Starting phenix.real_space_refine
on Sun May 11 22:30:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9muo_48639/05_2025/9muo_48639.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9muo_48639/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9muo_48639/05_2025/9muo_48639.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9muo_48639/05_2025/9muo_48639.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9muo_48639/05_2025/9muo_48639.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9muo_48639/05_2025/9muo_48639.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.37, per 1000 atoms: 0.88
  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: 2.26
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.95
  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: 2.29

  Time building geometry restraints manager: 2.62 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:             10.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     24.550
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.760
-------------------------------------------------------------------------------
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 : 14.39
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.012   0.001   TRP C  31 
 HIS   0.001   0.000   HIS C   8 
 PHE   0.015   0.001   PHE C   6 
 TYR   0.015   0.001   TYR D 122 
 ARG   0.007   0.001   ARG C 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.30607 (  261)
  hydrogen bonds       : angle       8.36780 (  699)
  covalent geometry    : bond        0.00456 ( 8648)
  covalent geometry    : angle       0.81399 (11783)

*********************** 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  : 0.983 
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: 0.8036 (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: 0.9076 (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: 0.8686 (pttm)
  outliers start: 13
  outliers final: 2
  residues processed: 264
  average time/residue: 0.2258
  time to fit residues: 78.7559
Evaluate side-chains
  187 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 183
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
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 82 optimal weight:    7.9990
   chunk 74 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9990
   chunk 25 optimal weight:    5.9990
   chunk 50 optimal weight:    9.9990
   chunk 39 optimal weight:    6.9990
   chunk 76 optimal weight:    0.0040
   chunk 29 optimal weight:   10.0000
   chunk 46 optimal weight:    7.9990
   chunk 57 optimal weight:    8.9990
   chunk 88 optimal weight:    0.0070
   overall best weight:    2.8016

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

Flipped N/Q/H residues before XYZ refinement:
A 234 ASN
B  46 GLN
B 234 ASN
C 234 ASN
D 234 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.094188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.066555 restraints weight = 19037.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3036 rms_B_bonded: 3.58
r_work: 0.2907 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8647
moved from start:          0.2694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8648  Z= 0.189
  Angle     :  0.672   7.630  11783  Z= 0.341
  Chirality :  0.047   0.230   1312
  Planarity :  0.006   0.053   1459
  Dihedral  :  9.955  81.247   1226
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 28.73 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.28), residues: 1000
  helix:  0.40 (0.30), residues: 324
  sheet: -0.12 (0.37), residues: 224
  loop :  0.17 (0.32), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C  70 
 HIS   0.005   0.001   HIS C  22 
 PHE   0.011   0.001   PHE C  60 
 TYR   0.026   0.002   TYR A  79 
 ARG   0.007   0.001   ARG D 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05112 (  261)
  hydrogen bonds       : angle       5.22399 (  699)
  covalent geometry    : bond        0.00446 ( 8648)
  covalent geometry    : angle       0.67240 (11783)

*********************** 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
  230 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 196
  time to evaluate  : 1.025 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 PHE cc_start: 0.8988 (t80) cc_final: 0.8431 (t80)
REVERT: A  143 GLN cc_start: 0.8974 (tm-30) cc_final: 0.8709 (tm-30)
REVERT: A  185 LYS cc_start: 0.9231 (ptpp) cc_final: 0.8852 (ptmt)
REVERT: B  119 ARG cc_start: 0.8870 (ttp-110) cc_final: 0.8637 (ptp-110)
REVERT: C   11 LYS cc_start: 0.9462 (mmtm) cc_final: 0.9107 (mttp)
REVERT: C   70 TRP cc_start: 0.8154 (OUTLIER) cc_final: 0.7831 (p-90)
REVERT: C  112 PHE cc_start: 0.9261 (t80) cc_final: 0.8951 (t80)
REVERT: C  129 ASN cc_start: 0.8427 (t0) cc_final: 0.7779 (t0)
REVERT: C  142 TRP cc_start: 0.9161 (m100) cc_final: 0.8260 (m100)
REVERT: C  143 GLN cc_start: 0.9211 (tt0) cc_final: 0.8537 (tm-30)
REVERT: C  195 ASN cc_start: 0.9399 (m-40) cc_final: 0.9075 (p0)
REVERT: C  209 TYR cc_start: 0.8800 (t80) cc_final: 0.8087 (t80)
REVERT: D   24 ARG cc_start: 0.8785 (ttp80) cc_final: 0.8354 (ttp80)
REVERT: D   97 ARG cc_start: 0.8716 (tpt-90) cc_final: 0.8451 (ttt180)
REVERT: D  101 ASP cc_start: 0.8853 (t0) cc_final: 0.8053 (p0)
REVERT: D  119 ARG cc_start: 0.9542 (ttp-110) cc_final: 0.9223 (ptp90)
REVERT: D  132 ARG cc_start: 0.8935 (tmt170) cc_final: 0.8618 (tmm-80)
REVERT: D  154 MET cc_start: 0.9131 (mtp) cc_final: 0.8589 (mtp)
REVERT: D  161 GLU cc_start: 0.8714 (tp30) cc_final: 0.8255 (tp30)
REVERT: D  185 LYS cc_start: 0.9047 (ptpp) cc_final: 0.8788 (pttm)
  outliers start: 34
  outliers final: 20
  residues processed: 220
  average time/residue: 0.2307
  time to fit residues: 67.4054
Evaluate side-chains
  201 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 180
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ILE
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 B residue   32 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain C residue   70 TRP
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  174 LEU
Chi-restraints excluded: chain D residue   30 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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0980
   chunk 43 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 20 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9990
   chunk 19 optimal weight:    8.9990
   chunk 26 optimal weight:    3.9990
   chunk 24 optimal weight:   10.0000
   chunk 53 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
A 234 ASN
D  22 HIS
D 234 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.096629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.069654 restraints weight = 19225.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 3.60
r_work: 0.2952 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.3142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8648  Z= 0.115
  Angle     :  0.612   8.358  11783  Z= 0.305
  Chirality :  0.045   0.148   1312
  Planarity :  0.005   0.046   1459
  Dihedral  :  9.375  78.564   1221
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 27.95 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.28), residues: 1000
  helix:  0.42 (0.30), residues: 328
  sheet: -0.44 (0.36), residues: 232
  loop :  0.39 (0.32), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C  70 
 HIS   0.004   0.001   HIS A  82 
 PHE   0.013   0.001   PHE C  57 
 TYR   0.020   0.002   TYR A  79 
 ARG   0.007   0.001   ARG D 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04195 (  261)
  hydrogen bonds       : angle       4.94140 (  699)
  covalent geometry    : bond        0.00265 ( 8648)
  covalent geometry    : angle       0.61170 (11783)

