Starting phenix.real_space_refine
on Tue May 13 19:36:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z2z_39745/05_2025/8z2z_39745.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z2z_39745/05_2025/8z2z_39745.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8z2z_39745/05_2025/8z2z_39745.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z2z_39745/05_2025/8z2z_39745.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z2z_39745/05_2025/8z2z_39745.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z2z_39745/05_2025/8z2z_39745.cif"
  }
  resolution = 3.25
  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=   0.001 sd=   0.059
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      80      5.16       5
     C    6972      2.51       5
     N    1776      2.21       5
     O    2032      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 52 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 10860
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2689
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 330, 2689
          Classifications: {'peptide': 330}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320}
    Chain: "A"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Classifications: {'peptide': 1}
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 5.94, per 1000 atoms: 0.55
  Number of scatterers: 10860
  At special positions: 0
  Unit cell: (138.61, 103.75, 80.51, 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      80     16.00
     O    2032      8.00
     N    1776      7.00
     C    6972      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.87
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2528

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 16 sheets defined
      33.3% alpha, 37.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 49 through 54
      removed outlier: 3.550A  pdb=" N   TYR A  52 " --> pdb=" O   SER A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 58
    Processing helix  chain 'A' and resid 59 through 68
      removed outlier: 4.188A  pdb=" N   HIS A  63 " --> pdb=" O   HIS A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 82
    Processing helix  chain 'A' and resid 83 through 88
      removed outlier: 3.651A  pdb=" N   PHE A  87 " --> pdb=" O   ASN A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 109
    Processing helix  chain 'A' and resid 122 through 133
    Processing helix  chain 'A' and resid 165 through 171
      removed outlier: 4.856A  pdb=" N   TYR A 170 " --> pdb=" O   CYS A 167 " (cutoff:3.500A)
      removed outlier: 7.192A  pdb=" N   GLU A 171 " --> pdb=" O   LEU A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 184
      removed outlier: 4.327A  pdb=" N   THR A 176 " --> pdb=" O   SER A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 213
    Processing helix  chain 'A' and resid 214 through 218
    Processing helix  chain 'A' and resid 224 through 232
      removed outlier: 3.807A  pdb=" N   VAL A 230 " --> pdb=" O   CYS A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 245
    Processing helix  chain 'B' and resid 49 through 54
      removed outlier: 3.549A  pdb=" N   TYR B  52 " --> pdb=" O   SER B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 58
    Processing helix  chain 'B' and resid 59 through 68
      removed outlier: 4.187A  pdb=" N   HIS B  63 " --> pdb=" O   HIS B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 82
    Processing helix  chain 'B' and resid 83 through 88
      removed outlier: 3.651A  pdb=" N   PHE B  87 " --> pdb=" O   ASN B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 109
    Processing helix  chain 'B' and resid 122 through 133
    Processing helix  chain 'B' and resid 165 through 171
      removed outlier: 4.856A  pdb=" N   TYR B 170 " --> pdb=" O   CYS B 167 " (cutoff:3.500A)
      removed outlier: 7.191A  pdb=" N   GLU B 171 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 184
      removed outlier: 4.325A  pdb=" N   THR B 176 " --> pdb=" O   SER B 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 213
    Processing helix  chain 'B' and resid 214 through 218
    Processing helix  chain 'B' and resid 224 through 232
      removed outlier: 3.807A  pdb=" N   VAL B 230 " --> pdb=" O   CYS B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 245
    Processing helix  chain 'C' and resid 49 through 54
      removed outlier: 3.550A  pdb=" N   TYR C  52 " --> pdb=" O   SER C  49 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 55 through 58
    Processing helix  chain 'C' and resid 59 through 68
      removed outlier: 4.187A  pdb=" N   HIS C  63 " --> pdb=" O   HIS C  59 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 69 through 82
    Processing helix  chain 'C' and resid 83 through 88
      removed outlier: 3.651A  pdb=" N   PHE C  87 " --> pdb=" O   ASN C  83 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 100 through 109
    Processing helix  chain 'C' and resid 122 through 133
    Processing helix  chain 'C' and resid 165 through 171
      removed outlier: 4.856A  pdb=" N   TYR C 170 " --> pdb=" O   CYS C 167 " (cutoff:3.500A)
      removed outlier: 7.192A  pdb=" N   GLU C 171 " --> pdb=" O   LEU C 168 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 172 through 184
      removed outlier: 4.326A  pdb=" N   THR C 176 " --> pdb=" O   SER C 172 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 205 through 213
    Processing helix  chain 'C' and resid 214 through 218
    Processing helix  chain 'C' and resid 224 through 232
      removed outlier: 3.807A  pdb=" N   VAL C 230 " --> pdb=" O   CYS C 226 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 241 through 245
    Processing helix  chain 'D' and resid 49 through 54
      removed outlier: 3.550A  pdb=" N   TYR D  52 " --> pdb=" O   SER D  49 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 58
    Processing helix  chain 'D' and resid 59 through 68
      removed outlier: 4.188A  pdb=" N   HIS D  63 " --> pdb=" O   HIS D  59 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 69 through 82
    Processing helix  chain 'D' and resid 83 through 88
