Starting phenix.real_space_refine
on Wed Sep 17 19:50:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z2z_39745/09_2025/8z2z_39745.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z2z_39745/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z2z_39745/09_2025/8z2z_39745.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z2z_39745/09_2025/8z2z_39745.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8z2z_39745/09_2025/8z2z_39745.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z2z_39745/09_2025/8z2z_39745.map"
  }
  resolution = 3.25
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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:
    B, C, D
  Time building chain proxies: 2.23, per 1000 atoms: 0.21
  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: 1.07
  Conformation dependent library (CDL) restraints added in 402.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.45
  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: 1.80

  Time building geometry restraints manager: 1.33 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.230
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     11.380
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  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:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.330
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.005   0.001   ARG B 298 
 TYR   0.010   0.001   TYR A 208 
 PHE   0.015   0.002   PHE A  60 
 TRP   0.006   0.001   TRP A 184 
 HIS   0.008   0.001   HIS D 282 

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

*********************** 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  : 0.466 
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: 0.1207
  time to fit residues: 38.0017
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  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:   20.0000
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:    0.5980
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.5980
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3823 r_free = 0.3823 target = 0.146542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.124753 restraints weight = 15014.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 2.63
r_work: 0.3431 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.2249

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= 0.133
  Angle     :  0.530   7.050  15068  Z= 0.286
  Chirality :  0.043   0.142   1668
  Planarity :  0.004   0.032   1884
  Dihedral  :  4.833  33.282   1460
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  7.89 %
    Favored  : 90.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.80 (0.23), residues: 1312
  helix: -0.84 (0.26), residues: 348
  sheet: -0.45 (0.26), residues: 384
  loop : -0.16 (0.27), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 371 
 TYR   0.011   0.001   TYR C 220 
 PHE   0.018   0.001   PHE C 292 
 TRP   0.015   0.001   TRP A 184 
 HIS   0.003   0.001   HIS D 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (11124)
  covalent geometry    : angle       0.52982 (15068)
  hydrogen bonds       : bond        0.03867 (  456)
  hydrogen bonds       : angle       5.38610 ( 1260)

*********************** 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
  183 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 169
  time to evaluate  : 0.438 
Fit side-chains
REVERT: A   74 LEU cc_start: 0.8127 (mt) cc_final: 0.7920 (mt)
REVERT: A  129 ILE cc_start: 0.8591 (mt) cc_final: 0.8325 (mp)
REVERT: A  204 GLU cc_start: 0.7058 (pt0) cc_final: 0.6836 (pt0)
REVERT: A  261 LYS cc_start: 0.8116 (mtmm) cc_final: 0.7826 (mtmt)
REVERT: A  330 GLU cc_start: 0.7004 (tt0) cc_final: 0.6743 (mm-30)
REVERT: A  332 PHE cc_start: 0.8069 (m-10) cc_final: 0.7858 (m-10)
REVERT: A  345 ARG cc_start: 0.8019 (mmt-90) cc_final: 0.7637 (mmm160)
REVERT: A  352 ASP cc_start: 0.7240 (m-30) cc_final: 0.7038 (t0)
REVERT: B  162 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7120 (tm-30)
REVERT: B  337 MET cc_start: 0.8432 (mtt) cc_final: 0.8220 (mtt)
REVERT: C  162 GLU cc_start: 0.7345 (tm-30) cc_final: 0.6984 (tm-30)
REVERT: C  188 ASP cc_start: 0.7617 (t0) cc_final: 0.7413 (t70)
REVERT: C  319 MET cc_start: 0.8921 (mtm) cc_final: 0.8713 (mtp)
REVERT: C  337 MET cc_start: 0.8447 (mtt) cc_final: 0.8231 (mtt)
REVERT: C  371 ARG cc_start: 0.7569 (ptt-90) cc_final: 0.7350 (ptt-90)
REVERT: D  129 ILE cc_start: 0.8508 (mt) cc_final: 0.8279 (mp)
REVERT: D  162 GLU cc_start: 0.5638 (tm-30) cc_final: 0.5337 (tm-30)
REVERT: D  204 GLU cc_start: 0.6809 (pt0) cc_final: 0.6577 (pt0)
REVERT: D  279 ASP cc_start: 0.7866 (t0) cc_final: 0.7494 (t70)
  outliers start: 14
  outliers final: 13
  residues processed: 178
  average time/residue: 0.1072
  time to fit residues: 27.5741
Evaluate side-chains
  148 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 135
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
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  153 VAL
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 4 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 102 optimal weight:    0.7980
   chunk 76 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 82 optimal weight:    3.9990
   chunk 3 optimal weight:    0.5980
   chunk 7 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 93 optimal weight:    0.6980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3817 r_free = 0.3817 target = 0.146502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.126945 restraints weight = 14972.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 2.26
r_work: 0.3467 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3316 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.2777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11124  Z= 0.130
  Angle     :  0.500   6.098  15068  Z= 0.269
  Chirality :  0.042   0.140   1668
  Planarity :  0.003   0.028   1884
  Dihedral  :  4.574  29.566   1460
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 10.49 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.57 (0.23), residues: 1312
  helix: -0.60 (0.27), residues: 348
  sheet: -0.20 (0.27), residues: 380
  loop : -0.15 (0.27), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 371 
 TYR   0.007   0.001   TYR C 220 
 PHE   0.016   0.001   PHE B 292 
 TRP   0.015   0.001   TRP A 184 
 HIS   0.003   0.001   HIS D 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (11124)
  covalent geometry    : angle       0.50010 (15068)
  hydrogen bonds       : bond        0.03563 (  456)
  hydrogen bonds       : angle       4.99935 ( 1260)