*********************** 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
  235 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 196
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 TYR cc_start: 0.9443 (t80) cc_final: 0.9195 (t80)
REVERT: A  166 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8293 (tp30)
REVERT: C    9 ASN cc_start: 0.8811 (t0) cc_final: 0.8085 (m-40)
REVERT: C   11 LYS cc_start: 0.9450 (mmtm) cc_final: 0.9035 (mtmt)
REVERT: C   14 LYS cc_start: 0.9410 (tppt) cc_final: 0.8791 (tppt)
REVERT: C   18 GLU cc_start: 0.9373 (tt0) cc_final: 0.9017 (pt0)
REVERT: C   47 ILE cc_start: 0.8515 (mm) cc_final: 0.8170 (mm)
REVERT: C   65 TYR cc_start: 0.8707 (t80) cc_final: 0.7855 (t80)
REVERT: C   70 TRP cc_start: 0.8165 (OUTLIER) cc_final: 0.7521 (p-90)
REVERT: C   71 CYS cc_start: 0.7550 (m) cc_final: 0.6736 (m)
REVERT: C  122 TYR cc_start: 0.8903 (p90) cc_final: 0.8577 (p90)
REVERT: C  129 ASN cc_start: 0.8354 (t0) cc_final: 0.7918 (t0)
REVERT: C  130 MET cc_start: 0.8631 (tpt) cc_final: 0.8291 (tpp)
REVERT: C  142 TRP cc_start: 0.9065 (m100) cc_final: 0.8267 (m100)
REVERT: C  166 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8607 (tp30)
REVERT: C  183 ASP cc_start: 0.8988 (p0) cc_final: 0.8661 (p0)
REVERT: C  195 ASN cc_start: 0.9439 (m-40) cc_final: 0.9088 (p0)
REVERT: C  209 TYR cc_start: 0.8652 (t80) cc_final: 0.7614 (t80)
REVERT: D   24 ARG cc_start: 0.8770 (ttp80) cc_final: 0.8237 (ttp80)
REVERT: D   31 TRP cc_start: 0.9107 (m100) cc_final: 0.8596 (m100)
REVERT: D   71 CYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8349 (p)
REVERT: D  101 ASP cc_start: 0.8832 (t0) cc_final: 0.8016 (p0)
REVERT: D  132 ARG cc_start: 0.8952 (tmt170) cc_final: 0.8583 (tmm-80)
REVERT: D  154 MET cc_start: 0.9184 (mtp) cc_final: 0.8627 (mtp)
REVERT: D  161 GLU cc_start: 0.8631 (tp30) cc_final: 0.8231 (tp30)
REVERT: D  183 ASP cc_start: 0.8960 (p0) cc_final: 0.8725 (p0)
REVERT: D  185 LYS cc_start: 0.8983 (ptpp) cc_final: 0.8706 (pttm)
  outliers start: 39
  outliers final: 22
  residues processed: 221
  average time/residue: 0.2230
  time to fit residues: 65.2528
Evaluate side-chains
  200 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 174
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 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  176 VAL
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  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   70 TRP
Chi-restraints excluded: chain C residue   81 LEU
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  176 VAL
Chi-restraints excluded: chain C residue  229 THR
Chi-restraints excluded: chain D residue   71 CYS
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  164 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 1 optimal weight:   10.0000
   chunk 29 optimal weight:    7.9990
   chunk 51 optimal weight:   10.0000
   chunk 58 optimal weight:   20.0000
   chunk 84 optimal weight:    0.7980
   chunk 82 optimal weight:    6.9990
   chunk 52 optimal weight:    0.0670
   chunk 21 optimal weight:    7.9990
   chunk 33 optimal weight:    0.0870
   chunk 19 optimal weight:    5.9990
   overall best weight:    1.5298

