Starting phenix.real_space_refine
on Mon Jul 28 16:49:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ka2_22756/07_2025/7ka2_22756.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ka2_22756/07_2025/7ka2_22756.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ka2_22756/07_2025/7ka2_22756.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ka2_22756/07_2025/7ka2_22756.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ka2_22756/07_2025/7ka2_22756.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ka2_22756/07_2025/7ka2_22756.cif"
  }
  resolution = 3.6
  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=   0.000 sd=   0.002
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: 4
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    6588      2.51       5
     N    1860      2.21       5
     O    1980      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10472
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 6.12, per 1000 atoms: 0.58
  Number of scatterers: 10472
  At special positions: 0
  Unit cell: (97.37, 79.17, 106.47, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      44     16.00
     O    1980      8.00
     N    1860      7.00
     C    6588      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: 3.93
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2520

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 8 sheets defined
      55.7% alpha, 13.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.35
  Creating SS restraints...
    Processing helix  chain 'B' and resid 8 through 24
    Processing helix  chain 'B' and resid 35 through 47
    Processing helix  chain 'B' and resid 51 through 64
    Processing helix  chain 'B' and resid 66 through 70
    Processing helix  chain 'B' and resid 80 through 85
    Processing helix  chain 'B' and resid 92 through 100
      removed outlier: 3.729A  pdb=" N   LYS B 100 " --> pdb=" O   VAL B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 140
    Processing helix  chain 'B' and resid 159 through 180
      removed outlier: 3.558A  pdb=" N   ASN B 180 " --> pdb=" O   ILE B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 219
      removed outlier: 3.539A  pdb=" N   CYS B 201 " --> pdb=" O   ASP B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 225
    Processing helix  chain 'B' and resid 244 through 258
    Processing helix  chain 'B' and resid 275 through 287
      removed outlier: 3.637A  pdb=" N   ALA B 279 " --> pdb=" O   SER B 275 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   SER B 280 " --> pdb=" O   GLU B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 314
      removed outlier: 3.706A  pdb=" N   GLN B 306 " --> pdb=" O   GLY B 302 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   SER B 308 " --> pdb=" O   ALA B 304 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   ALA B 309 " --> pdb=" O   LEU B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 318
      No H-bonds generated for 'chain 'B' and resid 316 through 318'
    Processing helix  chain 'B' and resid 319 through 340
    Processing helix  chain 'A' and resid 8 through 24
    Processing helix  chain 'A' and resid 35 through 47
    Processing helix  chain 'A' and resid 51 through 64
    Processing helix  chain 'A' and resid 66 through 70
    Processing helix  chain 'A' and resid 80 through 85
    Processing helix  chain 'A' and resid 92 through 100
      removed outlier: 3.730A  pdb=" N   LYS A 100 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 140
    Processing helix  chain 'A' and resid 159 through 180
      removed outlier: 3.558A  pdb=" N   ASN A 180 " --> pdb=" O   ILE A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 219
      removed outlier: 3.539A  pdb=" N   CYS A 201 " --> pdb=" O   ASP A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 225
    Processing helix  chain 'A' and resid 244 through 258
    Processing helix  chain 'A' and resid 275 through 287
      removed outlier: 3.636A  pdb=" N   ALA A 279 " --> pdb=" O   SER A 275 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   SER A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 314
      removed outlier: 3.705A  pdb=" N   GLN A 306 " --> pdb=" O   GLY A 302 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   SER A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   ALA A 309 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 318
      No H-bonds generated for 'chain 'A' and resid 316 through 318'
    Processing helix  chain 'A' and resid 319 through 340
    Processing helix  chain 'C' and resid 8 through 24
    Processing helix  chain 'C' and resid 35 through 47
    Processing helix  chain 'C' and resid 51 through 64
    Processing helix  chain 'C' and resid 66 through 70
    Processing helix  chain 'C' and resid 80 through 85
    Processing helix  chain 'C' and resid 92 through 100
      removed outlier: 3.729A  pdb=" N   LYS C 100 " --> pdb=" O   VAL C  96 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 129 through 140
    Processing helix  chain 'C' and resid 159 through 180
      removed outlier: 3.558A  pdb=" N   ASN C 180 " --> pdb=" O   ILE C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 197 through 219
      removed outlier: 3.538A  pdb=" N   CYS C 201 " --> pdb=" O   ASP C 197 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 225
    Processing helix  chain 'C' and resid 244 through 258
    Processing helix  chain 'C' and resid 275 through 287
      removed outlier: 3.637A  pdb=" N   ALA C 279 " --> pdb=" O   SER C 275 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   SER C 280 " --> pdb=" O   GLU C 276 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 302 through 314
      removed outlier: 3.705A  pdb=" N   GLN C 306 " --> pdb=" O   GLY C 302 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   SER C 308 " --> pdb=" O   ALA C 304 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   ALA C 309 " --> pdb=" O   LEU C 305 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 316 through 318
      No H-bonds generated for 'chain 'C' and resid 316 through 318'
    Processing helix  chain 'C' and resid 319 through 340
    Processing helix  chain 'D' and resid 8 through 24
    Processing helix  chain 'D' and resid 35 through 47
    Processing helix  chain 'D' and resid 51 through 64
    Processing helix  chain 'D' and resid 66 through 70
    Processing helix  chain 'D' and resid 80 through 85
    Processing helix  chain 'D' and resid 92 through 100
      removed outlier: 3.729A  pdb=" N   LYS D 100 " --> pdb=" O   VAL D  96 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 129 through 140
    Processing helix  chain 'D' and resid 159 through 180
      removed outlier: 3.558A  pdb=" N   ASN D 180 " --> pdb=" O   ILE D 176 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 197 through 219
      removed outlier: 3.539A  pdb=" N   CYS D 201 " --> pdb=" O   ASP D 197 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 222 through 225
    Processing helix  chain 'D' and resid 244 through 258
    Processing helix  chain 'D' and resid 275 through 287
      removed outlier: 3.637A  pdb=" N   ALA D 279 " --> pdb=" O   SER D 275 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   SER D 280 " --> pdb=" O   GLU D 276 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 302 through 314
      removed outlier: 3.706A  pdb=" N   GLN D 306 " --> pdb=" O   GLY D 302 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   SER D 308 " --> pdb=" O   ALA D 304 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   ALA D 309 " --> pdb=" O   LEU D 305 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 316 through 318
