residue   12 ASP
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue   70 TRP
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  174 LEU
Chi-restraints excluded: chain C residue  229 THR
Chi-restraints excluded: chain D residue   12 ASP
Chi-restraints excluded: chain D residue   27 LEU
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  164 VAL
Chi-restraints excluded: chain D residue  188 ASP
Chi-restraints excluded: chain D residue  206 VAL
Chi-restraints excluded: chain D residue  254 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 61 optimal weight:   20.0000
   chunk 8 optimal weight:    5.9990
   chunk 50 optimal weight:    0.1980
   chunk 22 optimal weight:    9.9990
   chunk 35 optimal weight:    0.9990
   chunk 96 optimal weight:    2.9990
   chunk 84 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 66 optimal weight:    9.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 234 ASN
** C  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3501 r_free = 0.3501 target = 0.091041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.064636 restraints weight = 19014.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.2992 rms_B_bonded: 3.57
r_work: 0.2854 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8553
moved from start:          0.4659

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= 0.118
  Angle     :  0.635  10.947  11783  Z= 0.315
  Chirality :  0.045   0.163   1312
  Planarity :  0.004   0.045   1459
  Dihedral  :  9.093  74.962   1221
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 28.62 %
    Favored  : 67.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.29), residues: 1000
  helix:  0.88 (0.32), residues: 322
  sheet: -0.76 (0.36), residues: 232
  loop :  0.75 (0.33), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 148 
 TYR   0.026   0.002   TYR A  79 
 PHE   0.012   0.001   PHE C  57 
 TRP   0.020   0.001   TRP C  31 
 HIS   0.002   0.000   HIS A  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 8648)
  covalent geometry    : angle       0.63458 (11783)
  hydrogen bonds       : bond        0.03204 (  261)
  hydrogen bonds       : angle       4.66625 (  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
  191 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 155
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 PHE cc_start: 0.8982 (t80) cc_final: 0.8417 (t80)
REVERT: A   79 TYR cc_start: 0.9273 (t80) cc_final: 0.8997 (t80)
REVERT: A   97 ARG cc_start: 0.8112 (mtp180) cc_final: 0.7859 (mtp180)
REVERT: A  109 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8077 (mmm160)
REVERT: A  119 ARG cc_start: 0.9046 (ttp-110) cc_final: 0.8304 (ptp90)
REVERT: A  122 TYR cc_start: 0.8717 (p90) cc_final: 0.8441 (p90)
REVERT: A  185 LYS cc_start: 0.9167 (ptpp) cc_final: 0.8736 (ptmt)
REVERT: A  239 GLU cc_start: 0.8403 (mt-10) cc_final: 0.7812 (mp0)
REVERT: B   33 ASP cc_start: 0.6518 (OUTLIER) cc_final: 0.6019 (p0)
REVERT: B   97 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.6936 (tpt-90)
REVERT: B  139 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8323 (tm-30)
REVERT: C   11 LYS cc_start: 0.9528 (mmtm) cc_final: 0.9184 (mttp)
REVERT: C   45 GLN cc_start: 0.8867 (pm20) cc_final: 0.8426 (pm20)
REVERT: C   70 TRP cc_start: 0.8089 (OUTLIER) cc_final: 0.6953 (p-90)
REVERT: C   71 CYS cc_start: 0.7742 (m) cc_final: 0.6920 (m)
REVERT: C  112 PHE cc_start: 0.9164 (t80) cc_final: 0.8808 (t80)
REVERT: C  161 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8342 (tp30)
REVERT: C  183 ASP cc_start: 0.9072 (p0) cc_final: 0.8618 (p0)
REVERT: C  185 LYS cc_start: 0.9051 (mmtm) cc_final: 0.8756 (mmtm)
REVERT: C  188 ASP cc_start: 0.9189 (m-30) cc_final: 0.8729 (t0)
REVERT: C  195 ASN cc_start: 0.9464 (m-40) cc_final: 0.9083 (p0)
REVERT: C  209 TYR cc_start: 0.8554 (t80) cc_final: 0.7878 (t80)
REVERT: D   24 ARG cc_start: 0.8846 (ttp80) cc_final: 0.8541 (ttp80)
REVERT: D  101 ASP cc_start: 0.8843 (t0) cc_final: 0.7991 (p0)
REVERT: D  132 ARG cc_start: 0.8941 (tmt170) cc_final: 0.8590 (tmm-80)
REVERT: D  139 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8275 (tm-30)
REVERT: D  185 LYS cc_start: 0.8828 (ptpp) cc_final: 0.8422 (ptpp)
  outliers start: 36
  outliers final: 30
  residues processed: 180
  average time/residue: 0.1100
  time to fit residues: 25.9504
Evaluate side-chains
  181 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 147
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ILE
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  109 ARG
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   33 ASP
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain B residue   97 ARG
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 B residue  206 VAL
Chi-restraints excluded: chain B residue  254 MET
Chi-restraints excluded: chain C residue   12 ASP
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue   70 TRP
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  174 LEU
Chi-restraints excluded: chain D residue   12 ASP
Chi-restraints excluded: chain D residue   27 LEU
Chi-restraints excluded: chain D residue   31 TRP
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  106 THR
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:    0.1980
   chunk 80 optimal weight:    0.4980
   chunk 11 optimal weight:    7.9990
   chunk 73 optimal weight:   10.0000
   chunk 51 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 27 optimal weight:    0.4980
   chunk 81 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 234 ASN
B  22 HIS
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.092461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.066073 restraints weight = 19056.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 3.63
r_work: 0.2874 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.4764

