Starting phenix.real_space_refine
on Tue Apr 29 07:42:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9muo_48639/04_2025/9muo_48639.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9muo_48639/04_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_48639/04_2025/9muo_48639.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9muo_48639/04_2025/9muo_48639.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9muo_48639/04_2025/9muo_48639.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9muo_48639/04_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-5669/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: 7.47, per 1000 atoms: 0.89
  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: 2.16
  Conformation dependent library (CDL) restraints added in 951.3 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 8 sheets defined
      39.9% alpha, 15.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  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: 2.12

  Time building geometry restraints manager: 2.51 seconds

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

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

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

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

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1036
       0.051 -    0.103: 202
       0.103 -    0.154: 70
       0.154 -    0.205: 3
       0.205 -    0.256: 1
  Chirality restraints: 1312
  Sorted by residual:
  chirality pdb=" C20 DQV B 301 "
            pdb=" C21 DQV B 301 "
            pdb=" C8  DQV B 301 "
            pdb=" O12 DQV B 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.55   -2.81    0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" C21 DQV B 301 "
            pdb=" C20 DQV B 301 "
            pdb=" C7  DQV B 301 "
            pdb=" O13 DQV B 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.73    2.54    0.19 2.00e-01 2.50e+01 9.23e-01
  chirality pdb=" CA  ILE B  32 "
            pdb=" N   ILE B  32 "
            pdb=" C   ILE B  32 "
            pdb=" CB  ILE B  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 8.10e-01
  ... (remaining 1309 not shown)

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

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

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             12.100
  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:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.010
  Find NCS groups from input model:        0.310
  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:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.850
-------------------------------------------------------------------------------
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  : 0.925 
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: 0.2204
  time to fit residues: 76.9503
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  : 0.998 
-------------------------------------------------------------------------------
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 = 0.3563 r_free = 0.3563 target = 0.094225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.066446 restraints weight = 19047.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 3.59
r_work: 0.2915 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
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  : 1.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 PHE cc_start: 0.8944 (t80) cc_final: 0.8389 (t80)
REVERT: A   79 TYR cc_start: 0.9488 (t80) cc_final: 0.9286 (t80)
REVERT: A  143 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8690 (tm-30)
REVERT: A  185 LYS cc_start: 0.9232 (ptpp) cc_final: 0.8814 (ptmt)
REVERT: B  119 ARG cc_start: 0.8888 (ttp-110) cc_final: 0.8678 (ptp-110)
REVERT: C   11 LYS cc_start: 0.9468 (mmtm) cc_final: 0.9092 (mttp)
REVERT: C   70 TRP cc_start: 0.8182 (OUTLIER) cc_final: 0.7868 (p-90)
REVERT: C  112 PHE cc_start: 0.9251 (t80) cc_final: 0.8938 (t80)
REVERT: C  119 ARG cc_start: 0.8840 (ttp-110) cc_final: 0.8635 (ptp90)
REVERT: C  129 ASN cc_start: 0.8414 (t0) cc_final: 0.7765 (t0)
REVERT: C  142 TRP cc_start: 0.9125 (m100) cc_final: 0.8199 (m100)
REVERT: C  143 GLN cc_start: 0.9204 (tt0) cc_final: 0.8533 (tm-30)
REVERT: C  144 ASN cc_start: 0.8722 (p0) cc_final: 0.8520 (p0)
REVERT: C  195 ASN cc_start: 0.9431 (m-40) cc_final: 0.9080 (p0)
REVERT: C  209 TYR cc_start: 0.8847 (t80) cc_final: 0.8069 (t80)
REVERT: D   24 ARG cc_start: 0.8715 (ttp80) cc_final: 0.8265 (ttp80)
REVERT: D   97 ARG cc_start: 0.8711 (tpt-90) cc_final: 0.8426 (ttt180)
REVERT: D  101 ASP cc_start: 0.8844 (t0) cc_final: 0.8027 (p0)
REVERT: D  119 ARG cc_start: 0.9557 (ttp-110) cc_final: 0.9233 (ptp90)
REVERT: D  132 ARG cc_start: 0.8955 (tmt170) cc_final: 0.8623 (tmm-80)
REVERT: D  154 MET cc_start: 0.9181 (mtp) cc_final: 0.8603 (mtp)
REVERT: D  161 GLU cc_start: 0.8698 (tp30) cc_final: 0.8213 (tp30)
REVERT: D  166 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8614 (tp30)
REVERT: D  185 LYS cc_start: 0.9043 (ptpp) cc_final: 0.8760 (pttm)
  outliers start: 34
  outliers final: 20
  residues processed: 220
  average time/residue: 0.2975
  time to fit residues: 87.9426
Evaluate side-chains
  203 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 181
  time to evaluate  : 1.313 
-------------------------------------------------------------------------------
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  166 GLU
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:    9.9990
   chunk 77 optimal weight:    9.9990
   chunk 43 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 20 optimal weight:   10.0000
   chunk 18 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 24 optimal weight:    9.9990
   chunk 53 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   overall best weight:    1.9186