      No H-bonds generated for 'chain 'D' and resid 316 through 318'
    Processing helix  chain 'D' and resid 319 through 340
    Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 32
      removed outlier: 7.121A  pdb=" N   GLY B  28 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   VAL B  76 " --> pdb=" O   GLY B  28 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   LEU B  30 " --> pdb=" O   VAL B  76 " (cutoff:3.500A)
      removed outlier: 5.888A  pdb=" N   LEU B  78 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   ALA B  32 " --> pdb=" O   LEU B  78 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   VAL B 104 " --> pdb=" O   ASP B 143 " (cutoff:3.500A)
      removed outlier: 5.915A  pdb=" N   ALA B 145 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
      removed outlier: 5.516A  pdb=" N   ILE B 106 " --> pdb=" O   ALA B 145 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   TRP B 147 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 8.139A  pdb=" N   ILE B 185 " --> pdb=" O   ASP B 143 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   ALA B 145 " --> pdb=" O   ILE B 185 " (cutoff:3.500A)
      removed outlier: 7.861A  pdb=" N   GLU B 187 " --> pdb=" O   ALA B 145 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   TRP B 147 " --> pdb=" O   GLU B 187 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   GLU B 189 " --> pdb=" O   TRP B 147 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   CYS B 149 " --> pdb=" O   GLU B 189 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   LEU B 191 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   LEU B 151 " --> pdb=" O   LEU B 191 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   LEU B 228 " --> pdb=" O   THR B 268 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ALA B  31 " --> pdb=" O   TYR B 301 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 112 through 114
    Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 32
      removed outlier: 7.121A  pdb=" N   GLY A  28 " --> pdb=" O   GLY A  74 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   VAL A  76 " --> pdb=" O   GLY A  28 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   LEU A  30 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
      removed outlier: 5.889A  pdb=" N   LEU A  78 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   ALA A  32 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   VAL A 104 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
      removed outlier: 5.915A  pdb=" N   ALA A 145 " --> pdb=" O   VAL A 104 " (cutoff:3.500A)
      removed outlier: 5.515A  pdb=" N   ILE A 106 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   TRP A 147 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 8.139A  pdb=" N   ILE A 185 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   ALA A 145 " --> pdb=" O   ILE A 185 " (cutoff:3.500A)
      removed outlier: 7.861A  pdb=" N   GLU A 187 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   TRP A 147 " --> pdb=" O   GLU A 187 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   GLU A 189 " --> pdb=" O   TRP A 147 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   CYS A 149 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   LEU A 191 " --> pdb=" O   CYS A 149 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   LEU A 151 " --> pdb=" O   LEU A 191 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   LEU A 228 " --> pdb=" O   THR A 268 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ALA A  31 " --> pdb=" O   TYR A 301 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114
    Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 32
      removed outlier: 7.120A  pdb=" N   GLY C  28 " --> pdb=" O   GLY C  74 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   VAL C  76 " --> pdb=" O   GLY C  28 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   LEU C  30 " --> pdb=" O   VAL C  76 " (cutoff:3.500A)
      removed outlier: 5.888A  pdb=" N   LEU C  78 " --> pdb=" O   LEU C  30 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   ALA C  32 " --> pdb=" O   LEU C  78 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   VAL C 104 " --> pdb=" O   ASP C 143 " (cutoff:3.500A)
      removed outlier: 5.915A  pdb=" N   ALA C 145 " --> pdb=" O   VAL C 104 " (cutoff:3.500A)
      removed outlier: 5.516A  pdb=" N   ILE C 106 " --> pdb=" O   ALA C 145 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   TRP C 147 " --> pdb=" O   ILE C 106 " (cutoff:3.500A)
      removed outlier: 8.139A  pdb=" N   ILE C 185 " --> pdb=" O   ASP C 143 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ALA C 145 " --> pdb=" O   ILE C 185 " (cutoff:3.500A)
      removed outlier: 7.861A  pdb=" N   GLU C 187 " --> pdb=" O   ALA C 145 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   TRP C 147 " --> pdb=" O   GLU C 187 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   GLU C 189 " --> pdb=" O   TRP C 147 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   CYS C 149 " --> pdb=" O   GLU C 189 " (cutoff:3.500A)
      removed outlier: 7.179A  pdb=" N   LEU C 191 " --> pdb=" O   CYS C 149 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   LEU C 151 " --> pdb=" O   LEU C 191 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   LEU C 228 " --> pdb=" O   THR C 268 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ALA C  31 " --> pdb=" O   TYR C 301 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114
    Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 32
      removed outlier: 7.120A  pdb=" N   GLY D  28 " --> pdb=" O   GLY D  74 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   VAL D  76 " --> pdb=" O   GLY D  28 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   LEU D  30 " --> pdb=" O   VAL D  76 " (cutoff:3.500A)
      removed outlier: 5.888A  pdb=" N   LEU D  78 " --> pdb=" O   LEU D  30 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   ALA D  32 " --> pdb=" O   LEU D  78 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   VAL D 104 " --> pdb=" O   ASP D 143 " (cutoff:3.500A)
      removed outlier: 5.915A  pdb=" N   ALA D 145 " --> pdb=" O   VAL D 104 " (cutoff:3.500A)
      removed outlier: 5.515A  pdb=" N   ILE D 106 " --> pdb=" O   ALA D 145 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   TRP D 147 " --> pdb=" O   ILE D 106 " (cutoff:3.500A)
      removed outlier: 8.139A  pdb=" N   ILE D 185 " --> pdb=" O   ASP D 143 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   ALA D 145 " --> pdb=" O   ILE D 185 " (cutoff:3.500A)
      removed outlier: 7.862A  pdb=" N   GLU D 187 " --> pdb=" O   ALA D 145 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   TRP D 147 " --> pdb=" O   GLU D 187 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   GLU D 189 " --> pdb=" O   TRP D 147 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   CYS D 149 " --> pdb=" O   GLU D 189 " (cutoff:3.500A)
      removed outlier: 7.179A  pdb=" N   LEU D 191 " --> pdb=" O   CYS D 149 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   LEU D 151 " --> pdb=" O   LEU D 191 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   LEU D 228 " --> pdb=" O   THR D 268 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ALA D  31 " --> pdb=" O   TYR D 301 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114

    564 hydrogen bonds defined for protein.
    1608 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: 3.44