      removed outlier: 3.650A  pdb=" N   PHE D  87 " --> pdb=" O   ASN D  83 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 109
    Processing helix  chain 'D' and resid 122 through 133
    Processing helix  chain 'D' and resid 165 through 171
      removed outlier: 4.857A  pdb=" N   TYR D 170 " --> pdb=" O   CYS D 167 " (cutoff:3.500A)
      removed outlier: 7.192A  pdb=" N   GLU D 171 " --> pdb=" O   LEU D 168 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 172 through 184
      removed outlier: 4.326A  pdb=" N   THR D 176 " --> pdb=" O   SER D 172 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 205 through 213
    Processing helix  chain 'D' and resid 214 through 218
    Processing helix  chain 'D' and resid 224 through 232
      removed outlier: 3.808A  pdb=" N   VAL D 230 " --> pdb=" O   CYS D 226 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 241 through 245
    Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 143
      removed outlier: 6.968A  pdb=" N   VAL A  91 " --> pdb=" O   ASP A 157 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   ILE A 159 " --> pdb=" O   VAL A  91 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   LEU A  93 " --> pdb=" O   ILE A 159 " (cutoff:3.500A)
      removed outlier: 5.430A  pdb=" N   SER A 161 " --> pdb=" O   LEU A  93 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   VAL A  95 " --> pdb=" O   SER A 161 " (cutoff:3.500A)
      removed outlier: 7.318A  pdb=" N   ASP A 157 " --> pdb=" O   ASP A 188 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 236 through 237
      removed outlier: 13.431A  pdb=" N   THR A 315 " --> pdb=" O   ASN A 289 " (cutoff:3.500A)
      removed outlier: 12.419A  pdb=" N   ASN A 289 " --> pdb=" O   THR A 315 " (cutoff:3.500A)
      removed outlier: 11.623A  pdb=" N   PHE A 317 " --> pdb=" O   TYR A 287 " (cutoff:3.500A)
      removed outlier: 11.187A  pdb=" N   TYR A 287 " --> pdb=" O   PHE A 317 " (cutoff:3.500A)
      removed outlier: 11.881A  pdb=" N   MET A 319 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
      removed outlier: 11.793A  pdb=" N   VAL A 285 " --> pdb=" O   MET A 319 " (cutoff:3.500A)
      removed outlier: 10.847A  pdb=" N   ASP A 321 " --> pdb=" O   ALA A 283 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   ALA A 283 " --> pdb=" O   ASP A 321 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   ALA A 196 " --> pdb=" O   GLU A 254 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   GLU A 254 " --> pdb=" O   ALA A 196 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   LEU A 198 " --> pdb=" O   ILE A 252 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 237
      removed outlier: 13.431A  pdb=" N   THR A 315 " --> pdb=" O   ASN A 289 " (cutoff:3.500A)
      removed outlier: 12.419A  pdb=" N   ASN A 289 " --> pdb=" O   THR A 315 " (cutoff:3.500A)
      removed outlier: 11.623A  pdb=" N   PHE A 317 " --> pdb=" O   TYR A 287 " (cutoff:3.500A)
      removed outlier: 11.187A  pdb=" N   TYR A 287 " --> pdb=" O   PHE A 317 " (cutoff:3.500A)
      removed outlier: 11.881A  pdb=" N   MET A 319 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
      removed outlier: 11.793A  pdb=" N   VAL A 285 " --> pdb=" O   MET A 319 " (cutoff:3.500A)
      removed outlier: 10.847A  pdb=" N   ASP A 321 " --> pdb=" O   ALA A 283 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   ALA A 283 " --> pdb=" O   ASP A 321 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   THR A 299 " --> pdb=" O   PHE A 292 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 268 through 274
      removed outlier: 6.026A  pdb=" N   GLU A 330 " --> pdb=" O   LYS A 356 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   LYS A 356 " --> pdb=" O   GLU A 330 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LEU A 347 " --> pdb=" O   MET A 370 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 139 through 143
      removed outlier: 6.968A  pdb=" N   VAL B  91 " --> pdb=" O   ASP B 157 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   ILE B 159 " --> pdb=" O   VAL B  91 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   LEU B  93 " --> pdb=" O   ILE B 159 " (cutoff:3.500A)
      removed outlier: 5.430A  pdb=" N   SER B 161 " --> pdb=" O   LEU B  93 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   VAL B  95 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 7.318A  pdb=" N   ASP B 157 " --> pdb=" O   ASP B 188 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 236 through 237
      removed outlier: 13.432A  pdb=" N   THR B 315 " --> pdb=" O   ASN B 289 " (cutoff:3.500A)
      removed outlier: 12.418A  pdb=" N   ASN B 289 " --> pdb=" O   THR B 315 " (cutoff:3.500A)
      removed outlier: 11.624A  pdb=" N   PHE B 317 " --> pdb=" O   TYR B 287 " (cutoff:3.500A)
      removed outlier: 11.186A  pdb=" N   TYR B 287 " --> pdb=" O   PHE B 317 " (cutoff:3.500A)
      removed outlier: 11.880A  pdb=" N   MET B 319 " --> pdb=" O   VAL B 285 " (cutoff:3.500A)
      removed outlier: 11.792A  pdb=" N   VAL B 285 " --> pdb=" O   MET B 319 " (cutoff:3.500A)
      removed outlier: 10.849A  pdb=" N   ASP B 321 " --> pdb=" O   ALA B 283 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   ALA B 283 " --> pdb=" O   ASP B 321 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   ALA B 196 " --> pdb=" O   GLU B 254 " (cutoff:3.500A)
      removed outlier: 4.719A  pdb=" N   GLU B 254 " --> pdb=" O   ALA B 196 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   LEU B 198 " --> pdb=" O   ILE B 252 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 236 through 237
      removed outlier: 13.432A  pdb=" N   THR B 315 " --> pdb=" O   ASN B 289 " (cutoff:3.500A)
      removed outlier: 12.418A  pdb=" N   ASN B 289 " --> pdb=" O   THR B 315 " (cutoff:3.500A)
      removed outlier: 11.624A  pdb=" N   PHE B 317 " --> pdb=" O   TYR B 287 " (cutoff:3.500A)
      removed outlier: 11.186A  pdb=" N   TYR B 287 " --> pdb=" O   PHE B 317 " (cutoff:3.500A)
      removed outlier: 11.880A  pdb=" N   MET B 319 " --> pdb=" O   VAL B 285 " (cutoff:3.500A)
      removed outlier: 11.792A  pdb=" N   VAL B 285 " --> pdb=" O   MET B 319 " (cutoff:3.500A)