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.094565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.068273 restraints weight = 18915.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3054 rms_B_bonded: 3.44
r_work: 0.2926 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.3527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8648  Z= 0.127
  Angle     :  0.604   7.923  11783  Z= 0.299
  Chirality :  0.045   0.148   1312
  Planarity :  0.004   0.049   1459
  Dihedral  :  9.097  82.726   1221
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 26.61 %
    Favored  : 68.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.29), residues: 1000
  helix:  0.60 (0.31), residues: 328
  sheet: -0.67 (0.36), residues: 240
  loop :  0.58 (0.33), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C  70 
 HIS   0.003   0.001   HIS B  22 
 PHE   0.022   0.001   PHE C 112 
 TYR   0.016   0.001   TYR C 244 
 ARG   0.007   0.001   ARG D 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03537 (  261)
  hydrogen bonds       : angle       4.76497 (  699)
  covalent geometry    : bond        0.00304 ( 8648)
  covalent geometry    : angle       0.60431 (11783)

*********************** 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
  224 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 184
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 ASP cc_start: 0.8870 (t0) cc_final: 0.8564 (t0)
REVERT: A  166 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8275 (tp30)
REVERT: A  185 LYS cc_start: 0.9195 (ptpp) cc_final: 0.8774 (ptmt)
REVERT: C   11 LYS cc_start: 0.9476 (mmtm) cc_final: 0.9056 (mttp)
REVERT: C   70 TRP cc_start: 0.8250 (OUTLIER) cc_final: 0.7429 (p-90)
REVERT: C   71 CYS cc_start: 0.7542 (m) cc_final: 0.6863 (m)
REVERT: C   97 ARG cc_start: 0.9278 (ttt180) cc_final: 0.9012 (ttt180)
REVERT: C  122 TYR cc_start: 0.8969 (p90) cc_final: 0.8522 (p90)
REVERT: C  129 ASN cc_start: 0.8482 (t0) cc_final: 0.7866 (t0)
REVERT: C  130 MET cc_start: 0.8628 (tpt) cc_final: 0.8360 (tpp)
REVERT: C  142 TRP cc_start: 0.9089 (m100) cc_final: 0.8301 (m100)
REVERT: C  183 ASP cc_start: 0.8978 (p0) cc_final: 0.8691 (p0)
REVERT: C  188 ASP cc_start: 0.8982 (m-30) cc_final: 0.8708 (t0)
REVERT: C  195 ASN cc_start: 0.9439 (m-40) cc_final: 0.9104 (p0)
REVERT: C  209 TYR cc_start: 0.8651 (t80) cc_final: 0.7645 (t80)
REVERT: D   24 ARG cc_start: 0.8818 (ttp80) cc_final: 0.8310 (ttp80)
REVERT: D   31 TRP cc_start: 0.9161 (m100) cc_final: 0.8629 (m100)
REVERT: D   71 CYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8449 (p)
REVERT: D  101 ASP cc_start: 0.8812 (t0) cc_final: 0.8013 (p0)
REVERT: D  132 ARG cc_start: 0.8949 (tmt170) cc_final: 0.8562 (tmm-80)
REVERT: D  183 ASP cc_start: 0.8992 (p0) cc_final: 0.8776 (p0)
REVERT: D  185 LYS cc_start: 0.8966 (ptpp) cc_final: 0.8675 (pttm)
  outliers start: 40
  outliers final: 26
  residues processed: 211
  average time/residue: 0.2364
  time to fit residues: 65.6991
Evaluate side-chains
  201 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 172
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
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   32 ILE
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue   81 LEU
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  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   77 GLN
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  174 LEU
Chi-restraints excluded: chain C residue  176 VAL
Chi-restraints excluded: chain C residue  229 THR
Chi-restraints excluded: chain D residue   71 CYS
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  119 ARG
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 54 optimal weight:    9.9990
   chunk 77 optimal weight:    8.9990
   chunk 55 optimal weight:   10.0000
   chunk 51 optimal weight:    8.9990
   chunk 46 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9990
   chunk 52 optimal weight:    8.9990
   chunk 23 optimal weight:    0.4980
   chunk 12 optimal weight:   20.0000
   overall best weight:    3.0988

-------------------------------------------------------------------------------
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  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.091231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.064498 restraints weight = 19175.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 3.39
r_work: 0.2876 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8688
moved from start:          0.4067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8648  Z= 0.192
  Angle     :  0.642   8.174  11783  Z= 0.319
  Chirality :  0.046   0.154   1312
  Planarity :  0.004   0.047   1459
  Dihedral  :  9.100  88.686   1221
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 26.17 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.29), residues: 1000
  helix:  0.84 (0.31), residues: 322
  sheet: -0.77 (0.36), residues: 240
  loop :  0.60 (0.33), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  31 
 HIS   0.003   0.001   HIS C   8 
 PHE   0.018   0.001   PHE C 112 
 TYR   0.035   0.002   TYR A  79 
 ARG   0.008   0.001   ARG D 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03636 (  261)
  hydrogen bonds       : angle       4.76522 (  699)
  covalent geometry    : bond        0.00452 ( 8648)
  covalent geometry    : angle       0.64177 (11783)