  Time building geometry restraints manager: 4.41 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: 3443
        1.34 -     1.46: 1851
        1.46 -     1.57: 5322
        1.57 -     1.69: 0
        1.69 -     1.81: 56
  Bond restraints: 10672
  Sorted by residual:
  bond pdb=" C   ASN D  70 "
       pdb=" N   PRO D  71 "
    ideal  model  delta    sigma   weight residual
    1.334  1.386 -0.052 2.34e-02 1.83e+03 4.92e+00
  bond pdb=" C   ASN C  70 "
       pdb=" N   PRO C  71 "
    ideal  model  delta    sigma   weight residual
    1.334  1.386 -0.052 2.34e-02 1.83e+03 4.87e+00
  bond pdb=" C   ASN B  70 "
       pdb=" N   PRO B  71 "
    ideal  model  delta    sigma   weight residual
    1.334  1.385 -0.051 2.34e-02 1.83e+03 4.77e+00
  bond pdb=" C   ASN A  70 "
       pdb=" N   PRO A  71 "
    ideal  model  delta    sigma   weight residual
    1.334  1.385 -0.051 2.34e-02 1.83e+03 4.74e+00
  bond pdb=" CB  GLU B  14 "
       pdb=" CG  GLU B  14 "
    ideal  model  delta    sigma   weight residual
    1.520  1.473  0.047 3.00e-02 1.11e+03 2.42e+00
  ... (remaining 10667 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 13401
        1.63 -     3.25: 883
        3.25 -     4.88: 115
        4.88 -     6.50: 53
        6.50 -     8.13: 12
  Bond angle restraints: 14464
  Sorted by residual:
  angle pdb=" C   ASN D 319 "
        pdb=" N   LEU D 320 "
        pdb=" CA  LEU D 320 "
      ideal   model   delta    sigma   weight residual
     121.19  129.32   -8.13 1.59e+00 3.96e-01 2.61e+01
  angle pdb=" C   ASN A 319 "
        pdb=" N   LEU A 320 "
        pdb=" CA  LEU A 320 "
      ideal   model   delta    sigma   weight residual
     121.19  129.31   -8.12 1.59e+00 3.96e-01 2.61e+01
  angle pdb=" C   ASN B 319 "
        pdb=" N   LEU B 320 "
        pdb=" CA  LEU B 320 "
      ideal   model   delta    sigma   weight residual
     121.19  129.27   -8.08 1.59e+00 3.96e-01 2.58e+01
  angle pdb=" C   ASN C 319 "
        pdb=" N   LEU C 320 "
        pdb=" CA  LEU C 320 "
      ideal   model   delta    sigma   weight residual
     121.19  129.26   -8.07 1.59e+00 3.96e-01 2.58e+01
  angle pdb=" CA  GLU C  49 "
        pdb=" CB  GLU C  49 "
        pdb=" CG  GLU C  49 "
      ideal   model   delta    sigma   weight residual
     114.10  121.78   -7.68 2.00e+00 2.50e-01 1.47e+01
  ... (remaining 14459 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.52: 5733
       16.52 -    33.03: 591
       33.03 -    49.55: 112
       49.55 -    66.07: 56
       66.07 -    82.58: 12
  Dihedral angle restraints: 6504
    sinusoidal: 2572
      harmonic: 3932
  Sorted by residual:
  dihedral pdb=" CA  VAL C 264 "
           pdb=" C   VAL C 264 "
           pdb=" N   THR C 265 "
           pdb=" CA  THR C 265 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.69  -25.31     0      5.00e+00 4.00e-02 2.56e+01
  dihedral pdb=" CA  VAL A 264 "
           pdb=" C   VAL A 264 "
           pdb=" N   THR A 265 "
           pdb=" CA  THR A 265 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.70  -25.30     0      5.00e+00 4.00e-02 2.56e+01
  dihedral pdb=" CA  VAL B 264 "
           pdb=" C   VAL B 264 "
           pdb=" N   THR B 265 "
           pdb=" CA  THR B 265 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.72  -25.28     0      5.00e+00 4.00e-02 2.56e+01
  ... (remaining 6501 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1094
       0.044 -    0.088: 390
       0.088 -    0.133: 116
       0.133 -    0.177: 32
       0.177 -    0.221: 12
  Chirality restraints: 1644
  Sorted by residual:
  chirality pdb=" CB  ILE B  46 "
            pdb=" CA  ILE B  46 "
            pdb=" CG1 ILE B  46 "
            pdb=" CG2 ILE B  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CB  ILE C  46 "
            pdb=" CA  ILE C  46 "
            pdb=" CG1 ILE C  46 "
            pdb=" CG2 ILE C  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CB  ILE A  46 "
            pdb=" CA  ILE A  46 "
            pdb=" CG1 ILE A  46 "
            pdb=" CG2 ILE A  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 1641 not shown)