      removed outlier: 10.849A  pdb=" N   ASP B 321 " --> pdb=" O   ALA B 283 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   ALA B 283 " --> pdb=" O   ASP B 321 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   THR B 299 " --> pdb=" O   PHE B 292 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 268 through 274
      removed outlier: 6.026A  pdb=" N   GLU B 330 " --> pdb=" O   LYS B 356 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   LYS B 356 " --> pdb=" O   GLU B 330 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LEU B 347 " --> pdb=" O   MET B 370 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 139 through 143
      removed outlier: 6.968A  pdb=" N   VAL C  91 " --> pdb=" O   ASP C 157 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   ILE C 159 " --> pdb=" O   VAL C  91 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   LEU C  93 " --> pdb=" O   ILE C 159 " (cutoff:3.500A)
      removed outlier: 5.430A  pdb=" N   SER C 161 " --> pdb=" O   LEU C  93 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   VAL C  95 " --> pdb=" O   SER C 161 " (cutoff:3.500A)
      removed outlier: 7.318A  pdb=" N   ASP C 157 " --> pdb=" O   ASP C 188 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 236 through 237
      removed outlier: 13.431A  pdb=" N   THR C 315 " --> pdb=" O   ASN C 289 " (cutoff:3.500A)
      removed outlier: 12.419A  pdb=" N   ASN C 289 " --> pdb=" O   THR C 315 " (cutoff:3.500A)
      removed outlier: 11.624A  pdb=" N   PHE C 317 " --> pdb=" O   TYR C 287 " (cutoff:3.500A)
      removed outlier: 11.187A  pdb=" N   TYR C 287 " --> pdb=" O   PHE C 317 " (cutoff:3.500A)
      removed outlier: 11.880A  pdb=" N   MET C 319 " --> pdb=" O   VAL C 285 " (cutoff:3.500A)
      removed outlier: 11.793A  pdb=" N   VAL C 285 " --> pdb=" O   MET C 319 " (cutoff:3.500A)
      removed outlier: 10.847A  pdb=" N   ASP C 321 " --> pdb=" O   ALA C 283 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   ALA C 283 " --> pdb=" O   ASP C 321 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   ALA C 196 " --> pdb=" O   GLU C 254 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   GLU C 254 " --> pdb=" O   ALA C 196 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   LEU C 198 " --> pdb=" O   ILE C 252 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 236 through 237
      removed outlier: 13.431A  pdb=" N   THR C 315 " --> pdb=" O   ASN C 289 " (cutoff:3.500A)
      removed outlier: 12.419A  pdb=" N   ASN C 289 " --> pdb=" O   THR C 315 " (cutoff:3.500A)
      removed outlier: 11.624A  pdb=" N   PHE C 317 " --> pdb=" O   TYR C 287 " (cutoff:3.500A)
      removed outlier: 11.187A  pdb=" N   TYR C 287 " --> pdb=" O   PHE C 317 " (cutoff:3.500A)
      removed outlier: 11.880A  pdb=" N   MET C 319 " --> pdb=" O   VAL C 285 " (cutoff:3.500A)
      removed outlier: 11.793A  pdb=" N   VAL C 285 " --> pdb=" O   MET C 319 " (cutoff:3.500A)
      removed outlier: 10.847A  pdb=" N   ASP C 321 " --> pdb=" O   ALA C 283 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   ALA C 283 " --> pdb=" O   ASP C 321 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   THR C 299 " --> pdb=" O   PHE C 292 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 268 through 274
      removed outlier: 6.027A  pdb=" N   GLU C 330 " --> pdb=" O   LYS C 356 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   LYS C 356 " --> pdb=" O   GLU C 330 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LEU C 347 " --> pdb=" O   MET C 370 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 139 through 143
      removed outlier: 6.830A  pdb=" N   VAL D  91 " --> pdb=" O   VAL D 156 " (cutoff:3.500A)
      removed outlier: 7.317A  pdb=" N   ASP D 157 " --> pdb=" O   ASP D 188 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 236 through 237
      removed outlier: 13.431A  pdb=" N   THR D 315 " --> pdb=" O   ASN D 289 " (cutoff:3.500A)
      removed outlier: 12.418A  pdb=" N   ASN D 289 " --> pdb=" O   THR D 315 " (cutoff:3.500A)
      removed outlier: 11.623A  pdb=" N   PHE D 317 " --> pdb=" O   TYR D 287 " (cutoff:3.500A)
      removed outlier: 11.186A  pdb=" N   TYR D 287 " --> pdb=" O   PHE D 317 " (cutoff:3.500A)
      removed outlier: 11.880A  pdb=" N   MET D 319 " --> pdb=" O   VAL D 285 " (cutoff:3.500A)
      removed outlier: 11.793A  pdb=" N   VAL D 285 " --> pdb=" O   MET D 319 " (cutoff:3.500A)
      removed outlier: 10.848A  pdb=" N   ASP D 321 " --> pdb=" O   ALA D 283 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   ALA D 283 " --> pdb=" O   ASP D 321 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   ALA D 196 " --> pdb=" O   GLU D 254 " (cutoff:3.500A)
      removed outlier: 4.719A  pdb=" N   GLU D 254 " --> pdb=" O   ALA D 196 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   LEU D 198 " --> pdb=" O   ILE D 252 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 236 through 237
      removed outlier: 13.431A  pdb=" N   THR D 315 " --> pdb=" O   ASN D 289 " (cutoff:3.500A)
      removed outlier: 12.418A  pdb=" N   ASN D 289 " --> pdb=" O   THR D 315 " (cutoff:3.500A)
      removed outlier: 11.623A  pdb=" N   PHE D 317 " --> pdb=" O   TYR D 287 " (cutoff:3.500A)
      removed outlier: 11.186A  pdb=" N   TYR D 287 " --> pdb=" O   PHE D 317 " (cutoff:3.500A)
      removed outlier: 11.880A  pdb=" N   MET D 319 " --> pdb=" O   VAL D 285 " (cutoff:3.500A)
      removed outlier: 11.793A  pdb=" N   VAL D 285 " --> pdb=" O   MET D 319 " (cutoff:3.500A)
      removed outlier: 10.848A  pdb=" N   ASP D 321 " --> pdb=" O   ALA D 283 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   ALA D 283 " --> pdb=" O   ASP D 321 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   THR D 299 " --> pdb=" O   PHE D 292 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 268 through 274
      removed outlier: 6.026A  pdb=" N   GLU D 330 " --> pdb=" O   LYS D 356 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   LYS D 356 " --> pdb=" O   GLU D 330 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LEU D 347 " --> pdb=" O   MET D 370 " (cutoff:3.500A)

    480 hydrogen bonds defined for protein.
