Starting phenix.real_space_refine
on Tue Jul 29 02:28:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z2z_39745/07_2025/8z2z_39745.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z2z_39745/07_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_39745/07_2025/8z2z_39745.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z2z_39745/07_2025/8z2z_39745.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z2z_39745/07_2025/8z2z_39745.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z2z_39745/07_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-5711/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: 6.25, per 1000 atoms: 0.58
  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: 2.69
  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: 1.35
  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: 3.29

  Time building geometry restraints manager: 3.19 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.190
  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:          0.500
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     26.610
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.470
-------------------------------------------------------------------------------
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  : 1.520 
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: 0.2597
  time to fit residues: 81.8158
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  : 1.425 
-------------------------------------------------------------------------------
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 = 0.3825 r_free = 0.3825 target = 0.146714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.125060 restraints weight = 14919.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 2.61
r_work: 0.3435 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
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  : 1.245 
Fit side-chains
REVERT: A  129 ILE cc_start: 0.8574 (mt) cc_final: 0.8307 (mp)
REVERT: A  204 GLU cc_start: 0.7079 (pt0) cc_final: 0.6858 (pt0)
REVERT: A  261 LYS cc_start: 0.8123 (mtmm) cc_final: 0.7834 (mtmt)
REVERT: A  330 GLU cc_start: 0.6973 (tt0) cc_final: 0.6702 (mm-30)
REVERT: A  345 ARG cc_start: 0.8010 (mmt-90) cc_final: 0.7641 (mmm160)
REVERT: A  352 ASP cc_start: 0.7240 (m-30) cc_final: 0.7035 (t0)
REVERT: A  358 GLN cc_start: 0.7950 (mt0) cc_final: 0.7749 (mt0)
REVERT: B  162 GLU cc_start: 0.7414 (tm-30) cc_final: 0.7070 (tm-30)
REVERT: B  337 MET cc_start: 0.8406 (mtt) cc_final: 0.8194 (mtt)
REVERT: C  162 GLU cc_start: 0.7346 (tm-30) cc_final: 0.6978 (tm-30)
REVERT: C  188 ASP cc_start: 0.7609 (t0) cc_final: 0.7397 (t70)
REVERT: C  319 MET cc_start: 0.8930 (mtm) cc_final: 0.8681 (mtp)
REVERT: C  337 MET cc_start: 0.8471 (mtt) cc_final: 0.8244 (mtt)
REVERT: C  371 ARG cc_start: 0.7568 (ptt-90) cc_final: 0.7350 (ptt-90)
REVERT: D  129 ILE cc_start: 0.8501 (mt) cc_final: 0.8255 (mp)
REVERT: D  162 GLU cc_start: 0.5660 (tm-30) cc_final: 0.5295 (tm-30)
REVERT: D  204 GLU cc_start: 0.6813 (pt0) cc_final: 0.6564 (pt0)
REVERT: D  279 ASP cc_start: 0.7855 (t0) cc_final: 0.7469 (t70)
  outliers start: 13
  outliers final: 12
  residues processed: 177
  average time/residue: 0.2275
  time to fit residues: 57.8879
Evaluate side-chains
  143 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 131
  time to evaluate  : 1.342 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 126 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 123 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 61 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9980
   chunk 113 optimal weight:    3.9990
   chunk 66 optimal weight:   20.0000
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3803 r_free = 0.3803 target = 0.145338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.125477 restraints weight = 15056.103|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 2.31
r_work: 0.3449 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3292 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11124  Z= 0.152
  Angle     :  0.519   6.265  15068  Z= 0.280
  Chirality :  0.043   0.142   1668
  Planarity :  0.003   0.028   1884
  Dihedral  :  4.662  30.719   1460
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 10.49 %
    Favored  : 87.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -0.63 (0.23), residues: 1312
  helix: -0.62 (0.27), residues: 348
  sheet: -0.25 (0.27), residues: 376
  loop : -0.19 (0.27), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 184 
 HIS   0.003   0.001   HIS A 282 
 PHE   0.017   0.001   PHE B 292 
 TYR   0.008   0.001   TYR D 287 
 ARG   0.003   0.000   ARG A 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03693 (  456)