*********************** 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
  171 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 147
  time to evaluate  : 0.446 
Fit side-chains
REVERT: A  204 GLU cc_start: 0.7295 (pt0) cc_final: 0.6969 (pt0)
REVERT: A  261 LYS cc_start: 0.8138 (mtmm) cc_final: 0.7906 (mtmt)
REVERT: A  314 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.8057 (mp10)
REVERT: A  330 GLU cc_start: 0.7373 (tt0) cc_final: 0.7067 (mm-30)
REVERT: A  332 PHE cc_start: 0.8327 (m-10) cc_final: 0.8109 (m-80)
REVERT: A  345 ARG cc_start: 0.8075 (mmt-90) cc_final: 0.7731 (mmm160)
REVERT: A  352 ASP cc_start: 0.7368 (m-30) cc_final: 0.7152 (t0)
REVERT: B  162 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7056 (tm-30)
REVERT: B  319 MET cc_start: 0.8914 (mtm) cc_final: 0.8703 (mtp)
REVERT: C  162 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7032 (tm-30)
REVERT: C  371 ARG cc_start: 0.7750 (ptt-90) cc_final: 0.7519 (ptt-90)
REVERT: D  204 GLU cc_start: 0.7158 (pt0) cc_final: 0.6853 (tt0)
REVERT: D  279 ASP cc_start: 0.7948 (t0) cc_final: 0.7473 (t0)
  outliers start: 24
  outliers final: 15
  residues processed: 160
  average time/residue: 0.1093
  time to fit residues: 25.3562
Evaluate side-chains
  144 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
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  238 ASP
Chi-restraints excluded: chain A residue  314 GLN
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain B residue  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 118 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 105 optimal weight:    0.8980
   chunk 125 optimal weight:    0.9980
   chunk 74 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 126 optimal weight:    0.5980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3808 r_free = 0.3808 target = 0.145935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.128222 restraints weight = 15092.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 1.91
r_work: 0.3474 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3337 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.3125