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= 0.118
  Angle     :  0.644  11.513  11783  Z= 0.324
  Chirality :  0.045   0.149   1312
  Planarity :  0.004   0.041   1459
  Dihedral  :  9.044  75.246   1221
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 29.62 %
    Favored  : 66.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.29), residues: 1000
  helix:  0.95 (0.32), residues: 320
  sheet: -0.72 (0.36), residues: 232
  loop :  0.74 (0.33), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 148 
 TYR   0.023   0.002   TYR A  79 
 PHE   0.010   0.001   PHE C  57 
 TRP   0.022   0.001   TRP B  31 
 HIS   0.003   0.000   HIS B  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 8648)
  covalent geometry    : angle       0.64407 (11783)
  hydrogen bonds       : bond        0.03242 (  261)
  hydrogen bonds       : angle       4.68702 (  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
  196 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 163
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 LYS cc_start: 0.9212 (mmtt) cc_final: 0.8891 (mptt)
REVERT: A   57 PHE cc_start: 0.8998 (t80) cc_final: 0.8423 (t80)
REVERT: A   97 ARG cc_start: 0.8086 (mtp180) cc_final: 0.7833 (mtp180)
REVERT: A  109 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8075 (mmm160)
REVERT: A  119 ARG cc_start: 0.9102 (ttp-110) cc_final: 0.8330 (ptp90)
REVERT: A  122 TYR cc_start: 0.8715 (p90) cc_final: 0.8433 (p90)
REVERT: A  185 LYS cc_start: 0.9132 (ptpp) cc_final: 0.8702 (ptmt)
REVERT: A  239 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7762 (mp0)
REVERT: B   33 ASP cc_start: 0.6439 (OUTLIER) cc_final: 0.5880 (p0)
REVERT: B   97 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.6946 (tpt-90)
REVERT: B  139 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8106 (tm-30)
REVERT: C   11 LYS cc_start: 0.9514 (mmtm) cc_final: 0.9169 (mttp)
REVERT: C   45 GLN cc_start: 0.8868 (pm20) cc_final: 0.8437 (pm20)
REVERT: C   65 TYR cc_start: 0.8598 (t80) cc_final: 0.8220 (t80)
REVERT: C   70 TRP cc_start: 0.8083 (OUTLIER) cc_final: 0.6842 (p-90)
REVERT: C   71 CYS cc_start: 0.7772 (m) cc_final: 0.6979 (m)
REVERT: C  112 PHE cc_start: 0.9164 (t80) cc_final: 0.8741 (t80)
REVERT: C  114 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8771 (mp0)
REVERT: C  161 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8357 (tp30)
REVERT: C  183 ASP cc_start: 0.9062 (p0) cc_final: 0.8604 (p0)
REVERT: C  185 LYS cc_start: 0.9006 (mmtm) cc_final: 0.8709 (mmtm)
REVERT: C  188 ASP cc_start: 0.9195 (m-30) cc_final: 0.8710 (t0)
REVERT: C  195 ASN cc_start: 0.9473 (m-40) cc_final: 0.9064 (p0)
REVERT: C  209 TYR cc_start: 0.8505 (t80) cc_final: 0.7788 (t80)
REVERT: D   24 ARG cc_start: 0.8824 (ttp80) cc_final: 0.8515 (ttp80)
REVERT: D   72 TRP cc_start: 0.8511 (OUTLIER) cc_final: 0.8265 (t-100)
REVERT: D  101 ASP cc_start: 0.8842 (t0) cc_final: 0.8032 (p0)
REVERT: D  132 ARG cc_start: 0.8936 (tmt170) cc_final: 0.8558 (tmm-80)
REVERT: D  139 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8265 (tm-30)
REVERT: D  185 LYS cc_start: 0.8808 (ptpp) cc_final: 0.8379 (ptpp)
  outliers start: 33
  outliers final: 27
  residues processed: 186
  average time/residue: 0.1137
  time to fit residues: 27.9861
Evaluate side-chains
  184 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 152
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
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  109 ARG
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   33 ASP
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain B residue   97 ARG
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 B residue  206 VAL
Chi-restraints excluded: chain C residue   12 ASP
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue   70 TRP
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  174 LEU
Chi-restraints excluded: chain D residue   27 LEU
Chi-restraints excluded: chain D residue   72 TRP
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  174 LEU
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:    5.9990
   chunk 63 optimal weight:    4.9990
   chunk 88 optimal weight:    0.7980
   chunk 29 optimal weight:   10.0000
   chunk 60 optimal weight:    4.9990
   chunk 33 optimal weight:    7.9990
   chunk 95 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0470
   chunk 45 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   overall best weight:    0.9684

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3516 r_free = 0.3516 target = 0.092348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.066186 restraints weight = 19068.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.3014 rms_B_bonded: 3.63
r_work: 0.2879 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.4830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8648  Z= 0.125
  Angle     :  0.660  11.476  11783  Z= 0.331
  Chirality :  0.045   0.161   1312
  Planarity :  0.004   0.044   1459
  Dihedral  :  9.012  76.228   1221
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 29.62 %
    Favored  : 66.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.29), residues: 1000
  helix:  1.01 (0.32), residues: 314
  sheet: -0.70 (0.36), residues: 232
  loop :  0.86 (0.33), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 148 
 TYR   0.020   0.002   TYR C  56 
 PHE   0.009   0.001   PHE C  57 
 TRP   0.031   0.002   TRP C  72 
 HIS   0.002   0.000   HIS A  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8648)
  covalent geometry    : angle       0.66006 (11783)
  hydrogen bonds       : bond        0.03252 (  261)
  hydrogen bonds       : angle       4.63308 (  699)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 2217.63 seconds
wall clock time: 38 minutes 51.44 seconds (2331.44 seconds total)