  hydrogen bonds       : angle       5.06127 ( 1260)
  covalent geometry    : bond        0.00359 (11124)
  covalent geometry    : angle       0.51926 (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
  158 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 135
  time to evaluate  : 1.266 
Fit side-chains
REVERT: A  204 GLU cc_start: 0.7399 (pt0) cc_final: 0.7087 (pt0)
REVERT: A  261 LYS cc_start: 0.8151 (mtmm) cc_final: 0.7931 (mtmt)
REVERT: A  330 GLU cc_start: 0.7396 (tt0) cc_final: 0.7127 (mm-30)
REVERT: A  345 ARG cc_start: 0.8053 (mmt-90) cc_final: 0.7724 (mmm160)
REVERT: A  352 ASP cc_start: 0.7444 (m-30) cc_final: 0.7205 (t0)
REVERT: B  162 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7069 (tm-30)
REVERT: B  319 MET cc_start: 0.8916 (mtm) cc_final: 0.8708 (mtp)
REVERT: C  162 GLU cc_start: 0.7391 (tm-30) cc_final: 0.7043 (tm-30)
REVERT: C  319 MET cc_start: 0.8958 (mtm) cc_final: 0.8744 (mtp)
REVERT: C  371 ARG cc_start: 0.7811 (ptt-90) cc_final: 0.7559 (ptt-90)
REVERT: D  104 MET cc_start: 0.7939 (mtp) cc_final: 0.7698 (mtt)
  outliers start: 23
  outliers final: 15
  residues processed: 149
  average time/residue: 0.2267
  time to fit residues: 49.3368
Evaluate side-chains
  135 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 1.414 
-------------------------------------------------------------------------------
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  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:    1.9990
   chunk 120 optimal weight:    0.0970
   chunk 51 optimal weight:    0.8980
   chunk 116 optimal weight:    0.0870
   chunk 94 optimal weight:    0.7980
   chunk 107 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 130 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.5556

-------------------------------------------------------------------------------
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 = 0.3820 r_free = 0.3820 target = 0.146886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.127667 restraints weight = 14884.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3592 rms_B_bonded: 2.24
r_work: 0.3483 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3331 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.3094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  11124  Z= 0.110
  Angle     :  0.480   5.336  15068  Z= 0.260
  Chirality :  0.042   0.143   1668
  Planarity :  0.003   0.029   1884
  Dihedral  :  4.467  29.521   1460
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 11.91 %
    Favored  : 86.33 %
  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: -0.46 (0.27), residues: 344
  sheet:  0.00 (0.28), residues: 356
  loop : -0.09 (0.26), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 184 
 HIS   0.002   0.001   HIS A 282 
 PHE   0.020   0.001   PHE B  60 
 TYR   0.007   0.001   TYR A 309 
 ARG   0.007   0.000   ARG B 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03146 (  456)
  hydrogen bonds       : angle       4.77263 ( 1260)
  covalent geometry    : bond        0.00250 (11124)
  covalent geometry    : angle       0.47998 (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
  160 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 139
  time to evaluate  : 1.256 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.7828 (mmmt) cc_final: 0.7595 (mmmt)
REVERT: A  261 LYS cc_start: 0.8164 (mtmm) cc_final: 0.7933 (mtmt)
REVERT: A  330 GLU cc_start: 0.7429 (tt0) cc_final: 0.7082 (mm-30)
REVERT: B  162 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7074 (tm-30)
REVERT: B  338 ARG cc_start: 0.7541 (ptp90) cc_final: 0.7017 (ptm-80)
REVERT: C  162 GLU cc_start: 0.7443 (tm-30) cc_final: 0.7022 (tm-30)
REVERT: C  346 ASP cc_start: 0.8062 (m-30) cc_final: 0.7564 (m-30)
REVERT: C  371 ARG cc_start: 0.7740 (ptt-90) cc_final: 0.7160 (ptt-90)
REVERT: D  104 MET cc_start: 0.7979 (mtp) cc_final: 0.7729 (mtt)
  outliers start: 21
  outliers final: 14
  residues processed: 150
  average time/residue: 0.2473
  time to fit residues: 52.3036
Evaluate side-chains
  136 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 1.423 
-------------------------------------------------------------------------------
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  239 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  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:    0.0570
   chunk 74 optimal weight:    0.9980
   chunk 63 optimal weight:    3.9990
   chunk 99 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 120 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 105 optimal weight:    2.9990
   chunk 90 optimal weight:    0.6980
   chunk 112 optimal weight:    0.7980