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.094178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.066886 restraints weight = 19289.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3027 rms_B_bonded: 3.55
r_work: 0.2892 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.3236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8648  Z= 0.141
  Angle     :  0.619   8.385  11783  Z= 0.309
  Chirality :  0.046   0.146   1312
  Planarity :  0.005   0.045   1459
  Dihedral  :  9.397  78.864   1221
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 27.28 %
    Favored  : 68.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.49 (0.30), residues: 326
  sheet: -0.47 (0.36), residues: 232
  loop :  0.31 (0.32), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C  70 
 HIS   0.002   0.001   HIS D  22 
 PHE   0.012   0.001   PHE C  57 
 TYR   0.018   0.002   TYR C 244 
 ARG   0.007   0.000   ARG D 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04223 (  261)
  hydrogen bonds       : angle       4.92803 (  699)
  covalent geometry    : bond        0.00335 ( 8648)
  covalent geometry    : angle       0.61901 (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
  230 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 190
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8377 (tp30)
REVERT: A  185 LYS cc_start: 0.9222 (ptpp) cc_final: 0.8794 (ptmt)
REVERT: B   58 LEU cc_start: 0.9075 (mp) cc_final: 0.8848 (mp)
REVERT: B  166 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8543 (tp30)
REVERT: C    9 ASN cc_start: 0.8833 (t0) cc_final: 0.8077 (m-40)
REVERT: C   11 LYS cc_start: 0.9461 (mmtm) cc_final: 0.9036 (mtmt)
REVERT: C   56 TYR cc_start: 0.8109 (m-80) cc_final: 0.7876 (m-10)
REVERT: C   70 TRP cc_start: 0.8149 (OUTLIER) cc_final: 0.7472 (p-90)
REVERT: C   71 CYS cc_start: 0.7595 (m) cc_final: 0.6781 (m)
REVERT: C  119 ARG cc_start: 0.8819 (ttp-110) cc_final: 0.8576 (ptp90)
REVERT: C  122 TYR cc_start: 0.8895 (p90) cc_final: 0.8502 (p90)
REVERT: C  129 ASN cc_start: 0.8356 (t0) cc_final: 0.7912 (t0)
REVERT: C  130 MET cc_start: 0.8606 (tpt) cc_final: 0.8267 (tpp)
REVERT: C  142 TRP cc_start: 0.9079 (m100) cc_final: 0.8307 (m100)
REVERT: C  166 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8375 (tp30)
REVERT: C  183 ASP cc_start: 0.8996 (p0) cc_final: 0.8662 (p0)
REVERT: C  195 ASN cc_start: 0.9448 (m-40) cc_final: 0.9094 (p0)
REVERT: C  209 TYR cc_start: 0.8780 (t80) cc_final: 0.7909 (t80)
REVERT: D   24 ARG cc_start: 0.8771 (ttp80) cc_final: 0.8225 (ttp80)
REVERT: D   31 TRP cc_start: 0.9135 (m100) cc_final: 0.8621 (m100)
REVERT: D   97 ARG cc_start: 0.8757 (tpt-90) cc_final: 0.8456 (ttt180)
REVERT: D  101 ASP cc_start: 0.8851 (t0) cc_final: 0.8029 (p0)
REVERT: D  119 ARG cc_start: 0.9502 (ttp-110) cc_final: 0.9182 (ptp-110)
REVERT: D  132 ARG cc_start: 0.8945 (tmt170) cc_final: 0.8578 (tmm-80)
REVERT: D  154 MET cc_start: 0.9239 (mtp) cc_final: 0.8658 (mtp)
REVERT: D  161 GLU cc_start: 0.8631 (tp30) cc_final: 0.8222 (tp30)
REVERT: D  183 ASP cc_start: 0.8953 (p0) cc_final: 0.8739 (p0)
REVERT: D  185 LYS cc_start: 0.8989 (ptpp) cc_final: 0.8656 (pttm)
  outliers start: 40
  outliers final: 25
  residues processed: 215
  average time/residue: 0.2392
  time to fit residues: 68.1344
Evaluate side-chains
  181 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 152
  time to evaluate  : 1.228 
-------------------------------------------------------------------------------
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  176 VAL
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain B residue   31 TRP
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  166 GLU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain C residue   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
Chi-restraints excluded: chain D residue  188 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 1 optimal weight:   10.0000
   chunk 29 optimal weight:    7.9990
   chunk 51 optimal weight:    9.9990
   chunk 58 optimal weight:   20.0000
   chunk 84 optimal weight:    0.8980
   chunk 82 optimal weight:    0.6980
   chunk 52 optimal weight:    0.5980
   chunk 21 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 19 optimal weight:    8.9990
   overall best weight:    2.4384

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

Flipped N/Q/H residues before XYZ refinement:
A 226 ASN
** B  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   8 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.092608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.065515 restraints weight = 18997.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 3.40
r_work: 0.2934 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8669
moved from start:          0.3709