*********************** 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
  206 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 161
  time to evaluate  : 1.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8353 (tp30)
REVERT: A  185 LYS cc_start: 0.9222 (ptpp) cc_final: 0.8825 (ptmt)
REVERT: C   11 LYS cc_start: 0.9505 (mmtm) cc_final: 0.9126 (mttp)
REVERT: C   70 TRP cc_start: 0.8151 (OUTLIER) cc_final: 0.7194 (p-90)
REVERT: C   71 CYS cc_start: 0.7657 (m) cc_final: 0.6991 (m)
REVERT: C   72 TRP cc_start: 0.8404 (m100) cc_final: 0.8172 (m100)
REVERT: C  119 ARG cc_start: 0.9062 (ptp90) cc_final: 0.8858 (ptp90)
REVERT: C  129 ASN cc_start: 0.8496 (t0) cc_final: 0.7909 (t0)
REVERT: C  130 MET cc_start: 0.8696 (tpt) cc_final: 0.8478 (tpp)
REVERT: C  142 TRP cc_start: 0.9137 (m100) cc_final: 0.8119 (m100)
REVERT: C  161 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8433 (tp30)
REVERT: C  183 ASP cc_start: 0.9043 (p0) cc_final: 0.8506 (p0)
REVERT: C  188 ASP cc_start: 0.9186 (m-30) cc_final: 0.8730 (t0)
REVERT: C  195 ASN cc_start: 0.9417 (m-40) cc_final: 0.9078 (p0)
REVERT: C  209 TYR cc_start: 0.8628 (t80) cc_final: 0.7963 (t80)
REVERT: C  257 LYS cc_start: 0.6933 (tptt) cc_final: 0.6685 (tmtt)
REVERT: D   24 ARG cc_start: 0.8929 (ttp80) cc_final: 0.8384 (ttp80)
REVERT: D  101 ASP cc_start: 0.8841 (t0) cc_final: 0.8021 (p0)
REVERT: D  130 MET cc_start: 0.8897 (tpp) cc_final: 0.8676 (tpp)
REVERT: D  132 ARG cc_start: 0.8943 (tmt170) cc_final: 0.8597 (tmm-80)
REVERT: D  185 LYS cc_start: 0.8955 (ptpp) cc_final: 0.8598 (ptpp)
  outliers start: 45
  outliers final: 35
  residues processed: 194
  average time/residue: 0.2405
  time to fit residues: 61.5975
Evaluate side-chains
  187 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 150
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
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 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   72 TRP
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  121 LYS
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  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   77 GLN
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  174 LEU
Chi-restraints excluded: chain C residue  221 THR
Chi-restraints excluded: chain D residue   12 ASP
Chi-restraints excluded: chain D residue   71 CYS
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 87 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 90 optimal weight:    8.9990
   chunk 34 optimal weight:   10.0000
   chunk 74 optimal weight:    1.9990
   chunk 81 optimal weight:    5.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
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 234 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.089352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.062382 restraints weight = 18994.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.2937 rms_B_bonded: 3.52
r_work: 0.2800 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.4311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8648  Z= 0.183
  Angle     :  0.636   7.808  11783  Z= 0.316
  Chirality :  0.046   0.151   1312
  Planarity :  0.004   0.041   1459
  Dihedral  :  9.101  84.069   1221
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 27.51 %
    Favored  : 67.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.29), residues: 1000
  helix:  0.86 (0.32), residues: 322
  sheet: -0.87 (0.36), residues: 240
  loop :  0.70 (0.33), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C  70 
 HIS   0.003   0.001   HIS A  82 
 PHE   0.016   0.001   PHE C 112 
 TYR   0.021   0.002   TYR C 122 
 ARG   0.008   0.001   ARG D 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03516 (  261)
  hydrogen bonds       : angle       4.69250 (  699)
  covalent geometry    : bond        0.00439 ( 8648)
  covalent geometry    : angle       0.63615 (11783)