   overall best weight:    0.6298

-------------------------------------------------------------------------------
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 = 0.3816 r_free = 0.3816 target = 0.146789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.129243 restraints weight = 14881.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 1.91
r_work: 0.3491 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3351 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.3329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11124  Z= 0.115
  Angle     :  0.474   4.852  15068  Z= 0.258
  Chirality :  0.042   0.148   1668
  Planarity :  0.003   0.029   1884
  Dihedral  :  4.407  29.156   1460
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 11.83 %
    Favored  : 85.91 %
  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: -0.28 (0.24), residues: 1312
  helix: -0.40 (0.28), residues: 344
  sheet:  0.04 (0.28), residues: 356
  loop : -0.01 (0.27), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 184 
 HIS   0.002   0.000   HIS D 282 
 PHE   0.016   0.001   PHE B 292 
 TYR   0.006   0.001   TYR B 220 
 ARG   0.007   0.000   ARG B 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03097 (  456)
  hydrogen bonds       : angle       4.70142 ( 1260)
  covalent geometry    : bond        0.00262 (11124)
  covalent geometry    : angle       0.47434 (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: 27
    poor density    : 125
  time to evaluate  : 1.366 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.7975 (mmmt) cc_final: 0.7763 (mmmt)
REVERT: A  104 MET cc_start: 0.7920 (mtm) cc_final: 0.7677 (mtt)
REVERT: B  162 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7038 (tm-30)
REVERT: B  338 ARG cc_start: 0.7476 (ptp90) cc_final: 0.7195 (ptm-80)
REVERT: C  162 GLU cc_start: 0.7410 (tm-30) cc_final: 0.6971 (tm-30)
REVERT: C  346 ASP cc_start: 0.8092 (m-30) cc_final: 0.7739 (m-30)
REVERT: D  104 MET cc_start: 0.7992 (mtp) cc_final: 0.7754 (mtt)
  outliers start: 27
  outliers final: 20
  residues processed: 141
  average time/residue: 0.2219
  time to fit residues: 45.7576
Evaluate side-chains
  138 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 1.334 
-------------------------------------------------------------------------------
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  245 LEU
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 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  164 MET
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:    0.0040
   chunk 96 optimal weight:    0.8980
   chunk 100 optimal weight:    0.0370
   chunk 35 optimal weight:    1.9990
   chunk 129 optimal weight:    2.9990
   chunk 131 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.4670

-------------------------------------------------------------------------------
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 = 0.3828 r_free = 0.3828 target = 0.147971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.130578 restraints weight = 14995.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 1.90
r_work: 0.3528 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3388 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.3514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  11124  Z= 0.101
  Angle     :  0.464   5.096  15068  Z= 0.254
  Chirality :  0.042   0.141   1668
  Planarity :  0.003   0.029   1884
  Dihedral  :  4.298  27.623   1460
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 13.00 %
    Favored  : 84.73 %
  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: -0.30 (0.24), residues: 1312
  helix: -0.36 (0.28), residues: 344
  sheet:  0.03 (0.29), residues: 336
  loop : -0.06 (0.26), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 312 
 HIS   0.002   0.000   HIS D 282 
 PHE   0.015   0.001   PHE B 292 
 TYR   0.006   0.001   TYR D 287 
 ARG   0.006   0.000   ARG B 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02899 (  456)
  hydrogen bonds       : angle       4.56846 ( 1260)
  covalent geometry    : bond        0.00226 (11124)
  covalent geometry    : angle       0.46442 (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
  156 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 129
  time to evaluate  : 1.240 
Fit side-chains
   revert: symmetry clash
REVERT: A  104 MET cc_start: 0.7969 (mtm) cc_final: 0.7725 (mtp)
REVERT: B  162 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7000 (tm-30)
REVERT: B  338 ARG cc_start: 0.7412 (ptp90) cc_final: 0.7128 (ptm-80)
REVERT: C  162 GLU cc_start: 0.7374 (tm-30) cc_final: 0.6967 (tm-30)
REVERT: C  346 ASP cc_start: 0.8023 (m-30) cc_final: 0.7691 (m-30)
REVERT: C  371 ARG cc_start: 0.7782 (ptt-90) cc_final: 0.7520 (ptt-90)