    1260 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: 3.40

  Time building geometry restraints manager: 3.32 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: 3416
        1.34 -     1.46: 2376
        1.46 -     1.57: 5208
        1.57 -     1.69: 0
        1.69 -     1.81: 124
  Bond restraints: 11124
  Sorted by residual:
  bond pdb=" C2  SAH A 401 "
       pdb=" N3  SAH A 401 "
    ideal  model  delta    sigma   weight residual
    1.322  1.374 -0.052 2.00e-02 2.50e+03 6.83e+00
  bond pdb=" C2  SAH C 401 "
       pdb=" N3  SAH C 401 "
    ideal  model  delta    sigma   weight residual
    1.322  1.374 -0.052 2.00e-02 2.50e+03 6.74e+00
  bond pdb=" C2  SAH D 401 "
       pdb=" N3  SAH D 401 "
    ideal  model  delta    sigma   weight residual
    1.322  1.374 -0.052 2.00e-02 2.50e+03 6.69e+00
  bond pdb=" C2  SAH B 401 "
       pdb=" N3  SAH B 401 "
    ideal  model  delta    sigma   weight residual
    1.322  1.374 -0.052 2.00e-02 2.50e+03 6.69e+00
  bond pdb=" C   LYS A 233 "
       pdb=" N   GLU A 234 "
    ideal  model  delta    sigma   weight residual
    1.331  1.289  0.042 1.63e-02 3.76e+03 6.67e+00
  ... (remaining 11119 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.50: 14829
        2.50 -     5.01: 207
        5.01 -     7.51: 16
        7.51 -    10.02: 12
       10.02 -    12.52: 4
  Bond angle restraints: 15068
  Sorted by residual:
  angle pdb=" CG  SAH C 401 "
        pdb=" SD  SAH C 401 "
        pdb=" C5' SAH C 401 "
      ideal   model   delta    sigma   weight residual
     101.77   89.25   12.52 3.00e+00 1.11e-01 1.74e+01
  angle pdb=" CG  SAH B 401 "
        pdb=" SD  SAH B 401 "
        pdb=" C5' SAH B 401 "
      ideal   model   delta    sigma   weight residual
     101.77   89.28   12.49 3.00e+00 1.11e-01 1.73e+01
  angle pdb=" CG  SAH D 401 "
        pdb=" SD  SAH D 401 "
        pdb=" C5' SAH D 401 "
      ideal   model   delta    sigma   weight residual
     101.77   89.28   12.49 3.00e+00 1.11e-01 1.73e+01
  angle pdb=" CG  SAH A 401 "
        pdb=" SD  SAH A 401 "
        pdb=" C5' SAH A 401 "
      ideal   model   delta    sigma   weight residual
     101.77   89.30   12.47 3.00e+00 1.11e-01 1.73e+01
  angle pdb=" N   GLU D 162 "
        pdb=" CA  GLU D 162 "
        pdb=" C   GLU D 162 "
      ideal   model   delta    sigma   weight residual
     110.44  105.77    4.67 1.20e+00 6.94e-01 1.52e+01
  ... (remaining 15063 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.56: 5955
       15.56 -    31.12: 463
       31.12 -    46.68: 126
       46.68 -    62.24: 24
       62.24 -    77.81: 8
  Dihedral angle restraints: 6576
    sinusoidal: 2656
      harmonic: 3920
  Sorted by residual:
  dihedral pdb=" CA  TRP A 312 "
           pdb=" C   TRP A 312 "
           pdb=" N   LYS A 313 "
           pdb=" CA  LYS A 313 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -142.88  -37.12     0      5.00e+00 4.00e-02 5.51e+01
  dihedral pdb=" CA  TRP D 312 "
           pdb=" C   TRP D 312 "
           pdb=" N   LYS D 313 "
           pdb=" CA  LYS D 313 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -142.93  -37.07     0      5.00e+00 4.00e-02 5.50e+01
  dihedral pdb=" CA  TRP B 312 "
           pdb=" C   TRP B 312 "
           pdb=" N   LYS B 313 "
           pdb=" CA  LYS B 313 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -142.95  -37.05     0      5.00e+00 4.00e-02 5.49e+01
  ... (remaining 6573 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 659
       0.025 -    0.050: 537
       0.050 -    0.074: 258
       0.074 -    0.099: 154
       0.099 -    0.124: 60
  Chirality restraints: 1668
  Sorted by residual:
  chirality pdb=" CA  ILE D 331 "
            pdb=" N   ILE D 331 "
            pdb=" C   ILE D 331 "
            pdb=" CB  ILE D 331 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.83e-01
  chirality pdb=" CA  ILE A 331 "
            pdb=" N   ILE A 331 "
            pdb=" C   ILE A 331 "
            pdb=" CB  ILE A 331 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.78e-01
  chirality pdb=" CA  ILE C 331 "
            pdb=" N   ILE C 331 "
            pdb=" C   ILE C 331 "
            pdb=" CB  ILE C 331 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.74e-01
  ... (remaining 1665 not shown)

  Planarity restraints: 1884
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 313 "   -0.007 2.00e-02 2.50e+03   1.44e-02 2.07e+00
        pdb=" C   LYS A 313 "    0.025 2.00e-02 2.50e+03
        pdb=" O   LYS A 313 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   GLN A 314 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS D 313 "    0.007 2.00e-02 2.50e+03   1.44e-02 2.06e+00
        pdb=" C   LYS D 313 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   LYS D 313 "    0.009 2.00e-02 2.50e+03
        pdb=" N   GLN D 314 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 313 "   -0.007 2.00e-02 2.50e+03   1.43e-02 2.03e+00
        pdb=" C   LYS C 313 "    0.025 2.00e-02 2.50e+03
        pdb=" O   LYS C 313 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   GLN C 314 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1881 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1537
        2.75 -     3.29: 10204
        3.29 -     3.83: 17368
        3.83 -     4.36: 22178
        4.36 -     4.90: 38330
  Nonbonded interactions: 89617
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN C 289 "
            pdb=" OG  SER C 302 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" OD1 ASN A 289 "
            pdb=" OG  SER A 302 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" OD1 ASN B 289 "
            pdb=" OG  SER B 302 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" OD1 ASN D 289 "
            pdb=" OG  SER D 302 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   HIS B  82 "
            pdb=" OH  TYR D 280 "
     model   vdw
     2.273 3.040
  ... (remaining 89612 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: 0.07
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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.060
  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:          0.460
  Check model and map are aligned:         0.090
  Set scattering table:                    0.100
  Process input model:                     26.510
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   33.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
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      :  0.007   0.052  11124  Z= 0.306
  Angle     :  0.795  12.522  15068  Z= 0.419
  Chirality :  0.046   0.124   1668
  Planarity :  0.003   0.033   1884
  Dihedral  : 12.728  77.805   4048
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

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: -0.97 (0.23), residues: 1312
  helix: -0.98 (0.27), residues: 336
  sheet: -0.73 (0.27), residues: 380
  loop : -0.14 (0.26), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 184 
 HIS   0.008   0.001   HIS D 282 
 PHE   0.015   0.002   PHE A  60 
 TYR   0.010   0.001   TYR A 208 
 ARG   0.005   0.001   ARG B 298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21364 (  456)
  hydrogen bonds       : angle       8.82448 ( 1260)
  covalent geometry    : bond        0.00700 (11124)
  covalent geometry    : angle       0.79468 (15068)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 1.307 
Fit side-chains