  Planarity restraints: 1880
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS D 329 "   -0.014 2.00e-02 2.50e+03   2.91e-02 8.45e+00
        pdb=" C   LYS D 329 "    0.050 2.00e-02 2.50e+03
        pdb=" O   LYS D 329 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ARG D 330 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 329 "    0.014 2.00e-02 2.50e+03   2.91e-02 8.45e+00
        pdb=" C   LYS C 329 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   LYS C 329 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ARG C 330 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 329 "   -0.014 2.00e-02 2.50e+03   2.90e-02 8.39e+00
        pdb=" C   LYS A 329 "    0.050 2.00e-02 2.50e+03
        pdb=" O   LYS A 329 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ARG A 330 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1877 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2592
        2.78 -     3.31: 9896
        3.31 -     3.84: 18124
        3.84 -     4.37: 21109
        4.37 -     4.90: 35941
  Nonbonded interactions: 87662
  Sorted by model distance:
  nonbonded pdb=" O   MET D 250 "
            pdb=" OG1 THR D 254 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   MET A 250 "
            pdb=" OG1 THR A 254 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   MET B 250 "
            pdb=" OG1 THR B 254 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   MET C 250 "
            pdb=" OG1 THR C 254 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   THR B  64 "
            pdb=" OG1 THR B  64 "
     model   vdw
     2.259 3.040
  ... (remaining 87657 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.820
  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:          0.440
  Check model and map are aligned:         0.100
  Set scattering table:                    0.100
  Process input model:                     28.580
  Find NCS groups from input model:        0.200
  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:             0.000
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
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      :  0.008   0.054  10672  Z= 0.353
  Angle     :  0.961   8.127  14464  Z= 0.549
  Chirality :  0.053   0.221   1644
  Planarity :  0.008   0.049   1880
  Dihedral  : 15.204  82.581   3984
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  :  6.47 %
    Favored  : 87.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -1.99 (0.20), residues: 1364
  helix: -1.10 (0.16), residues: 672
  sheet: -2.01 (0.33), residues: 200
  loop : -0.99 (0.26), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.004   TRP B 295 
 HIS   0.005   0.001   HIS C 156 
 PHE   0.017   0.003   PHE A 144 
 TYR   0.017   0.003   TYR A 213 
 ARG   0.007   0.001   ARG B 172 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16327 (  564)
  hydrogen bonds       : angle       6.81305 ( 1608)
  covalent geometry    : bond        0.00797 (10672)
  covalent geometry    : angle       0.96122 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  402 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 334
  time to evaluate  : 1.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  250 MET cc_start: 0.8742 (tpp) cc_final: 0.8428 (tpt)
REVERT: A  233 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.6805 (p)
REVERT: A  250 MET cc_start: 0.8667 (tpp) cc_final: 0.8419 (tpt)
REVERT: A  271 SER cc_start: 0.8415 (OUTLIER) cc_final: 0.7989 (p)
REVERT: A  301 TYR cc_start: 0.7412 (m-10) cc_final: 0.7003 (m-10)
REVERT: C   39 ILE cc_start: 0.9263 (tp) cc_final: 0.8931 (tp)
REVERT: C   60 GLN cc_start: 0.8489 (mt0) cc_final: 0.7667 (mt0)
REVERT: C  250 MET cc_start: 0.8731 (tpp) cc_final: 0.8468 (tpt)
REVERT: C  271 SER cc_start: 0.8465 (OUTLIER) cc_final: 0.8102 (p)
REVERT: C  301 TYR cc_start: 0.7570 (m-10) cc_final: 0.7022 (m-10)
  outliers start: 68
  outliers final: 6
  residues processed: 373
  average time/residue: 0.2669
  time to fit residues: 132.5852
Evaluate side-chains
  195 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 186
  time to evaluate  : 1.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  271 SER
Chi-restraints excluded: chain D residue   64 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 114 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 55 optimal weight:    0.8980
   chunk 106 optimal weight:    0.0470
   chunk 41 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 123 optimal weight:    0.6980
   overall best weight:    0.7280

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
B  60 GLN
B  80 HIS
B 125 GLN
B 168 ASN
A  60 GLN
A  80 HIS
A 125 GLN
A 168 ASN
A 306 GLN
C  60 GLN
C  80 HIS
C 125 GLN
D  80 HIS
D 168 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.095400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.072662 restraints weight = 28987.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.075018 restraints weight = 16884.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.076581 restraints weight = 12007.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.2999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10672  Z= 0.141
  Angle     :  0.644   8.555  14464  Z= 0.334
  Chirality :  0.043   0.168   1644
  Planarity :  0.004   0.032   1880
  Dihedral  :  4.902  28.077   1481
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 14.75 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.08 (0.22), residues: 1364
  helix:  0.75 (0.18), residues: 684
  sheet: -1.30 (0.35), residues: 188
  loop : -0.50 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 147 
 HIS   0.003   0.001   HIS B 220 
 PHE   0.015   0.002   PHE B  93 
 TYR   0.019   0.002   TYR C 203 
 ARG   0.004   0.001   ARG D  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04538 (  564)
  hydrogen bonds       : angle       4.56058 ( 1608)
  covalent geometry    : bond        0.00308 (10672)
  covalent geometry    : angle       0.64409 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 244
  time to evaluate  : 1.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  165 GLU cc_start: 0.7849 (tp30) cc_final: 0.7338 (tp30)
REVERT: B  311 LYS cc_start: 0.9474 (ttpp) cc_final: 0.9238 (ptmm)
REVERT: B  316 LYS cc_start: 0.8984 (mmmt) cc_final: 0.8739 (mmtm)
REVERT: A   60 GLN cc_start: 0.8879 (mt0) cc_final: 0.8533 (mt0)
REVERT: A   82 THR cc_start: 0.9033 (m) cc_final: 0.8781 (m)
REVERT: C   60 GLN cc_start: 0.8782 (mt0) cc_final: 0.8519 (mt0)
REVERT: C   82 THR cc_start: 0.9070 (m) cc_final: 0.8847 (m)
REVERT: C  250 MET cc_start: 0.8863 (tpp) cc_final: 0.8623 (tpt)
REVERT: C  301 TYR cc_start: 0.7492 (m-10) cc_final: 0.7266 (m-10)
  outliers start: 35
  outliers final: 19
  residues processed: 260
  average time/residue: 0.2283
  time to fit residues: 83.5385
Evaluate side-chains
  181 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 162
  time to evaluate  : 1.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  185 ILE
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   80 HIS
Chi-restraints excluded: chain A residue  143 ASP
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  185 ILE
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue  226 THR
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 126 optimal weight:    5.9990
   chunk 105 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 37 optimal weight:    9.9990
   chunk 96 optimal weight:    6.9990
   chunk 122 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0670
   chunk 2 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.4124