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= 0.162
  Angle     :  0.627   8.199  11783  Z= 0.313
  Chirality :  0.045   0.145   1312
  Planarity :  0.005   0.055   1459
  Dihedral  :  9.211  82.905   1221
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 26.73 %
    Favored  : 68.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.18 (0.29), residues: 1000
  helix:  0.63 (0.31), residues: 328
  sheet: -0.70 (0.36), residues: 240
  loop :  0.46 (0.33), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C  70 
 HIS   0.003   0.001   HIS B  22 
 PHE   0.023   0.001   PHE C 112 
 TYR   0.018   0.002   TYR C 244 
 ARG   0.009   0.001   ARG D 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03700 (  261)
  hydrogen bonds       : angle       4.83072 (  699)
  covalent geometry    : bond        0.00387 ( 8648)
  covalent geometry    : angle       0.62749 (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
  210 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 165
  time to evaluate  : 1.002 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8310 (tp30)
REVERT: A  185 LYS cc_start: 0.9232 (ptpp) cc_final: 0.8829 (ptmt)
REVERT: B   97 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7095 (tpt-90)
REVERT: C   11 LYS cc_start: 0.9483 (mmtm) cc_final: 0.9073 (mttp)
REVERT: C   56 TYR cc_start: 0.8012 (m-80) cc_final: 0.7796 (m-10)
REVERT: C   70 TRP cc_start: 0.8126 (OUTLIER) cc_final: 0.7256 (p-90)
REVERT: C   71 CYS cc_start: 0.7602 (m) cc_final: 0.6913 (m)
REVERT: C   97 ARG cc_start: 0.9265 (ttt180) cc_final: 0.9059 (ttt180)
REVERT: C  119 ARG cc_start: 0.8851 (ttp-110) cc_final: 0.8602 (ptp90)
REVERT: C  129 ASN cc_start: 0.8493 (t0) cc_final: 0.7862 (t0)
REVERT: C  130 MET cc_start: 0.8676 (tpt) cc_final: 0.8378 (tpp)
REVERT: C  142 TRP cc_start: 0.9096 (m100) cc_final: 0.8140 (m100)
REVERT: C  166 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8352 (tp30)
REVERT: C  183 ASP cc_start: 0.8957 (p0) cc_final: 0.8687 (p0)
REVERT: C  188 ASP cc_start: 0.8993 (m-30) cc_final: 0.8718 (t0)
REVERT: C  195 ASN cc_start: 0.9449 (m-40) cc_final: 0.9092 (p0)
REVERT: C  209 TYR cc_start: 0.8778 (t80) cc_final: 0.8040 (t80)
REVERT: D   24 ARG cc_start: 0.8899 (ttp80) cc_final: 0.8386 (ttp80)
REVERT: D   31 TRP cc_start: 0.9199 (m100) cc_final: 0.8652 (m100)
REVERT: D   71 CYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8512 (p)
REVERT: D   97 ARG cc_start: 0.8826 (tpt-90) cc_final: 0.8528 (ttt180)
REVERT: D  101 ASP cc_start: 0.8811 (t0) cc_final: 0.8014 (p0)
REVERT: D  119 ARG cc_start: 0.9460 (ttp-110) cc_final: 0.9141 (ptp-110)
REVERT: D  130 MET cc_start: 0.8901 (tpp) cc_final: 0.8676 (tpp)
REVERT: D  132 ARG cc_start: 0.8924 (tmt170) cc_final: 0.8574 (tmm-80)
REVERT: D  185 LYS cc_start: 0.8972 (ptpp) cc_final: 0.8719 (pttm)
  outliers start: 45
  outliers final: 29
  residues processed: 196
  average time/residue: 0.2621
  time to fit residues: 67.3529
Evaluate side-chains
  180 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 146
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
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   97 ARG
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  254 MET
Chi-restraints excluded: chain C residue   12 ASP
Chi-restraints excluded: chain C residue   70 TRP
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  166 GLU
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  174 LEU
Chi-restraints excluded: chain C residue  229 THR
Chi-restraints excluded: chain D residue   12 ASP
Chi-restraints excluded: chain D residue   71 CYS
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  124 GLU
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  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:    4.9990
   chunk 54 optimal weight:    8.9990
   chunk 77 optimal weight:    4.9990
   chunk 55 optimal weight:    5.9990
   chunk 51 optimal weight:    9.9990
   chunk 46 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   chunk 52 optimal weight:    9.9990
   chunk 23 optimal weight:    4.9990
   chunk 12 optimal weight:   10.0000
   overall best weight:    4.9990