*********************** 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
  212 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 164
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 LYS cc_start: 0.9204 (mmtt) cc_final: 0.8983 (mmtm)
REVERT: A  143 GLN cc_start: 0.8968 (tm-30) cc_final: 0.8697 (pp30)
REVERT: A  185 LYS cc_start: 0.9211 (ptpp) cc_final: 0.8758 (ptmt)
REVERT: B   33 ASP cc_start: 0.6343 (OUTLIER) cc_final: 0.5795 (p0)
REVERT: C   11 LYS cc_start: 0.9531 (mmtm) cc_final: 0.9157 (mttp)
REVERT: C   45 GLN cc_start: 0.9000 (pm20) cc_final: 0.8628 (pm20)
REVERT: C   70 TRP cc_start: 0.8147 (OUTLIER) cc_final: 0.7229 (p-90)
REVERT: C   71 CYS cc_start: 0.7666 (m) cc_final: 0.7404 (m)
REVERT: C   97 ARG cc_start: 0.9111 (ttt180) cc_final: 0.8746 (ttt180)
REVERT: C  122 TYR cc_start: 0.8974 (p90) cc_final: 0.8387 (p90)
REVERT: C  129 ASN cc_start: 0.8515 (t0) cc_final: 0.7918 (t0)
REVERT: C  161 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8473 (tp30)
REVERT: C  183 ASP cc_start: 0.9128 (p0) cc_final: 0.8632 (p0)
REVERT: C  188 ASP cc_start: 0.9219 (m-30) cc_final: 0.8737 (t0)
REVERT: C  195 ASN cc_start: 0.9488 (m-40) cc_final: 0.9108 (p0)
REVERT: C  209 TYR cc_start: 0.8745 (t80) cc_final: 0.8007 (t80)
REVERT: C  257 LYS cc_start: 0.7040 (tptt) cc_final: 0.6729 (tmtt)
REVERT: D   24 ARG cc_start: 0.8841 (ttp80) cc_final: 0.8309 (ttp80)
REVERT: D  101 ASP cc_start: 0.8865 (t0) cc_final: 0.8001 (p0)
REVERT: D  132 ARG cc_start: 0.8959 (tmt170) cc_final: 0.8597 (tmm-80)
REVERT: D  154 MET cc_start: 0.9344 (mtp) cc_final: 0.8821 (mtp)
REVERT: D  185 LYS cc_start: 0.8889 (ptpp) cc_final: 0.8458 (ptpp)
  outliers start: 48
  outliers final: 35
  residues processed: 199
  average time/residue: 0.2276
  time to fit residues: 59.9675
Evaluate side-chains
  191 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 154
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
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  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  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   77 GLN
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  174 LEU
Chi-restraints excluded: chain D residue   12 ASP
Chi-restraints excluded: chain D residue   27 LEU
Chi-restraints excluded: chain D residue   71 CYS
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  119 ARG
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 9 optimal weight:   10.0000
   chunk 11 optimal weight:    5.9990
   chunk 6 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 17 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 36 optimal weight:    6.9990
   chunk 94 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.090129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.063500 restraints weight = 19250.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.2952 rms_B_bonded: 3.63
r_work: 0.2814 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.4444

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= 0.132
  Angle     :  0.639  10.937  11783  Z= 0.316
  Chirality :  0.045   0.176   1312
  Planarity :  0.004   0.041   1459
  Dihedral  :  9.056  77.648   1221
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 27.84 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.29), residues: 1000
  helix:  0.93 (0.31), residues: 320
  sheet: -0.89 (0.36), residues: 240
  loop :  0.75 (0.33), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C  70 
 HIS   0.002   0.001   HIS A  82 
 PHE   0.014   0.001   PHE C 112 
 TYR   0.020   0.002   TYR C 122 
 ARG   0.007   0.001   ARG D 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03395 (  261)
  hydrogen bonds       : angle       4.65622 (  699)
  covalent geometry    : bond        0.00317 ( 8648)
  covalent geometry    : angle       0.63879 (11783)

*********************** 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
  211 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 169
  time to evaluate  : 1.031 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.5491 (pp30) cc_final: 0.4828 (pp30)
REVERT: A   99 GLN cc_start: 0.9281 (pp30) cc_final: 0.8769 (pm20)
REVERT: A  101 ASP cc_start: 0.8942 (t0) cc_final: 0.8558 (t0)
REVERT: A  119 ARG cc_start: 0.9340 (mtm110) cc_final: 0.8835 (ptp90)
REVERT: A  166 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8244 (tp30)
REVERT: A  185 LYS cc_start: 0.9175 (ptpp) cc_final: 0.8741 (ptmt)
REVERT: A  239 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7825 (mp0)
REVERT: B  130 MET cc_start: 0.8509 (tpp) cc_final: 0.7992 (tpp)
REVERT: C   11 LYS cc_start: 0.9527 (mmtm) cc_final: 0.9148 (mttp)
REVERT: C   45 GLN cc_start: 0.8955 (pm20) cc_final: 0.8562 (pm20)
REVERT: C   65 TYR cc_start: 0.8545 (t80) cc_final: 0.8271 (t80)
REVERT: C   70 TRP cc_start: 0.8170 (OUTLIER) cc_final: 0.7102 (p-90)
REVERT: C   71 CYS cc_start: 0.7766 (m) cc_final: 0.7039 (m)
REVERT: C  114 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8797 (mp0)
REVERT: C  122 TYR cc_start: 0.8963 (p90) cc_final: 0.8360 (p90)
REVERT: C  129 ASN cc_start: 0.8474 (t0) cc_final: 0.8000 (t0)
REVERT: C  142 TRP cc_start: 0.9003 (m100) cc_final: 0.8066 (m100)
REVERT: C  183 ASP cc_start: 0.9111 (p0) cc_final: 0.8591 (p0)
REVERT: C  188 ASP cc_start: 0.9237 (m-30) cc_final: 0.8744 (t0)
REVERT: C  195 ASN cc_start: 0.9472 (m-40) cc_final: 0.9088 (p0)
REVERT: C  209 TYR cc_start: 0.8642 (t80) cc_final: 0.7959 (t80)
REVERT: C  257 LYS cc_start: 0.7066 (tptt) cc_final: 0.6735 (tmtt)
REVERT: D   18 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8228 (tm-30)
REVERT: D   24 ARG cc_start: 0.8795 (ttp80) cc_final: 0.8219 (ttp80)
REVERT: D  101 ASP cc_start: 0.8835 (t0) cc_final: 0.8003 (p0)
REVERT: D  130 MET cc_start: 0.8753 (tpp) cc_final: 0.8553 (tpp)
REVERT: D  132 ARG cc_start: 0.8910 (tmt170) cc_final: 0.8518 (tmm-80)
REVERT: D  154 MET cc_start: 0.9363 (mtp) cc_final: 0.8830 (mtp)
REVERT: D  185 LYS cc_start: 0.8830 (ptpp) cc_final: 0.8451 (ptpp)
  outliers start: 42
  outliers final: 32
  residues processed: 198
  average time/residue: 0.2367
  time to fit residues: 61.8744
Evaluate side-chains
  192 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 158
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
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   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  174 LEU
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   77 GLN
Chi-restraints excluded: chain C residue   81 LEU
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  176 VAL
Chi-restraints excluded: chain D residue   27 LEU
Chi-restraints excluded: chain D residue   71 CYS
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 83 optimal weight:    0.0020
   chunk 8 optimal weight:    8.9990
   chunk 67 optimal weight:    0.0980
   chunk 29 optimal weight:   10.0000
   chunk 38 optimal weight:    2.9990
   chunk 33 optimal weight:    8.9990
   chunk 42 optimal weight:    3.9990
   chunk 28 optimal weight:   10.0000
   chunk 51 optimal weight:    3.9990
   chunk 1 optimal weight:    7.9990
   chunk 71 optimal weight:    8.9990
   overall best weight:    2.2194