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

Flipped N/Q/H residues before XYZ refinement:
B  80 HIS
B 168 ASN
** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  80 HIS
A 168 ASN
A 306 GLN
C  80 HIS
C 168 ASN
D 168 ASN
D 339 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.093033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.070516 restraints weight = 29943.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.072874 restraints weight = 17308.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.074374 restraints weight = 12176.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.3626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026  10672  Z= 0.156
  Angle     :  0.628   8.188  14464  Z= 0.325
  Chirality :  0.043   0.162   1644
  Planarity :  0.004   0.063   1880
  Dihedral  :  4.519  20.169   1472
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 15.74 %
    Favored  : 81.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.58 (0.22), residues: 1364
  helix:  1.44 (0.19), residues: 668
  sheet: -1.00 (0.36), residues: 188
  loop : -0.39 (0.27), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 147 
 HIS   0.012   0.001   HIS A  80 
 PHE   0.018   0.002   PHE B  93 
 TYR   0.016   0.002   TYR B 203 
 ARG   0.005   0.000   ARG D  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04127 (  564)
  hydrogen bonds       : angle       4.33569 ( 1608)
  covalent geometry    : bond        0.00353 (10672)
  covalent geometry    : angle       0.62771 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 188
  time to evaluate  : 1.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  134 CYS cc_start: 0.8372 (p) cc_final: 0.8043 (p)
REVERT: B  229 LYS cc_start: 0.9245 (tttt) cc_final: 0.8800 (tptp)
REVERT: B  250 MET cc_start: 0.8819 (tpt) cc_final: 0.8613 (tpt)
REVERT: A   60 GLN cc_start: 0.8843 (mt0) cc_final: 0.8530 (mt0)
REVERT: A   66 ASP cc_start: 0.9083 (t70) cc_final: 0.8794 (p0)
REVERT: A  301 TYR cc_start: 0.7418 (m-10) cc_final: 0.7176 (m-10)
REVERT: C   34 GLU cc_start: 0.8308 (mp0) cc_final: 0.8087 (mp0)
REVERT: C   60 GLN cc_start: 0.8741 (mt0) cc_final: 0.8458 (mt0)
REVERT: C   66 ASP cc_start: 0.9023 (t70) cc_final: 0.8620 (p0)
REVERT: C   67 ASP cc_start: 0.8953 (p0) cc_final: 0.8721 (t0)
REVERT: C  250 MET cc_start: 0.8822 (tpp) cc_final: 0.8604 (tpt)
REVERT: D  250 MET cc_start: 0.8819 (mmm) cc_final: 0.8448 (tpp)
  outliers start: 34
  outliers final: 21
  residues processed: 211
  average time/residue: 0.2081
  time to fit residues: 63.6837
Evaluate side-chains
  173 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 152
  time to evaluate  : 1.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  278 GLU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   80 HIS
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  326 GLU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain C residue   46 ILE
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   80 HIS
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  326 GLU
Chi-restraints excluded: chain D residue  339 GLN
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 106 optimal weight:    1.9990
   chunk 126 optimal weight:    0.9980
   chunk 68 optimal weight:    5.9990
   chunk 125 optimal weight:    3.9990
   chunk 131 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 109 optimal weight:    3.9990
   chunk 89 optimal weight:    1.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
B  80 HIS
** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 168 ASN
** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  80 HIS
C 168 ASN
** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  80 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.092222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.069910 restraints weight = 29508.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.072217 restraints weight = 17061.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.073669 restraints weight = 12024.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.3944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10672  Z= 0.160
  Angle     :  0.630  11.614  14464  Z= 0.320
  Chirality :  0.043   0.177   1644
  Planarity :  0.004   0.051   1880
  Dihedral  :  4.397  19.789   1472
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 17.81 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.75 (0.22), residues: 1364
  helix:  1.59 (0.19), residues: 672
  sheet: -0.79 (0.36), residues: 188
  loop : -0.39 (0.27), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 313 
 HIS   0.008   0.001   HIS C  80 
 PHE   0.012   0.002   PHE A  93 
 TYR   0.020   0.002   TYR B 203 
 ARG   0.004   0.000   ARG D  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03996 (  564)
  hydrogen bonds       : angle       4.27673 ( 1608)
  covalent geometry    : bond        0.00366 (10672)
  covalent geometry    : angle       0.62973 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 179
  time to evaluate  : 1.591 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  134 CYS cc_start: 0.8365 (p) cc_final: 0.8057 (p)
REVERT: B  250 MET cc_start: 0.8792 (tpt) cc_final: 0.8591 (tpt)
REVERT: B  311 LYS cc_start: 0.9732 (ptmm) cc_final: 0.9530 (ptmm)
REVERT: A   60 GLN cc_start: 0.8794 (mt0) cc_final: 0.8501 (mt0)
REVERT: A  301 TYR cc_start: 0.7432 (m-10) cc_final: 0.7222 (m-10)
REVERT: C   60 GLN cc_start: 0.8717 (mt0) cc_final: 0.8468 (mt0)
REVERT: C  250 MET cc_start: 0.8783 (tpp) cc_final: 0.8558 (tpt)
REVERT: D  164 MET cc_start: 0.8576 (tmm) cc_final: 0.8351 (ptt)
REVERT: D  250 MET cc_start: 0.8771 (mmm) cc_final: 0.8454 (tpp)
REVERT: D  306 GLN cc_start: 0.7562 (pp30) cc_final: 0.7202 (pp30)
  outliers start: 30
  outliers final: 22
  residues processed: 200
  average time/residue: 0.2910
  time to fit residues: 86.0266
Evaluate side-chains
  175 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 153
  time to evaluate  : 2.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  293 LYS
Chi-restraints excluded: chain B residue  326 GLU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   80 HIS
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  217 SER
Chi-restraints excluded: chain C residue  247 GLU
Chi-restraints excluded: chain C residue  326 GLU
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 83 optimal weight:    4.9990
   chunk 134 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 115 optimal weight:    0.7980
   chunk 114 optimal weight:    4.9990
   chunk 22 optimal weight:    0.5980
   chunk 94 optimal weight:    0.9980
   chunk 84 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B  60 GLN
B  80 HIS
** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  80 HIS
A 168 ASN
** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  80 HIS
C 168 ASN