-------------------------------------------------------------------------------
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  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.088393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.060895 restraints weight = 19440.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 3.42
r_work: 0.2806 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8795
moved from start:          0.4419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.065   8648  Z= 0.282
  Angle     :  0.702   8.696  11783  Z= 0.353
  Chirality :  0.048   0.144   1312
  Planarity :  0.005   0.046   1459
  Dihedral  :  9.329  89.942   1221
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 15.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  6.35 %
    Allowed  : 25.28 %
    Favored  : 68.37 %
  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:  0.14 (0.29), residues: 1000
  helix:  0.79 (0.31), residues: 320
  sheet: -1.01 (0.35), residues: 250
  loop :  0.50 (0.33), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  31 
 HIS   0.004   0.001   HIS C  22 
 PHE   0.019   0.002   PHE C 112 
 TYR   0.030   0.003   TYR C 244 
 ARG   0.009   0.001   ARG D 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03833 (  261)
  hydrogen bonds       : angle       4.91672 (  699)
  covalent geometry    : bond        0.00665 ( 8648)
  covalent geometry    : angle       0.70205 (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
  203 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 146
  time to evaluate  : 1.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 LYS cc_start: 0.9226 (ptpp) cc_final: 0.8875 (ptmt)
REVERT: B   97 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.7089 (tpt-90)
REVERT: C   11 LYS cc_start: 0.9531 (mmtm) cc_final: 0.9194 (mttp)
REVERT: C   70 TRP cc_start: 0.8088 (OUTLIER) cc_final: 0.6970 (p-90)
REVERT: C   71 CYS cc_start: 0.7801 (m) cc_final: 0.7132 (m)
REVERT: C   72 TRP cc_start: 0.8372 (m100) cc_final: 0.8079 (m100)
REVERT: C   97 ARG cc_start: 0.9308 (ttt180) cc_final: 0.9046 (ttt180)
REVERT: C  129 ASN cc_start: 0.8556 (t0) cc_final: 0.7951 (t0)
REVERT: C  130 MET cc_start: 0.8678 (tpt) cc_final: 0.8453 (tpp)
REVERT: C  166 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8522 (tp30)
REVERT: C  183 ASP cc_start: 0.9032 (p0) cc_final: 0.8570 (p0)
REVERT: C  188 ASP cc_start: 0.9189 (m-30) cc_final: 0.8716 (t0)
REVERT: C  195 ASN cc_start: 0.9376 (m-40) cc_final: 0.9060 (p0)
REVERT: D   24 ARG cc_start: 0.9022 (ttp80) cc_final: 0.8485 (ttp80)
REVERT: D  101 ASP cc_start: 0.8861 (t0) cc_final: 0.8022 (p0)
REVERT: D  119 ARG cc_start: 0.9456 (ttp-110) cc_final: 0.9210 (ttp-110)
REVERT: D  132 ARG cc_start: 0.8917 (tmt170) cc_final: 0.8616 (tmm-80)
REVERT: D  154 MET cc_start: 0.9240 (mtp) cc_final: 0.8781 (mtp)
REVERT: D  185 LYS cc_start: 0.8892 (ptpp) cc_final: 0.8576 (ptpp)
  outliers start: 57
  outliers final: 41
  residues processed: 189
  average time/residue: 0.2856
  time to fit residues: 70.4504
Evaluate side-chains
  184 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 140
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ILE
Chi-restraints excluded: chain A residue   47 ILE
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  164 VAL
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain B residue   30 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   97 ARG
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  206 VAL
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  254 MET
Chi-restraints excluded: chain C residue   12 ASP
Chi-restraints excluded: chain C residue   70 TRP
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  166 GLU
Chi-restraints excluded: chain C residue  174 LEU
Chi-restraints excluded: chain C residue  221 THR
Chi-restraints excluded: chain C residue  229 THR
Chi-restraints excluded: chain D residue   12 ASP
Chi-restraints excluded: chain D residue   47 ILE
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  124 GLU
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  174 LEU
Chi-restraints excluded: chain D residue  206 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   chunk 7 optimal weight:   20.0000
   chunk 71 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 84 optimal weight:    2.9990
   chunk 55 optimal weight:   10.0000
   chunk 90 optimal weight:    4.9990
   chunk 34 optimal weight:    0.6980
   chunk 74 optimal weight:    0.7980
   chunk 81 optimal weight:   10.0000
   overall best weight:    1.6984

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.090627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.064000 restraints weight = 18980.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.3017 rms_B_bonded: 3.42
r_work: 0.2889 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8670
moved from start:          0.4502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8648  Z= 0.134
  Angle     :  0.624   8.390  11783  Z= 0.311
  Chirality :  0.045   0.147   1312
  Planarity :  0.004   0.042   1459
  Dihedral  :  9.235  83.339   1221
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 27.95 %
    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:  0.34 (0.29), residues: 1000
  helix:  0.94 (0.31), residues: 320
  sheet: -1.05 (0.35), residues: 236
  loop :  0.69 (0.33), residues: 444