REVERT: D   90 LYS cc_start: 0.7846 (mmmt) cc_final: 0.7605 (tptm)
REVERT: D  104 MET cc_start: 0.8022 (mtp) cc_final: 0.7784 (mtt)
  outliers start: 27
  outliers final: 21
  residues processed: 142
  average time/residue: 0.2245
  time to fit residues: 46.3233
Evaluate side-chains
  141 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 1.250 
-------------------------------------------------------------------------------
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  245 LEU
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 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  164 MET
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:    0.8980
   chunk 128 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 100 optimal weight:    6.9990
   chunk 76 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   chunk 9 optimal weight:    0.4980
   chunk 90 optimal weight:    0.9980
   chunk 73 optimal weight:    0.6980
   chunk 92 optimal weight:    0.0040
   overall best weight:    0.6192

-------------------------------------------------------------------------------
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 = 0.3823 r_free = 0.3823 target = 0.147281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.129701 restraints weight = 15261.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 1.92
r_work: 0.3511 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3372 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.3588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11124  Z= 0.113
  Angle     :  0.477   5.998  15068  Z= 0.260
  Chirality :  0.042   0.145   1668
  Planarity :  0.003   0.029   1884
  Dihedral  :  4.290  27.058   1460
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 13.93 %
    Favored  : 83.89 %
  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: -0.23 (0.24), residues: 1312
  helix: -0.35 (0.28), residues: 344
  sheet:  0.11 (0.28), residues: 356
  loop : -0.00 (0.27), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 184 
 HIS   0.002   0.000   HIS D 282 
 PHE   0.016   0.001   PHE B 292 
 TYR   0.007   0.001   TYR A 287 
 ARG   0.005   0.000   ARG A 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02974 (  456)
  hydrogen bonds       : angle       4.55184 ( 1260)
  covalent geometry    : bond        0.00261 (11124)
  covalent geometry    : angle       0.47675 (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
  149 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 123
  time to evaluate  : 1.356 
Fit side-chains
   revert: symmetry clash
REVERT: B  162 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6944 (tm-30)
REVERT: B  338 ARG cc_start: 0.7453 (ptp90) cc_final: 0.7163 (ptm-80)
REVERT: C  162 GLU cc_start: 0.7398 (tm-30) cc_final: 0.6978 (tm-30)
REVERT: C  346 ASP cc_start: 0.8091 (m-30) cc_final: 0.7778 (m-30)
REVERT: D  104 MET cc_start: 0.8037 (mtp) cc_final: 0.7800 (mtt)
  outliers start: 26
  outliers final: 23
  residues processed: 134
  average time/residue: 0.2289
  time to fit residues: 44.7565
Evaluate side-chains
  141 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 1.386 
-------------------------------------------------------------------------------
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  245 LEU
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 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  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   56 SER
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:    4.9990
   chunk 32 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0370
   chunk 68 optimal weight:    3.9990
   chunk 118 optimal weight:    0.8980
   chunk 111 optimal weight:    0.4980
   chunk 9 optimal weight:    0.8980
   chunk 89 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    0.6658

-------------------------------------------------------------------------------
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 = 0.3814 r_free = 0.3814 target = 0.146626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.129152 restraints weight = 15001.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3602 rms_B_bonded: 1.90
r_work: 0.3509 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3371 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.3676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11124  Z= 0.118
  Angle     :  0.488   7.846  15068  Z= 0.264
  Chirality :  0.042   0.147   1668
  Planarity :  0.003   0.029   1884
  Dihedral  :  4.311  27.023   1460
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 14.77 %
    Favored  : 83.22 %
  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: -0.26 (0.24), residues: 1312