D  60 GLN
D  80 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.093726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.071279 restraints weight = 29085.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.073603 restraints weight = 16809.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.075021 restraints weight = 11913.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.4229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10672  Z= 0.122
  Angle     :  0.598  11.476  14464  Z= 0.302
  Chirality :  0.042   0.157   1644
  Planarity :  0.004   0.044   1880
  Dihedral  :  4.198  17.062   1472
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 18.26 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.78 (0.22), residues: 1364
  helix:  1.66 (0.19), residues: 680
  sheet: -1.23 (0.32), residues: 220
  loop : -0.16 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 313 
 HIS   0.002   0.000   HIS C 245 
 PHE   0.018   0.001   PHE B  79 
 TYR   0.021   0.001   TYR B 203 
 ARG   0.005   0.000   ARG B 303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03489 (  564)
  hydrogen bonds       : angle       4.11262 ( 1608)
  covalent geometry    : bond        0.00277 (10672)
  covalent geometry    : angle       0.59824 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 178
  time to evaluate  : 2.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  134 CYS cc_start: 0.8364 (p) cc_final: 0.7971 (p)
REVERT: B  250 MET cc_start: 0.8840 (tpt) cc_final: 0.8636 (tpt)
REVERT: B  316 LYS cc_start: 0.8973 (mmmt) cc_final: 0.8753 (mmtm)
REVERT: A   60 GLN cc_start: 0.8790 (mt0) cc_final: 0.8547 (mt0)
REVERT: A   68 ARG cc_start: 0.9097 (mtm180) cc_final: 0.8888 (mtm180)
REVERT: A  301 TYR cc_start: 0.7404 (m-10) cc_final: 0.7187 (m-10)
REVERT: A  321 LYS cc_start: 0.8956 (mmmt) cc_final: 0.8734 (mppt)
REVERT: C   60 GLN cc_start: 0.8759 (mt0) cc_final: 0.8472 (mt0)
REVERT: C   66 ASP cc_start: 0.9135 (t0) cc_final: 0.8688 (p0)
REVERT: C   67 ASP cc_start: 0.8909 (p0) cc_final: 0.8603 (t0)
REVERT: C  250 MET cc_start: 0.8794 (tpp) cc_final: 0.8564 (tpt)
REVERT: C  311 LYS cc_start: 0.9430 (ttpp) cc_final: 0.9209 (ttpp)
REVERT: D  164 MET cc_start: 0.8590 (tmm) cc_final: 0.8376 (ptt)
REVERT: D  229 LYS cc_start: 0.9259 (tptm) cc_final: 0.8964 (tppp)
REVERT: D  250 MET cc_start: 0.8801 (mmm) cc_final: 0.8474 (tpp)
REVERT: D  330 ARG cc_start: 0.9176 (mmm160) cc_final: 0.8653 (ttp-170)
  outliers start: 27
  outliers final: 20
  residues processed: 191
  average time/residue: 0.3816
  time to fit residues: 101.5084
Evaluate side-chains
  180 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 160
  time to evaluate  : 1.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  326 GLU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   80 HIS
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  326 GLU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  326 GLU
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   69 VAL
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  326 GLU
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 89 optimal weight:    3.9990
   chunk 53 optimal weight:    0.5980
   chunk 27 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 125 optimal weight:    7.9990
   chunk 132 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
B  60 GLN
B  80 HIS
** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 168 ASN
** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  80 HIS
C 168 ASN
D  60 GLN
D  80 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.093531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.071030 restraints weight = 29396.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.073372 restraints weight = 16934.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.074882 restraints weight = 11968.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.4388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10672  Z= 0.124
  Angle     :  0.609  11.367  14464  Z= 0.305
  Chirality :  0.042   0.149   1644
  Planarity :  0.004   0.041   1880
  Dihedral  :  4.139  17.698   1472
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 18.88 %
    Favored  : 78.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.88 (0.22), residues: 1364
  helix:  1.68 (0.19), residues: 684
  sheet: -0.54 (0.35), residues: 184
  loop : -0.44 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 313 
 HIS   0.007   0.001   HIS D  80 
 PHE   0.020   0.002   PHE B  79 
 TYR   0.019   0.001   TYR B 203 
 ARG   0.005   0.000   ARG C  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03410 (  564)
  hydrogen bonds       : angle       4.08693 ( 1608)
  covalent geometry    : bond        0.00287 (10672)
  covalent geometry    : angle       0.60947 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 172
  time to evaluate  : 1.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  134 CYS cc_start: 0.8396 (p) cc_final: 0.7999 (p)
REVERT: B  316 LYS cc_start: 0.8997 (mmmt) cc_final: 0.8775 (mmtm)
REVERT: A   60 GLN cc_start: 0.8784 (mt0) cc_final: 0.8579 (mt0)
REVERT: C   60 GLN cc_start: 0.8728 (mt0) cc_final: 0.8423 (mt0)
REVERT: C   66 ASP cc_start: 0.9149 (t0) cc_final: 0.8744 (p0)
REVERT: C   67 ASP cc_start: 0.8846 (p0) cc_final: 0.8581 (t0)
REVERT: C  250 MET cc_start: 0.8752 (tpp) cc_final: 0.8531 (tpt)
REVERT: C  311 LYS cc_start: 0.9485 (ttpp) cc_final: 0.9281 (ttpp)
REVERT: C  330 ARG cc_start: 0.9142 (mmm160) cc_final: 0.8833 (ttp-170)
REVERT: D  229 LYS cc_start: 0.9283 (tptm) cc_final: 0.9052 (tptt)
REVERT: D  250 MET cc_start: 0.8776 (mmm) cc_final: 0.8515 (tpp)
REVERT: D  301 TYR cc_start: 0.6949 (m-80) cc_final: 0.6683 (m-10)
REVERT: D  326 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8791 (pp20)
REVERT: D  330 ARG cc_start: 0.9166 (mmm160) cc_final: 0.8612 (ttp-170)
  outliers start: 31
  outliers final: 23
  residues processed: 193
  average time/residue: 0.2885
  time to fit residues: 77.1779
Evaluate side-chains
  182 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 158
  time to evaluate  : 1.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  326 GLU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   80 HIS
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  326 GLU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue   80 HIS
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  326 GLU
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   69 VAL
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  326 GLU
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 60 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 68 optimal weight:    6.9990
   chunk 109 optimal weight:    6.9990
   chunk 65 optimal weight:    0.0000
   chunk 130 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.9188