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   0.016   0.001   PHE C 112 
 TYR   0.022   0.002   TYR B 209 
 ARG   0.008   0.001   ARG D 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03376 (  261)
  hydrogen bonds       : angle       4.70526 (  699)
  covalent geometry    : bond        0.00323 ( 8648)
  covalent geometry    : angle       0.62406 (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
  197 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 150
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 LYS cc_start: 0.9229 (mmtt) cc_final: 0.9013 (mmtm)
REVERT: A   21 GLU cc_start: 0.9072 (tp30) cc_final: 0.8870 (tt0)
REVERT: A   25 GLN cc_start: 0.9354 (mm110) cc_final: 0.9139 (mm-40)
REVERT: A  129 ASN cc_start: 0.8183 (t0) cc_final: 0.7234 (t0)
REVERT: A  132 ARG cc_start: 0.8494 (tmm-80) cc_final: 0.8054 (tmm-80)
REVERT: A  185 LYS cc_start: 0.9207 (ptpp) cc_final: 0.8821 (ptmt)
REVERT: B   97 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7103 (tpt-90)
REVERT: C   11 LYS cc_start: 0.9516 (mmtm) cc_final: 0.9147 (mttp)
REVERT: C   45 GLN cc_start: 0.8967 (pm20) cc_final: 0.8615 (pm20)
REVERT: C   65 TYR cc_start: 0.8652 (t80) cc_final: 0.8386 (t80)
REVERT: C   70 TRP cc_start: 0.8030 (OUTLIER) cc_final: 0.6893 (p-90)
REVERT: C   97 ARG cc_start: 0.9273 (ttt180) cc_final: 0.9044 (ttt180)
REVERT: C  119 ARG cc_start: 0.9189 (ptp90) cc_final: 0.8847 (ptp90)
REVERT: C  129 ASN cc_start: 0.8585 (t0) cc_final: 0.7959 (t0)
REVERT: C  183 ASP cc_start: 0.9032 (p0) cc_final: 0.8624 (p0)
REVERT: C  188 ASP cc_start: 0.9183 (m-30) cc_final: 0.8721 (t0)
REVERT: C  195 ASN cc_start: 0.9393 (m-40) cc_final: 0.9057 (p0)
REVERT: C  209 TYR cc_start: 0.8794 (t80) cc_final: 0.8347 (t80)
REVERT: D   24 ARG cc_start: 0.8922 (ttp80) cc_final: 0.8645 (ttp80)
REVERT: D  101 ASP cc_start: 0.8860 (t0) cc_final: 0.8017 (p0)
REVERT: D  119 ARG cc_start: 0.9422 (ttp-110) cc_final: 0.8990 (ttp-110)
REVERT: D  132 ARG cc_start: 0.8934 (tmt170) cc_final: 0.8571 (tmm-80)
REVERT: D  154 MET cc_start: 0.9240 (mtp) cc_final: 0.8767 (mtp)
REVERT: D  185 LYS cc_start: 0.8842 (ptpp) cc_final: 0.8494 (ptpp)
  outliers start: 47
  outliers final: 34
  residues processed: 185
  average time/residue: 0.3136
  time to fit residues: 76.2069
Evaluate side-chains
  179 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 143
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
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  164 VAL
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain B residue   31 TRP
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain B residue   97 ARG
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain C residue   12 ASP
Chi-restraints excluded: chain C residue   70 TRP
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  166 GLU
Chi-restraints excluded: chain C residue  174 LEU
Chi-restraints excluded: chain C residue  229 THR
Chi-restraints excluded: chain D residue   12 ASP
Chi-restraints excluded: chain D residue   27 LEU
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  174 LEU
Chi-restraints excluded: chain D residue  188 ASP
Chi-restraints excluded: chain D residue  206 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 9 optimal weight:   50.0000
   chunk 11 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 17 optimal weight:    6.9990
   chunk 48 optimal weight:    0.8980
   chunk 36 optimal weight:    5.9990
   chunk 94 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   chunk 85 optimal weight:    0.2980
   overall best weight:    0.8382

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.091803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.065542 restraints weight = 19051.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 3.39
r_work: 0.2879 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.4540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8648  Z= 0.114
  Angle     :  0.620  11.594  11783  Z= 0.305
  Chirality :  0.045   0.151   1312
  Planarity :  0.004   0.048   1459
  Dihedral  :  9.076  76.617   1221
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 28.40 %
    Favored  : 67.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.44 (0.29), residues: 1000
  helix:  1.03 (0.31), residues: 320
  sheet: -1.09 (0.35), residues: 236
  loop :  0.80 (0.33), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C  70 
 HIS   0.003   0.001   HIS C 128 
 PHE   0.015   0.001   PHE C 112 
 TYR   0.011   0.002   TYR B 209 
 ARG   0.009   0.001   ARG D 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03177 (  261)
  hydrogen bonds       : angle       4.59910 (  699)
  covalent geometry    : bond        0.00268 ( 8648)
  covalent geometry    : angle       0.62025 (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
  204 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 166
  time to evaluate  : 0.923 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.5522 (pp30) cc_final: 0.4800 (pp30)
REVERT: A  119 ARG cc_start: 0.9269 (mtm110) cc_final: 0.8734 (ptp90)
REVERT: A  132 ARG cc_start: 0.8524 (tmm-80) cc_final: 0.8014 (tmm-80)
REVERT: A  185 LYS cc_start: 0.9200 (ptpp) cc_final: 0.8801 (ptmt)
REVERT: C   11 LYS cc_start: 0.9516 (mmtm) cc_final: 0.9184 (mttp)
REVERT: C   45 GLN cc_start: 0.8900 (pm20) cc_final: 0.8533 (pm20)
REVERT: C   70 TRP cc_start: 0.7836 (OUTLIER) cc_final: 0.7094 (p-90)
REVERT: C  129 ASN cc_start: 0.8545 (t0) cc_final: 0.8140 (t0)
REVERT: C  183 ASP cc_start: 0.8967 (p0) cc_final: 0.8430 (p0)
REVERT: C  195 ASN cc_start: 0.9411 (m-40) cc_final: 0.9084 (p0)
REVERT: C  209 TYR cc_start: 0.8685 (t80) cc_final: 0.7805 (t80)
REVERT: D   18 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8262 (tm-30)
REVERT: D   24 ARG cc_start: 0.8926 (ttp80) cc_final: 0.8617 (ttp80)
REVERT: D   31 TRP cc_start: 0.9112 (m100) cc_final: 0.8555 (m100)
REVERT: D  101 ASP cc_start: 0.8882 (t0) cc_final: 0.8010 (p0)
REVERT: D  119 ARG cc_start: 0.9385 (ttp-110) cc_final: 0.8954 (ttp-110)
REVERT: D  130 MET cc_start: 0.8827 (tpp) cc_final: 0.8598 (tpp)
REVERT: D  132 ARG cc_start: 0.8927 (tmt170) cc_final: 0.8546 (tmm-80)
REVERT: D  185 LYS cc_start: 0.8826 (ptpp) cc_final: 0.8448 (ptpp)
  outliers start: 38
  outliers final: 29
  residues processed: 192
  average time/residue: 0.2398
  time to fit residues: 60.8504
Evaluate side-chains
  181 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 151
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
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  164 VAL
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  106 THR
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  164 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   70 TRP
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  229 THR
Chi-restraints excluded: chain D residue   12 ASP
Chi-restraints excluded: chain D residue   27 LEU
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  124 GLU
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  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:    3.9990
   chunk 8 optimal weight:    8.9990
   chunk 67 optimal weight:    0.0570
   chunk 29 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 33 optimal weight:   10.0000
   chunk 42 optimal weight:    0.3980
   chunk 28 optimal weight:   10.0000
   chunk 51 optimal weight:    5.9990
   chunk 1 optimal weight:   10.0000
   chunk 71 optimal weight:    9.9990
   overall best weight:    2.6904