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

Flipped N/Q/H residues before XYZ refinement:
A  83 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 = 0.3466 r_free = 0.3466 target = 0.088978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.062075 restraints weight = 19278.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.2930 rms_B_bonded: 3.66
r_work: 0.2793 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.4606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8648  Z= 0.150
  Angle     :  0.631  10.395  11783  Z= 0.313
  Chirality :  0.045   0.161   1312
  Planarity :  0.004   0.044   1459
  Dihedral  :  9.039  76.090   1221
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 28.40 %
    Favored  : 67.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.29), residues: 1000
  helix:  0.96 (0.31), residues: 322
  sheet: -0.90 (0.36), residues: 240
  loop :  0.72 (0.33), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C  70 
 HIS   0.002   0.001   HIS D   8 
 PHE   0.013   0.001   PHE C 112 
 TYR   0.020   0.002   TYR C  56 
 ARG   0.008   0.000   ARG D 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03328 (  261)
  hydrogen bonds       : angle       4.66625 (  699)
  covalent geometry    : bond        0.00359 ( 8648)
  covalent geometry    : angle       0.63111 (11783)

*********************** 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
  192 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 153
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.5576 (pp30) cc_final: 0.4948 (pp30)
REVERT: A   99 GLN cc_start: 0.9290 (pp30) cc_final: 0.8744 (pm20)
REVERT: A  166 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8269 (tp30)
REVERT: A  185 LYS cc_start: 0.9178 (ptpp) cc_final: 0.8744 (ptmt)
REVERT: A  239 GLU cc_start: 0.8452 (mt-10) cc_final: 0.7845 (mp0)
REVERT: B  130 MET cc_start: 0.8425 (tpp) cc_final: 0.7952 (tpp)
REVERT: B  139 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8396 (tm-30)
REVERT: B  166 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8514 (tp30)
REVERT: C   11 LYS cc_start: 0.9529 (mmtm) cc_final: 0.9174 (mttp)
REVERT: C   45 GLN cc_start: 0.8919 (pm20) cc_final: 0.8529 (pm20)
REVERT: C   70 TRP cc_start: 0.8132 (OUTLIER) cc_final: 0.6980 (p-90)
REVERT: C   71 CYS cc_start: 0.7717 (m) cc_final: 0.6960 (m)
REVERT: C   97 ARG cc_start: 0.9112 (ttt180) cc_final: 0.8883 (ttt180)
REVERT: C  122 TYR cc_start: 0.9024 (p90) cc_final: 0.8472 (p90)
REVERT: C  183 ASP cc_start: 0.9121 (p0) cc_final: 0.8569 (p0)
REVERT: C  188 ASP cc_start: 0.9249 (m-30) cc_final: 0.8744 (t0)
REVERT: C  195 ASN cc_start: 0.9470 (m-40) cc_final: 0.9086 (p0)
REVERT: C  209 TYR cc_start: 0.8655 (t80) cc_final: 0.7998 (t80)
REVERT: C  257 LYS cc_start: 0.7116 (tptt) cc_final: 0.6820 (tmtt)
REVERT: D   24 ARG cc_start: 0.8799 (ttp80) cc_final: 0.8219 (ttp80)
REVERT: D  101 ASP cc_start: 0.8844 (t0) cc_final: 0.7983 (p0)
REVERT: D  130 MET cc_start: 0.8738 (tpp) cc_final: 0.8534 (tpp)
REVERT: D  132 ARG cc_start: 0.8916 (tmt170) cc_final: 0.8541 (tmm-80)
REVERT: D  185 LYS cc_start: 0.8829 (ptpp) cc_final: 0.8371 (ptpp)
  outliers start: 39
  outliers final: 31
  residues processed: 182
  average time/residue: 0.2313
  time to fit residues: 56.0929
Evaluate side-chains
  186 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 152
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
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   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 A residue  229 THR
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  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 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   77 GLN
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  174 LEU
Chi-restraints excluded: chain D residue   27 LEU
Chi-restraints excluded: chain D residue   71 CYS
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 87 optimal weight:    4.9990
   chunk 76 optimal weight:    9.9990
   chunk 32 optimal weight:    8.9990
   chunk 88 optimal weight:    2.9990
   chunk 69 optimal weight:    6.9990
   chunk 3 optimal weight:    0.0050
   chunk 55 optimal weight:    9.9990
   chunk 13 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    3.6002