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= 0.140
  Angle     :  0.499   5.867  15068  Z= 0.268
  Chirality :  0.043   0.143   1668
  Planarity :  0.003   0.029   1884
  Dihedral  :  4.524  31.226   1460
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 11.91 %
    Favored  : 86.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.44 (0.24), residues: 1312
  helix: -0.54 (0.27), residues: 344
  sheet: -0.05 (0.28), residues: 356
  loop : -0.10 (0.26), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 371 
 TYR   0.007   0.001   TYR A 287 
 PHE   0.017   0.001   PHE B 292 
 TRP   0.017   0.001   TRP A 184 
 HIS   0.003   0.001   HIS A 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (11124)
  covalent geometry    : angle       0.49864 (15068)
  hydrogen bonds       : bond        0.03354 (  456)
  hydrogen bonds       : angle       4.85387 ( 1260)

*********************** 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
  154 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 130
  time to evaluate  : 0.458 
Fit side-chains
REVERT: A   55 ASP cc_start: 0.6186 (OUTLIER) cc_final: 0.5800 (t0)
REVERT: A   90 LYS cc_start: 0.7976 (mmmt) cc_final: 0.7760 (mmmt)
REVERT: A  345 ARG cc_start: 0.8066 (mmt-90) cc_final: 0.7856 (mmm160)
REVERT: B  162 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7061 (tm-30)
REVERT: B  338 ARG cc_start: 0.7509 (ptp90) cc_final: 0.7183 (ptm-80)
REVERT: C  162 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7030 (tm-30)
REVERT: C  371 ARG cc_start: 0.7891 (ptt-90) cc_final: 0.7588 (ptt-90)
REVERT: D  204 GLU cc_start: 0.7123 (pt0) cc_final: 0.6911 (pt0)
  outliers start: 24
  outliers final: 15
  residues processed: 146
  average time/residue: 0.1142
  time to fit residues: 23.9565
Evaluate side-chains
  135 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 119
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
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  353 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  194 ASP
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  194 ASP
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain D residue  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 99 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 61 optimal weight:    8.9990
   chunk 50 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 73 optimal weight:    0.5980
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN
B 358 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.140505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.122585 restraints weight = 15253.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 1.90
r_work: 0.3401 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3262 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.3418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042  11124  Z= 0.264
  Angle     :  0.595   7.391  15068  Z= 0.319
  Chirality :  0.046   0.184   1668
  Planarity :  0.004   0.033   1884
  Dihedral  :  4.913  34.723   1460
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 13.09 %
    Favored  : 84.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.91 (0.24), residues: 1312
  helix: -0.90 (0.27), residues: 344
  sheet: -0.67 (0.26), residues: 400
  loop : -0.09 (0.28), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 371 
 TYR   0.011   0.001   TYR D 287 
 PHE   0.020   0.002   PHE B 292 
 TRP   0.011   0.002   TRP C 312 
 HIS   0.003   0.001   HIS D 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00642 (11124)
  covalent geometry    : angle       0.59518 (15068)
  hydrogen bonds       : bond        0.04055 (  456)
  hydrogen bonds       : angle       5.26340 ( 1260)

*********************** 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
  147 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 120
  time to evaluate  : 0.435 
Fit side-chains
REVERT: A  104 MET cc_start: 0.8121 (mtm) cc_final: 0.7825 (mtp)
REVERT: A  345 ARG cc_start: 0.8049 (mmt-90) cc_final: 0.7824 (mmm160)
REVERT: B  162 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7330 (tm-30)
REVERT: B  233 LYS cc_start: 0.7415 (mmtt) cc_final: 0.6803 (mtmt)
REVERT: B  319 MET cc_start: 0.8919 (mtm) cc_final: 0.8715 (mtp)
REVERT: B  338 ARG cc_start: 0.7548 (ptp90) cc_final: 0.7185 (ptm-80)
REVERT: C  162 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7261 (tm-30)
  outliers start: 27
  outliers final: 20
  residues processed: 138
  average time/residue: 0.1114
  time to fit residues: 22.0270
Evaluate side-chains
  135 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
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 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   55 ASP
Chi-restraints excluded: chain D residue   56 SER
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 109 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 119 optimal weight:    0.0770
   chunk 23 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 25 optimal weight:    0.1980
   chunk 118 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.4938