  helix: -0.38 (0.28), residues: 344
  sheet:  0.10 (0.28), residues: 356
  loop : -0.02 (0.27), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 312 
 HIS   0.002   0.000   HIS D 282 
 PHE   0.015   0.001   PHE B 292 
 TYR   0.007   0.001   TYR D 287 
 ARG   0.005   0.000   ARG A 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03012 (  456)
  hydrogen bonds       : angle       4.58257 ( 1260)
  covalent geometry    : bond        0.00276 (11124)
  covalent geometry    : angle       0.48836 (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
  147 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 1.287 
Fit side-chains
REVERT: B   89 ASP cc_start: 0.7487 (t0) cc_final: 0.7270 (p0)
REVERT: B  162 GLU cc_start: 0.7442 (tm-30) cc_final: 0.6906 (tm-30)
REVERT: B  233 LYS cc_start: 0.7223 (mmtt) cc_final: 0.6692 (mtmt)
REVERT: B  338 ARG cc_start: 0.7452 (ptp90) cc_final: 0.7156 (ptm-80)
REVERT: C  162 GLU cc_start: 0.7437 (tm-30) cc_final: 0.6973 (tm-30)
REVERT: C  346 ASP cc_start: 0.8078 (m-30) cc_final: 0.7763 (m-30)
REVERT: C  371 ARG cc_start: 0.7695 (ptt-90) cc_final: 0.7358 (ptt-90)
REVERT: D  104 MET cc_start: 0.8001 (mtp) cc_final: 0.7765 (mtt)
  outliers start: 24
  outliers final: 23
  residues processed: 133
  average time/residue: 0.2323
  time to fit residues: 44.3286
Evaluate side-chains
  144 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 121
  time to evaluate  : 1.246 
-------------------------------------------------------------------------------
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  245 LEU
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 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  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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 114 optimal weight:    1.9990
   chunk 108 optimal weight:    0.0010
   chunk 113 optimal weight:    3.9990
   chunk 94 optimal weight:    0.4980
   chunk 49 optimal weight:    0.4980
   chunk 2 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    0.9990

-------------------------------------------------------------------------------
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 = 0.3796 r_free = 0.3796 target = 0.144934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.127278 restraints weight = 15216.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 1.93
r_work: 0.3478 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3337 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.3705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11124  Z= 0.154
  Angle     :  0.518   7.445  15068  Z= 0.279
  Chirality :  0.043   0.148   1668
  Planarity :  0.003   0.029   1884
  Dihedral  :  4.425  28.245   1460
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 14.93 %
    Favored  : 82.97 %
  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: -0.46 (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   0.009   0.001   TRP C 312 
 HIS   0.002   0.001   HIS D 282 
 PHE   0.017   0.001   PHE B 292 
 TYR   0.008   0.001   TYR D 287 
 ARG   0.004   0.000   ARG A 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03261 (  456)
  hydrogen bonds       : angle       4.70885 ( 1260)
  covalent geometry    : bond        0.00367 (11124)
  covalent geometry    : angle       0.51846 (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
  142 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 117
  time to evaluate  : 1.257 
Fit side-chains
   revert: symmetry clash
REVERT: A  104 MET cc_start: 0.7555 (mtt) cc_final: 0.6934 (mtp)
REVERT: B  162 GLU cc_start: 0.7503 (tm-30) cc_final: 0.7019 (tm-30)
REVERT: B  233 LYS cc_start: 0.7307 (mmtt) cc_final: 0.6801 (mtmt)
REVERT: B  338 ARG cc_start: 0.7422 (ptp90) cc_final: 0.7149 (ptm-80)
REVERT: C  162 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7019 (tm-30)
REVERT: C  256 ASP cc_start: 0.8340 (t0) cc_final: 0.7997 (m-30)
REVERT: C  346 ASP cc_start: 0.8143 (m-30) cc_final: 0.7748 (m-30)
REVERT: C  371 ARG cc_start: 0.7772 (ptt-90) cc_final: 0.7411 (ptt-90)
REVERT: D  104 MET cc_start: 0.7987 (mtp) cc_final: 0.7747 (mtt)
  outliers start: 25
  outliers final: 23
  residues processed: 131
  average time/residue: 0.2211
  time to fit residues: 42.4139
Evaluate side-chains
  137 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 1.271 
-------------------------------------------------------------------------------
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  245 LEU
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   56 SER
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:    6.9990
   chunk 6 optimal weight:    0.7980
   chunk 66 optimal weight:   20.0000