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

Flipped N/Q/H residues before XYZ refinement:
B  60 GLN
B  80 HIS
** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  80 HIS
A 168 ASN
** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  80 HIS
C 168 ASN
D  80 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.093796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.071149 restraints weight = 29600.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.073516 restraints weight = 17058.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.074988 restraints weight = 11984.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.4512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10672  Z= 0.122
  Angle     :  0.614  11.847  14464  Z= 0.302
  Chirality :  0.042   0.145   1644
  Planarity :  0.004   0.040   1880
  Dihedral  :  4.072  16.373   1472
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 18.62 %
    Favored  : 78.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.93 (0.22), residues: 1364
  helix:  1.72 (0.19), residues: 684
  sheet: -0.55 (0.35), residues: 184
  loop : -0.40 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 313 
 HIS   0.007   0.001   HIS D  80 
 PHE   0.015   0.002   PHE B  79 
 TYR   0.024   0.002   TYR B 137 
 ARG   0.005   0.000   ARG C  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03367 (  564)
  hydrogen bonds       : angle       4.01156 ( 1608)
  covalent geometry    : bond        0.00285 (10672)
  covalent geometry    : angle       0.61443 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 163
  time to evaluate  : 1.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 PHE cc_start: 0.8938 (t80) cc_final: 0.8659 (t80)
REVERT: B  134 CYS cc_start: 0.8371 (p) cc_final: 0.7963 (p)
REVERT: B  250 MET cc_start: 0.8713 (mmm) cc_final: 0.8441 (tpp)
REVERT: A   60 GLN cc_start: 0.8804 (mt0) cc_final: 0.8567 (mt0)
REVERT: C   60 GLN cc_start: 0.8734 (mt0) cc_final: 0.8472 (mt0)
REVERT: C  250 MET cc_start: 0.8769 (tpp) cc_final: 0.8537 (tpt)
REVERT: C  311 LYS cc_start: 0.9534 (ttpp) cc_final: 0.9317 (ttpp)
REVERT: C  330 ARG cc_start: 0.9126 (mmm160) cc_final: 0.8832 (ttp-170)
REVERT: D  229 LYS cc_start: 0.9290 (tptm) cc_final: 0.8978 (tppp)
REVERT: D  301 TYR cc_start: 0.6982 (m-80) cc_final: 0.6645 (m-10)
REVERT: D  326 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8720 (pp20)
REVERT: D  330 ARG cc_start: 0.9190 (mmm160) cc_final: 0.8630 (ttp-170)
  outliers start: 30
  outliers final: 18
  residues processed: 185
  average time/residue: 0.2138
  time to fit residues: 56.7545
Evaluate side-chains
  175 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 156
  time to evaluate  : 1.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  326 GLU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   80 HIS
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue   80 HIS
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  326 GLU
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  326 GLU
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 109 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 80 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 37 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 121 optimal weight:    0.0670
   chunk 119 optimal weight:    3.9990
   chunk 49 optimal weight:    8.9990
   overall best weight:    1.7922

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

Flipped N/Q/H residues before XYZ refinement:
B  60 GLN
B  80 HIS
** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 168 ASN
** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  80 HIS
C 168 ASN
D  80 HIS
D 125 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.091861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.069689 restraints weight = 29723.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.072014 restraints weight = 16927.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.073447 restraints weight = 11845.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.4646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10672  Z= 0.170
  Angle     :  0.648  12.007  14464  Z= 0.323
  Chirality :  0.043   0.152   1644
  Planarity :  0.004   0.043   1880
  Dihedral  :  4.159  19.399   1472
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 19.42 %
    Favored  : 78.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.98 (0.22), residues: 1364
  helix:  1.74 (0.19), residues: 684
  sheet: -0.52 (0.35), residues: 184
  loop : -0.34 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 147 
 HIS   0.005   0.001   HIS A  80 
 PHE   0.016   0.002   PHE B  79 
 TYR   0.022   0.002   TYR B 137 
 ARG   0.006   0.000   ARG C  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03593 (  564)
  hydrogen bonds       : angle       4.07026 ( 1608)
  covalent geometry    : bond        0.00393 (10672)
  covalent geometry    : angle       0.64817 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 162
  time to evaluate  : 1.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  134 CYS cc_start: 0.8366 (p) cc_final: 0.7941 (p)
REVERT: B  229 LYS cc_start: 0.9361 (tttt) cc_final: 0.9149 (tptm)
REVERT: B  250 MET cc_start: 0.8730 (mmm) cc_final: 0.8437 (tpp)
REVERT: A   60 GLN cc_start: 0.8757 (mt0) cc_final: 0.8507 (mt0)
REVERT: A  311 LYS cc_start: 0.9722 (ptmm) cc_final: 0.9471 (ptmm)
REVERT: C  250 MET cc_start: 0.8790 (tpp) cc_final: 0.8553 (tpt)
REVERT: C  311 LYS cc_start: 0.9543 (ttpp) cc_final: 0.9327 (ttpp)
REVERT: D  229 LYS cc_start: 0.9310 (tptm) cc_final: 0.8995 (tppp)
REVERT: D  250 MET cc_start: 0.8781 (mmm) cc_final: 0.8543 (tpp)
REVERT: D  301 TYR cc_start: 0.7092 (m-80) cc_final: 0.6713 (m-10)
REVERT: D  330 ARG cc_start: 0.9193 (mmm160) cc_final: 0.8716 (ttp-170)
REVERT: D  339 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8273 (pm20)
  outliers start: 27
  outliers final: 20
  residues processed: 180
  average time/residue: 0.2158
  time to fit residues: 56.0427
Evaluate side-chains
  171 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 150
  time to evaluate  : 1.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  326 GLU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  217 SER
Chi-restraints excluded: chain C residue  326 GLU
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   69 VAL
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  339 GLN
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 94 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 75 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 132 optimal weight:    6.9990
   chunk 123 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 97 optimal weight:    3.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
B  60 GLN
B  80 HIS
B 287 ASN
** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 168 ASN
** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  80 HIS
C 168 ASN
D  80 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.091734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.069529 restraints weight = 29897.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.071877 restraints weight = 16859.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.073330 restraints weight = 11744.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.4799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10672  Z= 0.158
  Angle     :  0.651  12.208  14464  Z= 0.326
  Chirality :  0.043   0.154   1644
  Planarity :  0.004   0.041   1880
  Dihedral  :  4.155  19.432   1472
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 20.41 %
    Favored  : 77.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.99 (0.22), residues: 1364
  helix:  1.72 (0.19), residues: 684
  sheet: -0.49 (0.35), residues: 184
  loop : -0.30 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 313 
 HIS   0.003   0.000   HIS D  80 
 PHE   0.042   0.002   PHE B  79 
 TYR   0.021   0.002   TYR B 137 
 ARG   0.010   0.000   ARG B  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03565 (  564)
  hydrogen bonds       : angle       4.13040 ( 1608)
  covalent geometry    : bond        0.00369 (10672)
  covalent geometry    : angle       0.65121 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 158
  time to evaluate  : 2.041 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  134 CYS cc_start: 0.8371 (p) cc_final: 0.7948 (p)
REVERT: B  229 LYS cc_start: 0.9372 (tttt) cc_final: 0.8932 (tptt)
REVERT: B  250 MET cc_start: 0.8714 (mmm) cc_final: 0.8476 (tpp)
REVERT: A   60 GLN cc_start: 0.8751 (mt0) cc_final: 0.8493 (mt0)
REVERT: A  311 LYS cc_start: 0.9744 (ptmm) cc_final: 0.9496 (ptmm)
REVERT: A  330 ARG cc_start: 0.9122 (mmm160) cc_final: 0.8856 (ttm170)
REVERT: C  250 MET cc_start: 0.8771 (tpp) cc_final: 0.8535 (tpt)
REVERT: C  311 LYS cc_start: 0.9590 (ttpp) cc_final: 0.9326 (ttpp)
REVERT: D  229 LYS cc_start: 0.9310 (tptm) cc_final: 0.8999 (tppp)
REVERT: D  250 MET cc_start: 0.8773 (mmm) cc_final: 0.8555 (tpp)
REVERT: D  301 TYR cc_start: 0.7082 (m-80) cc_final: 0.6696 (m-10)
REVERT: D  330 ARG cc_start: 0.9172 (mmm160) cc_final: 0.8719 (ttp-170)
REVERT: D  339 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8345 (pm20)
  outliers start: 24
  outliers final: 18
  residues processed: 174
  average time/residue: 0.2730
  time to fit residues: 67.9493
Evaluate side-chains
  167 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 148
  time to evaluate  : 2.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  217 SER
Chi-restraints excluded: chain C residue  326 GLU
Chi-restraints excluded: chain D residue   69 VAL
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  339 GLN
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 93 optimal weight:    0.8980
   chunk 106 optimal weight:    3.9990
   chunk 108 optimal weight:    0.6980
   chunk 41 optimal weight:    9.9990
   chunk 19 optimal weight:    2.9990
   chunk 105 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 112 optimal weight:    0.0270
   overall best weight:    0.7038