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

Flipped N/Q/H residues before XYZ refinement:
** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3427 r_free = 0.3427 target = 0.086821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.059830 restraints weight = 19407.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.2881 rms_B_bonded: 3.61
r_work: 0.2741 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.4883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   8648  Z= 0.213
  Angle     :  0.673  10.674  11783  Z= 0.338
  Chirality :  0.046   0.163   1312
  Planarity :  0.005   0.052   1459
  Dihedral  :  9.204  76.551   1221
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 14.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 28.62 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.29), residues: 1000
  helix:  0.91 (0.31), residues: 320
  sheet: -1.08 (0.35), residues: 250
  loop :  0.73 (0.33), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B  31 
 HIS   0.003   0.001   HIS D   8 
 PHE   0.015   0.001   PHE B  60 
 TYR   0.024   0.002   TYR C 244 
 ARG   0.008   0.001   ARG D 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03502 (  261)
  hydrogen bonds       : angle       4.74680 (  699)
  covalent geometry    : bond        0.00509 ( 8648)
  covalent geometry    : angle       0.67303 (11783)

*********************** 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
  193 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 151
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 LYS cc_start: 0.9214 (mmtt) cc_final: 0.8916 (mptt)
REVERT: A   55 GLN cc_start: 0.5585 (pp30) cc_final: 0.4891 (pp30)
REVERT: A   99 GLN cc_start: 0.9298 (pp30) cc_final: 0.8716 (pm20)
REVERT: A  101 ASP cc_start: 0.9081 (t0) cc_final: 0.8766 (t0)
REVERT: A  132 ARG cc_start: 0.9002 (tmt170) cc_final: 0.8692 (tmm-80)
REVERT: A  166 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8293 (tp30)
REVERT: A  185 LYS cc_start: 0.9186 (ptpp) cc_final: 0.8751 (ptmt)
REVERT: B  130 MET cc_start: 0.8360 (tpp) cc_final: 0.8011 (tpp)
REVERT: B  139 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8194 (tm-30)
REVERT: B  166 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8576 (tp30)
REVERT: C   11 LYS cc_start: 0.9521 (mmtm) cc_final: 0.9214 (mttp)
REVERT: C   45 GLN cc_start: 0.8943 (pm20) cc_final: 0.8564 (pm20)
REVERT: C   70 TRP cc_start: 0.8103 (OUTLIER) cc_final: 0.6906 (p-90)
REVERT: C   71 CYS cc_start: 0.7800 (m) cc_final: 0.7030 (m)
REVERT: C  183 ASP cc_start: 0.9074 (p0) cc_final: 0.8789 (p0)
REVERT: C  188 ASP cc_start: 0.9246 (m-30) cc_final: 0.8745 (t0)
REVERT: C  195 ASN cc_start: 0.9473 (m-40) cc_final: 0.9081 (p0)
REVERT: C  209 TYR cc_start: 0.8777 (t80) cc_final: 0.8022 (t80)
REVERT: C  257 LYS cc_start: 0.7325 (tptt) cc_final: 0.6984 (tmtt)
REVERT: D   18 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8170 (tm-30)
REVERT: D   24 ARG cc_start: 0.8812 (ttp80) cc_final: 0.8212 (ttp80)
REVERT: D  101 ASP cc_start: 0.8830 (t0) cc_final: 0.7925 (p0)
REVERT: D  126 ASP cc_start: 0.8683 (p0) cc_final: 0.8447 (p0)
REVERT: D  132 ARG cc_start: 0.8918 (tmt170) cc_final: 0.8566 (tmm-80)
REVERT: D  154 MET cc_start: 0.9361 (mtp) cc_final: 0.9055 (mtp)
REVERT: D  185 LYS cc_start: 0.8853 (ptpp) cc_final: 0.8409 (ptpp)
  outliers start: 42
  outliers final: 32
  residues processed: 182
  average time/residue: 0.2285
  time to fit residues: 55.4423
Evaluate side-chains
  175 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 140
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
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   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 A residue  229 THR
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  166 GLU
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  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   77 GLN
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   71 CYS
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  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 47 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0770
   chunk 11 optimal weight:    0.0030
   chunk 32 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 2 optimal weight:   10.0000
   chunk 30 optimal weight:    6.9990
   chunk 17 optimal weight:    4.9990
   chunk 71 optimal weight:    5.9990
   chunk 33 optimal weight:   10.0000
   overall best weight:    1.4154