-------------------------------------------------------------------------------
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 = 0.3798 r_free = 0.3798 target = 0.145298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.125967 restraints weight = 15048.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 2.26
r_work: 0.3455 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3303 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.3576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  11124  Z= 0.106
  Angle     :  0.481   6.483  15068  Z= 0.262
  Chirality :  0.042   0.149   1668
  Planarity :  0.003   0.027   1884
  Dihedral  :  4.519  31.122   1460
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 14.93 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.61 (0.24), residues: 1312
  helix: -0.76 (0.27), residues: 344
  sheet: -0.19 (0.28), residues: 356
  loop : -0.12 (0.27), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 371 
 TYR   0.007   0.001   TYR B 220 
 PHE   0.015   0.001   PHE B 292 
 TRP   0.013   0.001   TRP C 312 
 HIS   0.002   0.000   HIS A 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 (11124)
  covalent geometry    : angle       0.48148 (15068)
  hydrogen bonds       : bond        0.03059 (  456)
  hydrogen bonds       : angle       4.77266 ( 1260)

*********************** 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
  148 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 128
  time to evaluate  : 0.430 
Fit side-chains
REVERT: A  104 MET cc_start: 0.8170 (mtm) cc_final: 0.7905 (mtm)
REVERT: A  345 ARG cc_start: 0.8053 (mmt-90) cc_final: 0.7646 (mmm160)
REVERT: B  162 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7031 (tm-30)
REVERT: B  233 LYS cc_start: 0.6946 (mmtt) cc_final: 0.6424 (mtmt)
REVERT: B  256 ASP cc_start: 0.8469 (t0) cc_final: 0.8027 (m-30)
REVERT: B  314 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.6971 (mp10)
REVERT: B  319 MET cc_start: 0.8918 (mtm) cc_final: 0.8696 (mtp)
REVERT: B  338 ARG cc_start: 0.7420 (ptp90) cc_final: 0.6942 (ptm-80)
REVERT: C  162 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7030 (tm-30)
REVERT: C  358 GLN cc_start: 0.7866 (mt0) cc_final: 0.7633 (pt0)
REVERT: C  371 ARG cc_start: 0.7618 (ptt-90) cc_final: 0.7279 (ptt-90)
  outliers start: 20
  outliers final: 12
  residues processed: 138
  average time/residue: 0.1102
  time to fit residues: 22.0049
Evaluate side-chains
  133 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
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  353 LEU
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  314 GLN
Chi-restraints excluded: chain B residue  334 THR
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 93 optimal weight:    3.9990
   chunk 1 optimal weight:    0.2980
   chunk 113 optimal weight:    5.9990
   chunk 131 optimal weight:    0.8980
   chunk 121 optimal weight:    0.0000
   chunk 29 optimal weight:    0.7980
   chunk 99 optimal weight:   10.0000
   overall best weight:    0.5784

-------------------------------------------------------------------------------
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 = 0.3804 r_free = 0.3804 target = 0.145814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.128436 restraints weight = 14978.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3608 rms_B_bonded: 1.90
r_work: 0.3510 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3373 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.3692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11124  Z= 0.112
  Angle     :  0.487   6.240  15068  Z= 0.268
  Chirality :  0.042   0.149   1668
  Planarity :  0.003   0.028   1884
  Dihedral  :  4.406  28.798   1460
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 15.02 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.52 (0.24), residues: 1312
  helix: -0.62 (0.27), residues: 344
  sheet: -0.15 (0.28), residues: 356
  loop : -0.11 (0.27), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 371 
 TYR   0.007   0.001   TYR D 309 
 PHE   0.015   0.001   PHE B 292 
 TRP   0.013   0.001   TRP C 312 
 HIS   0.002   0.000   HIS D 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (11124)
  covalent geometry    : angle       0.48740 (15068)
  hydrogen bonds       : bond        0.02999 (  456)
  hydrogen bonds       : angle       4.70006 ( 1260)