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3453 r_free = 0.3453 target = 0.088515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.061556 restraints weight = 19134.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.2926 rms_B_bonded: 3.66
r_work: 0.2783 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
moved from start:          0.4708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8648  Z= 0.171
  Angle     :  0.646   9.799  11783  Z= 0.321
  Chirality :  0.045   0.149   1312
  Planarity :  0.005   0.046   1459
  Dihedral  :  9.075  74.845   1221
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 13.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 28.84 %
    Favored  : 66.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.43 (0.29), residues: 1000
  helix:  1.01 (0.32), residues: 324
  sheet: -0.95 (0.36), residues: 240
  loop :  0.73 (0.33), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  31 
 HIS   0.004   0.001   HIS A  82 
 PHE   0.014   0.001   PHE C 112 
 TYR   0.027   0.002   TYR C  56 
 ARG   0.008   0.000   ARG D 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03260 (  261)
  hydrogen bonds       : angle       4.62304 (  699)
  covalent geometry    : bond        0.00412 ( 8648)
  covalent geometry    : angle       0.64558 (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
  182 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 144
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.5670 (pp30) cc_final: 0.4988 (pp30)
REVERT: A  132 ARG cc_start: 0.8522 (tmm-80) cc_final: 0.7979 (tmm-80)
REVERT: A  185 LYS cc_start: 0.9205 (ptpp) cc_final: 0.8772 (ptmt)
REVERT: A  239 GLU cc_start: 0.8561 (mt-10) cc_final: 0.7935 (mp0)
REVERT: B   97 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7033 (tpt-90)
REVERT: C   11 LYS cc_start: 0.9526 (mmtm) cc_final: 0.9219 (mttp)
REVERT: C   45 GLN cc_start: 0.8923 (pm20) cc_final: 0.8546 (pm20)
REVERT: C   70 TRP cc_start: 0.7805 (OUTLIER) cc_final: 0.7341 (p-90)
REVERT: C  119 ARG cc_start: 0.9166 (ptp90) cc_final: 0.8941 (ptp90)
REVERT: C  188 ASP cc_start: 0.9184 (m-30) cc_final: 0.8825 (t0)
REVERT: C  195 ASN cc_start: 0.9472 (m-40) cc_final: 0.9086 (p0)
REVERT: C  209 TYR cc_start: 0.8711 (t80) cc_final: 0.7841 (t80)
REVERT: D   24 ARG cc_start: 0.8795 (ttp80) cc_final: 0.8512 (ttp80)
REVERT: D   31 TRP cc_start: 0.9053 (m100) cc_final: 0.8396 (m100)
REVERT: D  101 ASP cc_start: 0.8863 (t0) cc_final: 0.8327 (t0)
REVERT: D  119 ARG cc_start: 0.9423 (ttp-110) cc_final: 0.9051 (ttp-110)
REVERT: D  126 ASP cc_start: 0.8698 (p0) cc_final: 0.8477 (p0)
REVERT: D  132 ARG cc_start: 0.8945 (tmt170) cc_final: 0.8575 (tmm-80)
REVERT: D  185 LYS cc_start: 0.8827 (ptpp) cc_final: 0.8346 (ptpp)
  outliers start: 38
  outliers final: 31
  residues processed: 172
  average time/residue: 0.2551
  time to fit residues: 57.9513
Evaluate side-chains
  170 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 137
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
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  164 VAL
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   97 ARG
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  164 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   70 TRP
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  254 MET
Chi-restraints excluded: chain D residue   12 ASP
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  124 GLU
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  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:    3.9990
   chunk 87 optimal weight:    0.7980
   chunk 76 optimal weight:    5.9990
   chunk 32 optimal weight:    8.9990
   chunk 88 optimal weight:    3.9990
   chunk 69 optimal weight:    0.8980
   chunk 3 optimal weight:    0.3980
   chunk 55 optimal weight:    9.9990
   chunk 13 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 38 optimal weight:    8.9990