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

Flipped N/Q/H residues before XYZ refinement:
A 143 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 = 0.3457 r_free = 0.3457 target = 0.088858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.063051 restraints weight = 18795.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.2937 rms_B_bonded: 3.53
r_work: 0.2799 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.4917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8648  Z= 0.131
  Angle     :  0.649  10.288  11783  Z= 0.323
  Chirality :  0.045   0.167   1312
  Planarity :  0.005   0.050   1459
  Dihedral  :  9.155  77.083   1221
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 29.51 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.29), residues: 1000
  helix:  1.02 (0.32), residues: 314
  sheet: -1.10 (0.36), residues: 236
  loop :  0.95 (0.33), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B  31 
 HIS   0.002   0.000   HIS A  22 
 PHE   0.012   0.001   PHE C 112 
 TYR   0.022   0.002   TYR C  56 
 ARG   0.019   0.001   ARG C 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03291 (  261)
  hydrogen bonds       : angle       4.69798 (  699)
  covalent geometry    : bond        0.00318 ( 8648)
  covalent geometry    : angle       0.64909 (11783)

********************** 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
  192 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 158
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 LYS cc_start: 0.9242 (mmtt) cc_final: 0.8940 (mptt)
REVERT: A   55 GLN cc_start: 0.5441 (pp30) cc_final: 0.4873 (pp30)
REVERT: A   99 GLN cc_start: 0.9251 (pp30) cc_final: 0.8630 (pm20)
REVERT: A  101 ASP cc_start: 0.9122 (t0) cc_final: 0.8812 (t0)
REVERT: A  132 ARG cc_start: 0.8997 (tmt170) cc_final: 0.8716 (tmm-80)
REVERT: A  139 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8477 (tp30)
REVERT: A  166 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8283 (tp30)
REVERT: A  185 LYS cc_start: 0.9156 (ptpp) cc_final: 0.8729 (ptmt)
REVERT: A  239 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7838 (mp0)
REVERT: B  139 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8327 (tm-30)
REVERT: C   11 LYS cc_start: 0.9511 (mmtm) cc_final: 0.9225 (mttp)
REVERT: C   45 GLN cc_start: 0.8922 (pm20) cc_final: 0.8562 (pm20)
REVERT: C   70 TRP cc_start: 0.8039 (OUTLIER) cc_final: 0.6826 (p-90)
REVERT: C   71 CYS cc_start: 0.7730 (m) cc_final: 0.6996 (m)
REVERT: C  114 GLU cc_start: 0.9257 (mt-10) cc_final: 0.8784 (mp0)
REVERT: C  119 ARG cc_start: 0.9048 (ptp90) cc_final: 0.8795 (ptp90)
REVERT: C  150 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8867 (mm-30)
REVERT: C  183 ASP cc_start: 0.9067 (p0) cc_final: 0.8791 (p0)
REVERT: C  188 ASP cc_start: 0.9213 (m-30) cc_final: 0.8712 (t0)
REVERT: C  195 ASN cc_start: 0.9436 (m-40) cc_final: 0.9042 (p0)
REVERT: C  209 TYR cc_start: 0.8650 (t80) cc_final: 0.8004 (t80)
REVERT: C  257 LYS cc_start: 0.7326 (tptt) cc_final: 0.6972 (tmtt)
REVERT: D   24 ARG cc_start: 0.8846 (ttp80) cc_final: 0.8518 (ttp80)
REVERT: D  101 ASP cc_start: 0.8857 (t0) cc_final: 0.8033 (p0)
REVERT: D  126 ASP cc_start: 0.8654 (p0) cc_final: 0.8388 (p0)
REVERT: D  132 ARG cc_start: 0.8893 (tmt170) cc_final: 0.8507 (tmm-80)
REVERT: D  154 MET cc_start: 0.9330 (mtp) cc_final: 0.9024 (mtp)
REVERT: D  185 LYS cc_start: 0.8833 (ptpp) cc_final: 0.8407 (ptpp)
  outliers start: 34
  outliers final: 28
  residues processed: 182
  average time/residue: 0.2282
  time to fit residues: 55.3804
Evaluate side-chains
  179 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 149
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
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   81 LEU
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  143 GLN
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  106 THR
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain C residue   12 ASP
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  174 LEU
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 77 optimal weight:    0.3980
   chunk 30 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 43 optimal weight:    9.9990
   chunk 29 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 94 optimal weight:    0.6980
   chunk 3 optimal weight:    0.4980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 234 ASN
** 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 = 0.3465 r_free = 0.3465 target = 0.089400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.062624 restraints weight = 19161.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.2942 rms_B_bonded: 3.70
r_work: 0.2801 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8561
moved from start:          0.4949

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= 0.128
  Angle     :  0.651  11.439  11783  Z= 0.323
  Chirality :  0.045   0.180   1312
  Planarity :  0.005   0.049   1459
  Dihedral  :  9.108  74.933   1221
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 30.18 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.29), residues: 1000
  helix:  0.89 (0.32), residues: 320
  sheet: -1.11 (0.36), residues: 236
  loop :  0.95 (0.33), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  31 
 HIS   0.002   0.000   HIS D   8 
 PHE   0.012   0.001   PHE C 112 
 TYR   0.018   0.002   TYR C  79 
 ARG   0.016   0.001   ARG C 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03338 (  261)
  hydrogen bonds       : angle       4.70702 (  699)
  covalent geometry    : bond        0.00308 ( 8648)
  covalent geometry    : angle       0.65073 (11783)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4222.65 seconds
wall clock time: 74 minutes 9.17 seconds (4449.17 seconds total)