*********************** 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
  148 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
REVERT: A  345 ARG cc_start: 0.8047 (mmt-90) cc_final: 0.7740 (mmm160)
REVERT: B  162 GLU cc_start: 0.7397 (tm-30) cc_final: 0.6885 (tm-30)
REVERT: B  233 LYS cc_start: 0.7257 (mmtt) cc_final: 0.6781 (mtmt)
REVERT: B  256 ASP cc_start: 0.8378 (t0) cc_final: 0.8056 (m-30)
REVERT: B  338 ARG cc_start: 0.7422 (ptp90) cc_final: 0.7154 (ptm-80)
REVERT: C  162 GLU cc_start: 0.7384 (tm-30) cc_final: 0.6884 (tm-30)
REVERT: C  241 ASP cc_start: 0.7737 (t0) cc_final: 0.7398 (t0)
REVERT: C  314 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.6923 (mp10)
REVERT: C  346 ASP cc_start: 0.8171 (m-30) cc_final: 0.7742 (m-30)
REVERT: C  371 ARG cc_start: 0.7794 (ptt-90) cc_final: 0.7291 (ptt-90)
  outliers start: 21
  outliers final: 18
  residues processed: 138
  average time/residue: 0.1051
  time to fit residues: 21.0208
Evaluate side-chains
  140 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 121
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
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  353 LEU
Chi-restraints excluded: chain A residue  362 LEU
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  334 THR
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  194 ASP
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain C residue  314 GLN
Chi-restraints excluded: chain C residue  334 THR
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 16 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 100 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0980
   chunk 3 optimal weight:    0.9980
   chunk 118 optimal weight:    0.8980
   chunk 49 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   chunk 83 optimal weight:    0.7980
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3796 r_free = 0.3796 target = 0.145107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.127612 restraints weight = 15042.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 1.91
r_work: 0.3486 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3347 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.3754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  11124  Z= 0.125
  Angle     :  0.489   6.624  15068  Z= 0.267
  Chirality :  0.042   0.178   1668
  Planarity :  0.003   0.028   1884
  Dihedral  :  4.424  29.590   1460
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 15.44 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.53 (0.24), residues: 1312
  helix: -0.64 (0.28), residues: 344
  sheet: -0.14 (0.28), residues: 356
  loop : -0.12 (0.27), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 371 
 TYR   0.007   0.001   TYR D 287 
 PHE   0.015   0.001   PHE B 292 
 TRP   0.012   0.001   TRP C 312 
 HIS   0.002   0.001   HIS D 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (11124)
  covalent geometry    : angle       0.48850 (15068)
  hydrogen bonds       : bond        0.03079 (  456)
  hydrogen bonds       : angle       4.68938 ( 1260)