REVERT: A   57 TYR cc_start: 0.7412 (m-80) cc_final: 0.7205 (m-80)
REVERT: A  234 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7440 (mt-10)
REVERT: B  162 GLU cc_start: 0.7205 (tm-30) cc_final: 0.6941 (tm-30)
REVERT: B  330 GLU cc_start: 0.6316 (tt0) cc_final: 0.6062 (mt-10)
REVERT: B  371 ARG cc_start: 0.7885 (ptt-90) cc_final: 0.7623 (ptt-90)
REVERT: D  234 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7502 (mt-10)
REVERT: D  290 ILE cc_start: 0.8828 (mm) cc_final: 0.8350 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 226
  average time/residue: 0.2444
  time to fit residues: 76.6603
Evaluate side-chains
  138 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 1.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    0.6980
   chunk 100 optimal weight:    6.9990
   chunk 55 optimal weight:    0.5980
   chunk 34 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 103 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 77 optimal weight:    0.5980
   chunk 119 optimal weight:    0.4980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  83 ASN
C  59 HIS
D  83 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.146677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.125062 restraints weight = 14921.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 2.61
r_work: 0.3437 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11124  Z= 0.131
  Angle     :  0.529   7.018  15068  Z= 0.286
  Chirality :  0.043   0.141   1668
  Planarity :  0.004   0.032   1884
  Dihedral  :  4.831  33.321   1460
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  7.72 %
    Favored  : 91.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

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: -0.71 (0.23), residues: 1312
  helix: -0.82 (0.26), residues: 348
  sheet: -0.38 (0.26), residues: 404
  loop : -0.06 (0.27), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 184 
 HIS   0.003   0.001   HIS D 282 
 PHE   0.017   0.001   PHE C 292 
 TYR   0.011   0.001   TYR C 220 
 ARG   0.005   0.001   ARG D 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03984 (  456)
  hydrogen bonds       : angle       5.42198 ( 1260)
  covalent geometry    : bond        0.00298 (11124)
  covalent geometry    : angle       0.52859 (15068)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 168
  time to evaluate  : 1.206 
Fit side-chains
REVERT: A  129 ILE cc_start: 0.8577 (mt) cc_final: 0.8312 (mp)
REVERT: A  204 GLU cc_start: 0.7077 (pt0) cc_final: 0.6857 (pt0)
REVERT: A  261 LYS cc_start: 0.8130 (mtmm) cc_final: 0.7844 (mtmt)
REVERT: A  330 GLU cc_start: 0.6972 (tt0) cc_final: 0.6706 (mm-30)
REVERT: A  345 ARG cc_start: 0.8015 (mmt-90) cc_final: 0.7649 (mmm160)
REVERT: A  352 ASP cc_start: 0.7244 (m-30) cc_final: 0.7043 (t0)
REVERT: B  162 GLU cc_start: 0.7415 (tm-30) cc_final: 0.7072 (tm-30)
REVERT: B  337 MET cc_start: 0.8400 (mtt) cc_final: 0.8192 (mtt)
REVERT: C  162 GLU cc_start: 0.7349 (tm-30) cc_final: 0.6983 (tm-30)
REVERT: C  188 ASP cc_start: 0.7604 (t0) cc_final: 0.7393 (t70)
REVERT: C  319 MET cc_start: 0.8930 (mtm) cc_final: 0.8681 (mtp)
REVERT: C  337 MET cc_start: 0.8470 (mtt) cc_final: 0.8244 (mtt)
REVERT: C  371 ARG cc_start: 0.7572 (ptt-90) cc_final: 0.7355 (ptt-90)
REVERT: D  129 ILE cc_start: 0.8505 (mt) cc_final: 0.8259 (mp)
REVERT: D  162 GLU cc_start: 0.5658 (tm-30) cc_final: 0.5294 (tm-30)
REVERT: D  204 GLU cc_start: 0.6808 (pt0) cc_final: 0.6560 (pt0)
REVERT: D  279 ASP cc_start: 0.7851 (t0) cc_final: 0.7466 (t70)
  outliers start: 13
  outliers final: 12
  residues processed: 177
  average time/residue: 0.2343
  time to fit residues: 58.7765
Evaluate side-chains
  142 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 130
  time to evaluate  : 1.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ILE
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  226 CYS
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain B residue  194 ASP
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain C residue  194 ASP
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue  335 ILE
Chi-restraints excluded: chain D residue  353 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 126 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 123 optimal weight:    0.9990
   chunk 95 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 61 optimal weight:    6.9990
   chunk 11 optimal weight:    0.2980
   chunk 113 optimal weight:    3.9990
   chunk 66 optimal weight:   20.0000
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
D 133 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.146120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.126539 restraints weight = 15049.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 2.26
r_work: 0.3468 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3314 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.2822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11124  Z= 0.134
  Angle     :  0.506   6.467  15068  Z= 0.273
  Chirality :  0.043   0.141   1668
  Planarity :  0.003   0.028   1884
  Dihedral  :  4.584  29.661   1460
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 10.32 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.24), residues: 1312
  helix: -0.51 (0.28), residues: 344
  sheet: -0.19 (0.27), residues: 376
  loop : -0.11 (0.27), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 184 
 HIS   0.003   0.001   HIS A 282 
 PHE   0.016   0.001   PHE C 292 
 TYR   0.009   0.001   TYR B 220 
 ARG   0.003   0.000   ARG A 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03590 (  456)
  hydrogen bonds       : angle       4.97013 ( 1260)
  covalent geometry    : bond        0.00310 (11124)
  covalent geometry    : angle       0.50619 (15068)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 143
  time to evaluate  : 1.340 
Fit side-chains
   revert: symmetry clash
REVERT: A  204 GLU cc_start: 0.7259 (pt0) cc_final: 0.6930 (pt0)
REVERT: A  261 LYS cc_start: 0.8134 (mtmm) cc_final: 0.7900 (mtmt)
REVERT: A  330 GLU cc_start: 0.7358 (tt0) cc_final: 0.7079 (mm-30)
REVERT: A  332 PHE cc_start: 0.8347 (m-10) cc_final: 0.8140 (m-80)
REVERT: A  345 ARG cc_start: 0.8051 (mmt-90) cc_final: 0.7704 (mmm160)
REVERT: A  352 ASP cc_start: 0.7385 (m-30) cc_final: 0.7154 (t0)
REVERT: B  162 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7103 (tm-30)
REVERT: B  319 MET cc_start: 0.8897 (mtm) cc_final: 0.8687 (mtp)
REVERT: C  162 GLU cc_start: 0.7371 (tm-30) cc_final: 0.6985 (tm-30)
REVERT: C  371 ARG cc_start: 0.7761 (ptt-90) cc_final: 0.7517 (ptt-90)
REVERT: D  104 MET cc_start: 0.7965 (mtp) cc_final: 0.7765 (mtt)
REVERT: D  204 GLU cc_start: 0.7183 (pt0) cc_final: 0.6976 (pt0)
REVERT: D  279 ASP cc_start: 0.7948 (t0) cc_final: 0.7704 (t70)
REVERT: D  337 MET cc_start: 0.7695 (ttm) cc_final: 0.7425 (ttm)
  outliers start: 26
  outliers final: 16
  residues processed: 159
  average time/residue: 0.2266
  time to fit residues: 51.6825
Evaluate side-chains
  144 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 1.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  226 CYS
Chi-restraints excluded: chain A residue  314 GLN
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  194 ASP
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  194 ASP
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain D residue  335 ILE