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.090079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.063937 restraints weight = 19308.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.2949 rms_B_bonded: 3.62
r_work: 0.2811 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.4790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8648  Z= 0.140
  Angle     :  0.653  11.146  11783  Z= 0.326
  Chirality :  0.045   0.189   1312
  Planarity :  0.005   0.046   1459
  Dihedral  :  9.123  76.271   1221
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 29.51 %
    Favored  : 66.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.41 (0.29), residues: 1000
  helix:  0.95 (0.31), residues: 324
  sheet: -0.96 (0.36), residues: 240
  loop :  0.75 (0.33), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP C  31 
 HIS   0.003   0.001   HIS A  82 
 PHE   0.014   0.001   PHE C 112 
 TYR   0.023   0.002   TYR C  56 
 ARG   0.008   0.001   ARG D 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03287 (  261)
  hydrogen bonds       : angle       4.58123 (  699)
  covalent geometry    : bond        0.00340 ( 8648)
  covalent geometry    : angle       0.65350 (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
  186 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 151
  time to evaluate  : 1.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 LYS cc_start: 0.9235 (mmtt) cc_final: 0.8911 (mptt)
REVERT: A   55 GLN cc_start: 0.5569 (pp30) cc_final: 0.4937 (pp30)
REVERT: A  132 ARG cc_start: 0.8553 (tmm-80) cc_final: 0.7971 (tmm-80)
REVERT: A  185 LYS cc_start: 0.9202 (ptpp) cc_final: 0.8772 (ptmt)
REVERT: A  239 GLU cc_start: 0.8495 (mt-10) cc_final: 0.7882 (mp0)
REVERT: B   97 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.6997 (tpt-90)
REVERT: C   11 LYS cc_start: 0.9520 (mmtm) cc_final: 0.9221 (mttp)
REVERT: C   45 GLN cc_start: 0.8904 (pm20) cc_final: 0.8523 (pm20)
REVERT: C   70 TRP cc_start: 0.7749 (OUTLIER) cc_final: 0.7318 (p-90)
REVERT: C  114 GLU cc_start: 0.9265 (mt-10) cc_final: 0.8802 (mp0)
REVERT: C  119 ARG cc_start: 0.9186 (ptp90) cc_final: 0.8949 (ptp90)
REVERT: C  188 ASP cc_start: 0.9170 (m-30) cc_final: 0.8814 (t0)
REVERT: C  195 ASN cc_start: 0.9448 (m-40) cc_final: 0.9060 (p0)
REVERT: C  209 TYR cc_start: 0.8696 (t80) cc_final: 0.7891 (t80)
REVERT: D   24 ARG cc_start: 0.8820 (ttp80) cc_final: 0.8494 (ttp80)
REVERT: D   31 TRP cc_start: 0.9060 (m100) cc_final: 0.8424 (m100)
REVERT: D  101 ASP cc_start: 0.8859 (t0) cc_final: 0.8337 (t0)
REVERT: D  119 ARG cc_start: 0.9417 (ttp-110) cc_final: 0.9040 (ttp-110)
REVERT: D  126 ASP cc_start: 0.8691 (p0) cc_final: 0.8434 (p0)
REVERT: D  132 ARG cc_start: 0.8924 (tmt170) cc_final: 0.8533 (tmm-80)
REVERT: D  185 LYS cc_start: 0.8809 (ptpp) cc_final: 0.8417 (pttm)
  outliers start: 35
  outliers final: 31
  residues processed: 177
  average time/residue: 0.3171
  time to fit residues: 74.7048
Evaluate side-chains
  176 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 143
  time to evaluate  : 1.378 
-------------------------------------------------------------------------------
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  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   97 ARG
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  164 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   70 TRP
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 C residue  229 THR
Chi-restraints excluded: chain D residue   12 ASP
Chi-restraints excluded: chain D residue   27 LEU
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  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:    7.9990
   chunk 39 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 32 optimal weight:    8.9990
   chunk 38 optimal weight:    8.9990
   chunk 75 optimal weight:    0.0770
   chunk 2 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   overall best weight:    1.1142