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

Flipped N/Q/H residues before XYZ refinement:
B  60 GLN
B  80 HIS
** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 168 ASN
** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  80 HIS
C 168 ASN
D  80 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.093118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.071940 restraints weight = 29621.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.074341 restraints weight = 16202.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.075785 restraints weight = 11027.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.4946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10672  Z= 0.123
  Angle     :  0.658  11.869  14464  Z= 0.327
  Chirality :  0.043   0.143   1644
  Planarity :  0.004   0.052   1880
  Dihedral  :  4.087  21.688   1472
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 21.40 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.93 (0.23), residues: 1364
  helix:  1.58 (0.19), residues: 708
  sheet: -0.93 (0.33), residues: 216
  loop :  0.02 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 313 
 HIS   0.005   0.000   HIS D  80 
 PHE   0.037   0.002   PHE B  79 
 TYR   0.021   0.002   TYR B 137 
 ARG   0.008   0.000   ARG C  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03332 (  564)
  hydrogen bonds       : angle       4.09277 ( 1608)
  covalent geometry    : bond        0.00287 (10672)
  covalent geometry    : angle       0.65828 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 159
  time to evaluate  : 1.771 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  130 LEU cc_start: 0.9221 (tp) cc_final: 0.8576 (tt)
REVERT: B  134 CYS cc_start: 0.8393 (p) cc_final: 0.7794 (p)
REVERT: B  182 ILE cc_start: 0.8551 (mp) cc_final: 0.8068 (mt)
REVERT: B  250 MET cc_start: 0.8729 (mmm) cc_final: 0.8518 (tpp)
REVERT: B  297 LEU cc_start: 0.8140 (tp) cc_final: 0.7860 (tt)
REVERT: A   60 GLN cc_start: 0.8762 (mt0) cc_final: 0.8477 (mt0)
REVERT: A  311 LYS cc_start: 0.9720 (ptmm) cc_final: 0.9474 (ptmm)
REVERT: A  325 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8108 (pp20)
REVERT: C  250 MET cc_start: 0.8780 (tpp) cc_final: 0.8545 (tpt)
REVERT: C  311 LYS cc_start: 0.9596 (ttpp) cc_final: 0.9323 (ttpp)
REVERT: C  330 ARG cc_start: 0.9156 (mmm160) cc_final: 0.8871 (ttp-170)
REVERT: D  229 LYS cc_start: 0.9290 (tptm) cc_final: 0.8985 (tppp)
REVERT: D  250 MET cc_start: 0.8763 (mmm) cc_final: 0.8546 (tpp)
REVERT: D  301 TYR cc_start: 0.7078 (m-80) cc_final: 0.6688 (m-10)
  outliers start: 19
  outliers final: 13
  residues processed: 172
  average time/residue: 0.2763
  time to fit residues: 69.1858
Evaluate side-chains
  166 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 153
  time to evaluate  : 1.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain C residue   80 HIS
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  217 SER
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 135 optimal weight:    0.1980
   chunk 95 optimal weight:    0.0060
   chunk 43 optimal weight:    2.9990
   chunk 45 optimal weight:    0.3980
   chunk 21 optimal weight:    2.9990
   chunk 40 optimal weight:    9.9990
   chunk 62 optimal weight:    0.0040
   chunk 38 optimal weight:    8.9990
   overall best weight:    0.3210

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

Flipped N/Q/H residues before XYZ refinement:
B  60 GLN
B  80 HIS
** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  80 HIS
** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  80 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.094134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.073453 restraints weight = 29485.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.075787 restraints weight = 16853.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.077224 restraints weight = 11736.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.5032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  10672  Z= 0.118
  Angle     :  0.668  12.517  14464  Z= 0.334
  Chirality :  0.043   0.235   1644
  Planarity :  0.004   0.094   1880
  Dihedral  :  4.054  21.149   1472
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 22.12 %
    Favored  : 76.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.05 (0.23), residues: 1364
  helix:  1.64 (0.19), residues: 704
  sheet: -0.34 (0.37), residues: 184
  loop : -0.21 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 313 
 HIS   0.005   0.001   HIS C  80 
 PHE   0.036   0.002   PHE B  79 
 TYR   0.021   0.002   TYR B 137 
 ARG   0.008   0.000   ARG C  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03270 (  564)
  hydrogen bonds       : angle       4.09598 ( 1608)
  covalent geometry    : bond        0.00266 (10672)
  covalent geometry    : angle       0.66793 (14464)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3746.28 seconds
wall clock time: 72 minutes 13.77 seconds (4333.77 seconds total)