Chi-restraints excluded: chain D residue  353 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 120 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 116 optimal weight:    3.9990
   chunk 94 optimal weight:    3.9990
   chunk 107 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 86 optimal weight:    1.9990
   chunk 130 optimal weight:    0.6980
   chunk 91 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 358 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.145357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.127703 restraints weight = 15022.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 1.90
r_work: 0.3481 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3344 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.3116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11124  Z= 0.132
  Angle     :  0.487   5.196  15068  Z= 0.264
  Chirality :  0.042   0.144   1668
  Planarity :  0.003   0.028   1884
  Dihedral  :  4.490  31.405   1460
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 11.91 %
    Favored  : 86.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.40 (0.24), residues: 1312
  helix: -0.47 (0.28), residues: 344
  sheet: -0.04 (0.28), residues: 356
  loop : -0.09 (0.26), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 184 
 HIS   0.002   0.001   HIS A 282 
 PHE   0.017   0.001   PHE B 292 
 TYR   0.007   0.001   TYR A 287 
 ARG   0.006   0.000   ARG B 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03288 (  456)
  hydrogen bonds       : angle       4.80061 ( 1260)
  covalent geometry    : bond        0.00307 (11124)
  covalent geometry    : angle       0.48719 (15068)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 131
  time to evaluate  : 1.358 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.7911 (mmmt) cc_final: 0.7701 (mmmt)
REVERT: A  104 MET cc_start: 0.7994 (mtm) cc_final: 0.7724 (mtt)
REVERT: A  345 ARG cc_start: 0.8096 (mmt-90) cc_final: 0.7890 (mmm160)
REVERT: B  162 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7045 (tm-30)
REVERT: B  338 ARG cc_start: 0.7544 (ptp90) cc_final: 0.7223 (ptm-80)
REVERT: C  162 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7052 (tm-30)
REVERT: C  371 ARG cc_start: 0.7893 (ptt-90) cc_final: 0.7589 (ptt-90)
REVERT: D  104 MET cc_start: 0.7904 (mtp) cc_final: 0.7638 (mtt)
REVERT: D  204 GLU cc_start: 0.7078 (pt0) cc_final: 0.6872 (pt0)
REVERT: D  337 MET cc_start: 0.7605 (ttm) cc_final: 0.7394 (ttm)
  outliers start: 24
  outliers final: 16
  residues processed: 145
  average time/residue: 0.2339
  time to fit residues: 48.4881
Evaluate side-chains
  138 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 1.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  226 CYS
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  194 ASP
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  194 ASP
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain D residue  315 THR
Chi-restraints excluded: chain D residue  335 ILE
Chi-restraints excluded: chain D residue  353 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 21 optimal weight:    0.0170
   chunk 74 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 99 optimal weight:    4.9990
   chunk 95 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 120 optimal weight:    0.9980
   chunk 57 optimal weight:    0.8980
   chunk 105 optimal weight:    0.4980
   chunk 90 optimal weight:    0.6980
   chunk 112 optimal weight:    1.9990
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.146685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.129050 restraints weight = 14887.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 1.92
r_work: 0.3498 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3358 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.3345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11124  Z= 0.113
  Angle     :  0.470   5.505  15068  Z= 0.255
  Chirality :  0.042   0.148   1668
  Planarity :  0.004   0.076   1884
  Dihedral  :  4.420  29.660   1460
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 12.58 %
    Favored  : 85.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.31 (0.24), residues: 1312
  helix: -0.39 (0.28), residues: 344
  sheet:  0.00 (0.28), residues: 356
  loop : -0.03 (0.27), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 312 
 HIS   0.002   0.001   HIS A 282 
 PHE   0.016   0.001   PHE B 292 
 TYR   0.007   0.001   TYR D 287 
 ARG   0.012   0.000   ARG D 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03057 (  456)
  hydrogen bonds       : angle       4.64867 ( 1260)
  covalent geometry    : bond        0.00261 (11124)
  covalent geometry    : angle       0.47046 (15068)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 129
  time to evaluate  : 1.274 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 LYS cc_start: 0.7979 (mmmt) cc_final: 0.7768 (mmmt)
REVERT: A  104 MET cc_start: 0.8053 (mtm) cc_final: 0.7814 (mtt)
REVERT: A  345 ARG cc_start: 0.8054 (mmt-90) cc_final: 0.7761 (mmm160)
REVERT: B  162 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7015 (tm-30)
REVERT: B  338 ARG cc_start: 0.7454 (ptp90) cc_final: 0.7032 (ptm-80)
REVERT: C  162 GLU cc_start: 0.7433 (tm-30) cc_final: 0.6986 (tm-30)
REVERT: C  346 ASP cc_start: 0.8092 (m-30) cc_final: 0.7727 (m-30)
REVERT: D  104 MET cc_start: 0.7994 (mtp) cc_final: 0.7756 (mtt)
REVERT: D  337 MET cc_start: 0.7474 (ttm) cc_final: 0.7269 (ttm)
  outliers start: 23
  outliers final: 17
  residues processed: 142
  average time/residue: 0.2221
  time to fit residues: 45.6043
Evaluate side-chains
  140 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 123
  time to evaluate  : 1.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  262 VAL
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain D residue   62 ILE
Chi-restraints excluded: chain D residue  335 ILE
Chi-restraints excluded: chain D residue  353 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 25 optimal weight:    0.2980
   chunk 96 optimal weight:    0.0000
   chunk 100 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 129 optimal weight:    4.9990
   chunk 131 optimal weight:    0.7980
   chunk 68 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.5386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.147156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.129709 restraints weight = 14999.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 1.92
r_work: 0.3513 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3372 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.3493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  11124  Z= 0.105
  Angle     :  0.464   5.688  15068  Z= 0.253
  Chirality :  0.042   0.148   1668
  Planarity :  0.003   0.044   1884
  Dihedral  :  4.338  29.241   1460
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 13.17 %
    Favored  : 84.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.25 (0.24), residues: 1312
  helix: -0.33 (0.28), residues: 344
  sheet:  0.05 (0.28), residues: 356
  loop : -0.01 (0.27), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 312 
 HIS   0.002   0.000   HIS A 282 
 PHE   0.015   0.001   PHE C 292 
 TYR   0.006   0.001   TYR D 287 
 ARG   0.009   0.000   ARG D 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02935 (  456)
  hydrogen bonds       : angle       4.55640 ( 1260)
  covalent geometry    : bond        0.00238 (11124)
  covalent geometry    : angle       0.46441 (15068)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 1.200 