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.091339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.064717 restraints weight = 18888.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.2996 rms_B_bonded: 3.56
r_work: 0.2861 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8594
moved from start:          0.4835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8648  Z= 0.123
  Angle     :  0.664  10.917  11783  Z= 0.328
  Chirality :  0.045   0.194   1312
  Planarity :  0.005   0.048   1459
  Dihedral  :  9.072  75.718   1221
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 29.40 %
    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:  0.50 (0.29), residues: 1000
  helix:  1.06 (0.32), residues: 318
  sheet: -1.09 (0.36), residues: 236
  loop :  0.88 (0.33), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  31 
 HIS   0.002   0.000   HIS A  82 
 PHE   0.014   0.001   PHE C 112 
 TYR   0.023   0.002   TYR A  79 
 ARG   0.009   0.000   ARG D 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03101 (  261)
  hydrogen bonds       : angle       4.52042 (  699)
  covalent geometry    : bond        0.00298 ( 8648)
  covalent geometry    : angle       0.66389 (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
  187 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 152
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 LYS cc_start: 0.9244 (mmtt) cc_final: 0.8928 (mptt)
REVERT: A   55 GLN cc_start: 0.5373 (pp30) cc_final: 0.4791 (pp30)
REVERT: A   99 GLN cc_start: 0.9218 (pp30) cc_final: 0.8767 (pm20)
REVERT: A  122 TYR cc_start: 0.8579 (p90) cc_final: 0.8173 (p90)
REVERT: A  132 ARG cc_start: 0.8650 (tmm-80) cc_final: 0.8048 (tmm-80)
REVERT: A  185 LYS cc_start: 0.9203 (ptpp) cc_final: 0.8787 (ptmt)
REVERT: A  239 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7832 (mp0)
REVERT: B   67 LYS cc_start: 0.7592 (mmtt) cc_final: 0.7080 (mmtp)
REVERT: B   97 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.6984 (tpt-90)
REVERT: B  139 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8346 (tm-30)
REVERT: C   11 LYS cc_start: 0.9515 (mmtm) cc_final: 0.9260 (mttp)
REVERT: C   45 GLN cc_start: 0.8877 (pm20) cc_final: 0.8506 (pm20)
REVERT: C   70 TRP cc_start: 0.7702 (OUTLIER) cc_final: 0.7251 (p-90)
REVERT: C  114 GLU cc_start: 0.9260 (mt-10) cc_final: 0.8790 (mp0)
REVERT: C  143 GLN cc_start: 0.8989 (tt0) cc_final: 0.8748 (tt0)
REVERT: C  188 ASP cc_start: 0.9146 (m-30) cc_final: 0.8780 (t0)
REVERT: C  195 ASN cc_start: 0.9450 (m-40) cc_final: 0.9048 (p0)
REVERT: C  209 TYR cc_start: 0.8575 (t80) cc_final: 0.7814 (t80)
REVERT: D   24 ARG cc_start: 0.8852 (ttp80) cc_final: 0.8520 (ttp80)
REVERT: D   31 TRP cc_start: 0.9074 (m100) cc_final: 0.8460 (m100)
REVERT: D  101 ASP cc_start: 0.8858 (t0) cc_final: 0.8373 (t0)
REVERT: D  119 ARG cc_start: 0.9388 (ttp-110) cc_final: 0.9010 (ttp-110)
REVERT: D  126 ASP cc_start: 0.8688 (p0) cc_final: 0.8406 (p0)
REVERT: D  132 ARG cc_start: 0.8931 (tmt170) cc_final: 0.8493 (tmm-80)
REVERT: D  185 LYS cc_start: 0.8831 (ptpp) cc_final: 0.8480 (pttm)
  outliers start: 35
  outliers final: 30
  residues processed: 175
  average time/residue: 0.2442
  time to fit residues: 56.3419
Evaluate side-chains
  174 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 142
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
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  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   97 ARG
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  164 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   70 TRP
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   12 ASP
Chi-restraints excluded: chain D residue   27 LEU
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  124 GLU
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  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 36 optimal weight:    8.9990
   chunk 77 optimal weight:    0.8980
   chunk 30 optimal weight:    5.9990
   chunk 12 optimal weight:    8.9990
   chunk 43 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 13 optimal weight:    6.9990
   chunk 94 optimal weight:    0.4980
   chunk 3 optimal weight:    7.9990
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

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 = 0.090120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.063280 restraints weight = 19234.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 3.71
r_work: 0.2821 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.4921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8648  Z= 0.136
  Angle     :  0.668  10.800  11783  Z= 0.333
  Chirality :  0.045   0.191   1312
  Planarity :  0.005   0.047   1459
  Dihedral  :  9.080  76.080   1221
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 13.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 29.40 %
    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:  0.49 (0.29), residues: 1000
  helix:  1.03 (0.32), residues: 320
  sheet: -0.94 (0.36), residues: 240
  loop :  0.82 (0.33), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B  31 
 HIS   0.004   0.001   HIS A  82 
 PHE   0.013   0.001   PHE C 112 
 TYR   0.023   0.002   TYR C  56 
 ARG   0.009   0.001   ARG D 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03168 (  261)
  hydrogen bonds       : angle       4.57241 (  699)
  covalent geometry    : bond        0.00331 ( 8648)
  covalent geometry    : angle       0.66847 (11783)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4744.20 seconds
wall clock time: 84 minutes 30.33 seconds (5070.33 seconds total)