   chunk 96 optimal weight:    0.0470
   chunk 111 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 116 optimal weight:    0.0030
   chunk 62 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.5288

-------------------------------------------------------------------------------
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 = 0.3821 r_free = 0.3821 target = 0.147187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.129739 restraints weight = 15022.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 1.91
r_work: 0.3509 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3372 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.3838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  11124  Z= 0.106
  Angle     :  0.486   7.511  15068  Z= 0.262
  Chirality :  0.042   0.147   1668
  Planarity :  0.003   0.029   1884
  Dihedral  :  4.291  27.237   1460
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 15.44 %
    Favored  : 82.72 %
  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: -0.31 (0.24), residues: 1312
  helix: -0.41 (0.28), residues: 344
  sheet:  0.04 (0.28), residues: 356
  loop : -0.05 (0.27), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 312 
 HIS   0.002   0.000   HIS D 282 
 PHE   0.014   0.001   PHE B 292 
 TYR   0.006   0.001   TYR D 287 
 ARG   0.003   0.000   ARG A 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02932 (  456)
  hydrogen bonds       : angle       4.55020 ( 1260)
  covalent geometry    : bond        0.00241 (11124)
  covalent geometry    : angle       0.48590 (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
  143 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 1.391 
Fit side-chains
REVERT: A  104 MET cc_start: 0.7504 (mtt) cc_final: 0.6891 (mtp)
REVERT: B  162 GLU cc_start: 0.7460 (tm-30) cc_final: 0.6940 (tm-30)
REVERT: B  224 MET cc_start: 0.7765 (mtt) cc_final: 0.7366 (mtt)
REVERT: B  233 LYS cc_start: 0.7232 (mmtt) cc_final: 0.6745 (mtmt)
REVERT: B  256 ASP cc_start: 0.8346 (t0) cc_final: 0.8039 (m-30)
REVERT: B  338 ARG cc_start: 0.7441 (ptp90) cc_final: 0.7120 (ptm-80)
REVERT: C  162 GLU cc_start: 0.7455 (tm-30) cc_final: 0.6957 (tm-30)
REVERT: C  256 ASP cc_start: 0.8310 (t0) cc_final: 0.7990 (m-30)
REVERT: C  346 ASP cc_start: 0.8061 (m-30) cc_final: 0.7674 (m-30)
REVERT: C  371 ARG cc_start: 0.7688 (ptt-90) cc_final: 0.7307 (ptt-90)
REVERT: D  104 MET cc_start: 0.7938 (mtp) cc_final: 0.7687 (mtt)
  outliers start: 22
  outliers final: 21
  residues processed: 129
  average time/residue: 0.2285
  time to fit residues: 42.8363
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  : 1.263 
-------------------------------------------------------------------------------
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  245 LEU
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 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   56 SER
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:    0.0020
   chunk 10 optimal weight:    0.0970
   chunk 122 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 91 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   chunk 78 optimal weight:    0.1980
   chunk 27 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.3986

-------------------------------------------------------------------------------
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 = 0.3836 r_free = 0.3836 target = 0.148395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.131060 restraints weight = 14982.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 1.93
r_work: 0.3531 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3393 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.3922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  11124  Z= 0.098
  Angle     :  0.489   7.940  15068  Z= 0.264
  Chirality :  0.042   0.147   1668
  Planarity :  0.003   0.030   1884
  Dihedral  :  4.204  26.153   1460
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 15.60 %
    Favored  : 82.63 %
  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:  0.11 (0.25), residues: 1312
  helix: -0.01 (0.29), residues: 320
  sheet:  0.10 (0.30), residues: 336
  loop :  0.28 (0.27), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 312 
 HIS   0.002   0.000   HIS D 282 
 PHE   0.014   0.001   PHE B 292 
 TYR   0.006   0.001   TYR A 309 
 ARG   0.003   0.000   ARG A 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02816 (  456)
  hydrogen bonds       : angle       4.50304 ( 1260)
  covalent geometry    : bond        0.00217 (11124)
  covalent geometry    : angle       0.48907 (15068)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5926.53 seconds
wall clock time: 102 minutes 54.06 seconds (6174.06 seconds total)