Fit side-chains
   revert: symmetry clash
REVERT: A  104 MET cc_start: 0.8018 (mtm) cc_final: 0.7807 (mtt)
REVERT: A  291 GLU cc_start: 0.7238 (mp0) cc_final: 0.6928 (mt-10)
REVERT: A  337 MET cc_start: 0.7604 (mtp) cc_final: 0.7290 (mtm)
REVERT: B  162 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7037 (tm-30)
REVERT: B  256 ASP cc_start: 0.8380 (t0) cc_final: 0.8038 (m-30)
REVERT: B  338 ARG cc_start: 0.7422 (ptp90) cc_final: 0.7127 (ptm-80)
REVERT: C  162 GLU cc_start: 0.7435 (tm-30) cc_final: 0.7008 (tm-30)
REVERT: C  346 ASP cc_start: 0.8059 (m-30) cc_final: 0.7721 (m-30)
REVERT: C  371 ARG cc_start: 0.7755 (ptt-90) cc_final: 0.7452 (ptt-90)
REVERT: D  104 MET cc_start: 0.8036 (mtp) cc_final: 0.7781 (mtt)
  outliers start: 27
  outliers final: 21
  residues processed: 146
  average time/residue: 0.2190
  time to fit residues: 46.3576
Evaluate side-chains
  143 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 122
  time to evaluate  : 1.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  194 ASP
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  262 VAL
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  194 ASP
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain D residue   62 ILE
Chi-restraints excluded: chain D residue  164 MET
Chi-restraints excluded: chain D residue  315 THR
Chi-restraints excluded: chain D residue  335 ILE
Chi-restraints excluded: chain D residue  353 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 57 optimal weight:    0.7980
   chunk 128 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0980
   chunk 100 optimal weight:    6.9990
   chunk 76 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0050
   chunk 90 optimal weight:    0.8980
   chunk 73 optimal weight:    0.5980
   chunk 92 optimal weight:    0.0370
   overall best weight:    0.3072

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.149110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.131760 restraints weight = 15219.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 1.94
r_work: 0.3542 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3403 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.3688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  11124  Z= 0.088
  Angle     :  0.462   6.907  15068  Z= 0.250
  Chirality :  0.041   0.149   1668
  Planarity :  0.003   0.035   1884
  Dihedral  :  4.200  27.830   1460
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 14.43 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  0.21 (0.25), residues: 1312
  helix:  0.14 (0.29), residues: 320
  sheet:  0.15 (0.30), residues: 336
  loop :  0.32 (0.27), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 312 
 HIS   0.002   0.000   HIS D 282 
 PHE   0.014   0.001   PHE B 292 
 TYR   0.006   0.001   TYR D 309 
 ARG   0.007   0.000   ARG D 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02714 (  456)
  hydrogen bonds       : angle       4.42377 ( 1260)
  covalent geometry    : bond        0.00189 (11124)
  covalent geometry    : angle       0.46201 (15068)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 136
  time to evaluate  : 1.457 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.7792 (mmmt) cc_final: 0.7589 (mtpp)
REVERT: A  291 GLU cc_start: 0.7166 (mp0) cc_final: 0.6827 (mt-10)
REVERT: B  162 GLU cc_start: 0.7439 (tm-30) cc_final: 0.6972 (tm-30)
REVERT: B  256 ASP cc_start: 0.8364 (t0) cc_final: 0.8028 (m-30)
REVERT: B  291 GLU cc_start: 0.7332 (mp0) cc_final: 0.7054 (mp0)
REVERT: B  338 ARG cc_start: 0.7429 (ptp90) cc_final: 0.7139 (ptm-80)
REVERT: C  162 GLU cc_start: 0.7368 (tm-30) cc_final: 0.6941 (tm-30)
REVERT: C  346 ASP cc_start: 0.8021 (m-30) cc_final: 0.7705 (m-30)
REVERT: D  104 MET cc_start: 0.8023 (mtp) cc_final: 0.7774 (mtt)
  outliers start: 22
  outliers final: 18
  residues processed: 147
  average time/residue: 0.2201
  time to fit residues: 46.7868
Evaluate side-chains
  145 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  194 ASP
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  194 ASP
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain D residue   62 ILE
Chi-restraints excluded: chain D residue  164 MET
Chi-restraints excluded: chain D residue  315 THR
Chi-restraints excluded: chain D residue  335 ILE
Chi-restraints excluded: chain D residue  353 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 112 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 42 optimal weight:    0.0050
   chunk 68 optimal weight:    3.9990
   chunk 118 optimal weight:    1.9990
   chunk 111 optimal weight:    2.9990
   chunk 9 optimal weight:    0.3980
   chunk 89 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    1.0800

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

Flipped N/Q/H residues before XYZ refinement:
A  63 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.144352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.126749 restraints weight = 15058.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3569 rms_B_bonded: 1.92
r_work: 0.3474 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.3650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11124  Z= 0.163
  Angle     :  0.517   7.735  15068  Z= 0.278
  Chirality :  0.043   0.151   1668
  Planarity :  0.003   0.044   1884
  Dihedral  :  4.431  28.459   1460
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 14.26 %
    Favored  : 83.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.24), residues: 1312
  helix: -0.39 (0.28), residues: 344
  sheet: -0.06 (0.28), residues: 356
  loop : -0.05 (0.27), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 312 
 HIS   0.005   0.001   HIS A  85 
 PHE   0.017   0.001   PHE C 292 
 TYR   0.009   0.001   TYR D 287 
 ARG   0.008   0.001   ARG D 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03250 (  456)
  hydrogen bonds       : angle       4.68244 ( 1260)
  covalent geometry    : bond        0.00390 (11124)
  covalent geometry    : angle       0.51691 (15068)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 117
  time to evaluate  : 1.214 
Fit side-chains
   revert: symmetry clash
REVERT: A  291 GLU cc_start: 0.7312 (mp0) cc_final: 0.6912 (mt-10)
REVERT: B  162 GLU cc_start: 0.7498 (tm-30) cc_final: 0.6931 (tm-30)
REVERT: B  338 ARG cc_start: 0.7477 (ptp90) cc_final: 0.7179 (ptm-80)
REVERT: C  162 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7039 (tm-30)
REVERT: C  346 ASP cc_start: 0.8133 (m-30) cc_final: 0.7759 (m-30)
REVERT: C  371 ARG cc_start: 0.7712 (ptt-90) cc_final: 0.7355 (ptt-90)
REVERT: D  104 MET cc_start: 0.8076 (mtp) cc_final: 0.7824 (mtt)
  outliers start: 25
  outliers final: 21
  residues processed: 133
  average time/residue: 0.2221
  time to fit residues: 42.8703
Evaluate side-chains
  130 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 1.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  226 CYS
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  194 ASP
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  262 VAL
Chi-restraints excluded: chain B residue  334 THR
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  194 ASP
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain D residue   62 ILE
Chi-restraints excluded: chain D residue  164 MET
Chi-restraints excluded: chain D residue  335 ILE
Chi-restraints excluded: chain D residue  353 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0570
   chunk 114 optimal weight:    3.9990
   chunk 108 optimal weight:    0.9980
   chunk 113 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 75 optimal weight:    0.0060
   overall best weight:    0.6116

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.146280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.128840 restraints weight = 15179.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 1.92
r_work: 0.3498 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3360 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.3777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11124  Z= 0.115
  Angle     :  0.495   7.524  15068  Z= 0.268
  Chirality :  0.042   0.150   1668
  Planarity :  0.003   0.036   1884
  Dihedral  :  4.359  27.944   1460
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 15.27 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.24), residues: 1312
  helix: -0.44 (0.28), residues: 344
  sheet: -0.03 (0.28), residues: 356
  loop : -0.07 (0.27), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 312 
 HIS   0.004   0.001   HIS A  85 
 PHE   0.015   0.001   PHE B 292 
 TYR   0.006   0.001   TYR D 287 
 ARG   0.008   0.000   ARG D 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02989 (  456)
  hydrogen bonds       : angle       4.60684 ( 1260)
  covalent geometry    : bond        0.00267 (11124)
  covalent geometry    : angle       0.49453 (15068)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 1.183 
Fit side-chains
   revert: symmetry clash
REVERT: A  291 GLU cc_start: 0.7283 (mp0) cc_final: 0.6933 (mt-10)
REVERT: B  162 GLU cc_start: 0.7428 (tm-30) cc_final: 0.6884 (tm-30)
REVERT: B  233 LYS cc_start: 0.7229 (mmtt) cc_final: 0.6714 (mtmt)
REVERT: B  256 ASP cc_start: 0.8357 (t0) cc_final: 0.8046 (m-30)
REVERT: B  338 ARG cc_start: 0.7464 (ptp90) cc_final: 0.7160 (ptm-80)
REVERT: C  162 GLU cc_start: 0.7385 (tm-30) cc_final: 0.6910 (tm-30)
REVERT: C  256 ASP cc_start: 0.8307 (t0) cc_final: 0.7979 (m-30)
REVERT: C  346 ASP cc_start: 0.8085 (m-30) cc_final: 0.7704 (m-30)
REVERT: C  371 ARG cc_start: 0.7692 (ptt-90) cc_final: 0.7327 (ptt-90)
REVERT: D  104 MET cc_start: 0.8031 (mtp) cc_final: 0.7791 (mtt)
  outliers start: 20
  outliers final: 20
  residues processed: 124
  average time/residue: 0.2172
  time to fit residues: 39.0316
Evaluate side-chains
  136 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 1.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  194 ASP
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  194 ASP
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain D residue   62 ILE
Chi-restraints excluded: chain D residue  164 MET
Chi-restraints excluded: chain D residue  315 THR
Chi-restraints excluded: chain D residue  335 ILE
Chi-restraints excluded: chain D residue  353 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 66 optimal weight:   20.0000
   chunk 96 optimal weight:    0.0470
   chunk 111 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0970
   chunk 116 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   overall best weight:    0.6076

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.146827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.129465 restraints weight = 15051.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.3601 rms_B_bonded: 1.91
r_work: 0.3506 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3369 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.3848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11124  Z= 0.114
  Angle     :  0.491   7.535  15068  Z= 0.266
  Chirality :  0.042   0.150   1668
  Planarity :  0.003   0.036   1884
  Dihedral  :  4.319  27.731   1460
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 15.10 %
    Favored  : 83.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.38 (0.24), residues: 1312
  helix: -0.44 (0.28), residues: 344
  sheet: -0.03 (0.28), residues: 356
  loop : -0.07 (0.27), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 312 
 HIS   0.003   0.000   HIS A  85 
 PHE   0.015   0.001   PHE B 292 
 TYR   0.006   0.001   TYR A 309 
 ARG   0.007   0.000   ARG D 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02945 (  456)
  hydrogen bonds       : angle       4.59346 ( 1260)
  covalent geometry    : bond        0.00265 (11124)
  covalent geometry    : angle       0.49109 (15068)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 1.279 
Fit side-chains
REVERT: A  291 GLU cc_start: 0.7275 (mp0) cc_final: 0.6956 (mt-10)
REVERT: B   89 ASP cc_start: 0.7447 (t0) cc_final: 0.7212 (p0)
REVERT: B  162 GLU cc_start: 0.7509 (tm-30) cc_final: 0.6988 (tm-30)
REVERT: B  233 LYS cc_start: 0.7236 (mmtt) cc_final: 0.6750 (mtmt)
REVERT: B  256 ASP cc_start: 0.8348 (t0) cc_final: 0.8044 (m-30)
REVERT: B  338 ARG cc_start: 0.7469 (ptp90) cc_final: 0.7165 (ptm-80)
REVERT: C  162 GLU cc_start: 0.7375 (tm-30) cc_final: 0.6944 (tm-30)
REVERT: C  256 ASP cc_start: 0.8289 (t0) cc_final: 0.7985 (m-30)
REVERT: C  346 ASP cc_start: 0.8070 (m-30) cc_final: 0.7695 (m-30)
REVERT: C  371 ARG cc_start: 0.7710 (ptt-90) cc_final: 0.7328 (ptt-90)
REVERT: D  104 MET cc_start: 0.7958 (mtp) cc_final: 0.7720 (mtt)
  outliers start: 21
  outliers final: 21
  residues processed: 125
  average time/residue: 0.2421
  time to fit residues: 43.1082
Evaluate side-chains
  138 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 1.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  194 ASP
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  262 VAL
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  194 ASP
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain D residue   62 ILE
Chi-restraints excluded: chain D residue  164 MET
Chi-restraints excluded: chain D residue  315 THR
Chi-restraints excluded: chain D residue  335 ILE
Chi-restraints excluded: chain D residue  353 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 122 optimal weight:    3.9990
   chunk 81 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 78 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   overall best weight:    1.2984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.142971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.125305 restraints weight = 15104.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 1.91
r_work: 0.3456 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.3810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  11124  Z= 0.189
  Angle     :  0.550   8.357  15068  Z= 0.296
  Chirality :  0.044   0.152   1668
  Planarity :  0.004   0.043   1884
  Dihedral  :  4.590  30.331   1460
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 15.10 %
    Favored  : 82.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.59 (0.24), residues: 1312
  helix: -0.62 (0.28), residues: 344
  sheet: -0.22 (0.28), residues: 356
  loop : -0.16 (0.27), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 312 
 HIS   0.003   0.001   HIS A  85 
 PHE   0.017   0.002   PHE B 292 
 TYR   0.009   0.001   TYR D 287 
 ARG   0.007   0.000   ARG D 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03462 (  456)
  hydrogen bonds       : angle       4.86000 ( 1260)
  covalent geometry    : bond        0.00456 (11124)
  covalent geometry    : angle       0.55033 (15068)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5437.40 seconds
wall clock time: 95 minutes 24.23 seconds (5724.23 seconds total)