*********************** 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
  152 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 127
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
REVERT: A  104 MET cc_start: 0.7772 (mtm) cc_final: 0.7371 (mtp)
REVERT: A  205 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7696 (m-30)
REVERT: A  345 ARG cc_start: 0.8109 (mmt-90) cc_final: 0.7807 (mmm160)
REVERT: B  162 GLU cc_start: 0.7469 (tm-30) cc_final: 0.6945 (tm-30)
REVERT: B  233 LYS cc_start: 0.7245 (mmtt) cc_final: 0.6749 (mtmt)
REVERT: B  256 ASP cc_start: 0.8388 (t0) cc_final: 0.8051 (m-30)
REVERT: B  314 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.6853 (mp10)
REVERT: B  319 MET cc_start: 0.8824 (mtm) cc_final: 0.8619 (mtp)
REVERT: B  338 ARG cc_start: 0.7417 (ptp90) cc_final: 0.7122 (ptm-80)
REVERT: C  162 GLU cc_start: 0.7388 (tm-30) cc_final: 0.6920 (tm-30)
REVERT: C  241 ASP cc_start: 0.7748 (t0) cc_final: 0.7393 (t0)
REVERT: C  256 ASP cc_start: 0.8355 (t0) cc_final: 0.7993 (m-30)
REVERT: C  314 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.6942 (mp10)
REVERT: C  338 ARG cc_start: 0.7447 (ptp90) cc_final: 0.7086 (ptm-80)
REVERT: C  346 ASP cc_start: 0.8133 (m-30) cc_final: 0.7703 (m-30)
REVERT: C  358 GLN cc_start: 0.7650 (mt0) cc_final: 0.7449 (pt0)
  outliers start: 25
  outliers final: 19
  residues processed: 142
  average time/residue: 0.1062
  time to fit residues: 21.5783
Evaluate side-chains
  144 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 122
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
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  205 ASP
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  362 LEU
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  314 GLN
Chi-restraints excluded: chain B residue  334 THR
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  194 ASP
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain C residue  314 GLN
Chi-restraints excluded: chain C residue  334 THR
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 2 optimal weight:    0.3980
   chunk 89 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0370
   chunk 76 optimal weight:    0.4980
   chunk 29 optimal weight:    2.9990
   chunk 126 optimal weight:    2.9990
   chunk 118 optimal weight:    0.0980
   overall best weight:    0.4060

-------------------------------------------------------------------------------
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 = 0.3819 r_free = 0.3819 target = 0.147111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.129749 restraints weight = 14915.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 1.91
r_work: 0.3515 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3376 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.3876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  11124  Z= 0.097
  Angle     :  0.476   6.543  15068  Z= 0.259
  Chirality :  0.042   0.150   1668
  Planarity :  0.003   0.028   1884
  Dihedral  :  4.274  27.519   1460
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 15.60 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.50 (0.24), residues: 1312
  helix: -0.54 (0.28), residues: 344
  sheet: -0.17 (0.29), residues: 336
  loop : -0.11 (0.26), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 371 
 TYR   0.007   0.001   TYR D 309 
 PHE   0.014   0.001   PHE B 292 
 TRP   0.013   0.001   TRP C 312 
 HIS   0.002   0.000   HIS D 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 (11124)
  covalent geometry    : angle       0.47625 (15068)
  hydrogen bonds       : bond        0.02829 (  456)
  hydrogen bonds       : angle       4.53568 ( 1260)

*********************** 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
  151 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
REVERT: A  104 MET cc_start: 0.7732 (mtm) cc_final: 0.7390 (mtp)
REVERT: A  345 ARG cc_start: 0.8092 (mmt-90) cc_final: 0.7759 (mmm160)
REVERT: B  162 GLU cc_start: 0.7460 (tm-30) cc_final: 0.6970 (tm-30)
REVERT: B  233 LYS cc_start: 0.7153 (mmtt) cc_final: 0.6677 (mtmt)
REVERT: B  256 ASP cc_start: 0.8363 (t0) cc_final: 0.8041 (m-30)
REVERT: B  314 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.6943 (mp10)
REVERT: B  338 ARG cc_start: 0.7440 (ptp90) cc_final: 0.7117 (ptm-80)
REVERT: C  162 GLU cc_start: 0.7452 (tm-30) cc_final: 0.7020 (tm-30)
REVERT: C  241 ASP cc_start: 0.7705 (t0) cc_final: 0.7369 (t0)
REVERT: C  256 ASP cc_start: 0.8299 (t0) cc_final: 0.7963 (m-30)
REVERT: C  314 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.6985 (mp10)
REVERT: C  346 ASP cc_start: 0.8047 (m-30) cc_final: 0.7714 (m-30)
REVERT: C  358 GLN cc_start: 0.7653 (mt0) cc_final: 0.7376 (pt0)
  outliers start: 23
  outliers final: 19
  residues processed: 138
  average time/residue: 0.1095
  time to fit residues: 21.8221
Evaluate side-chains
  144 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
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  164 MET
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  164 MET
Chi-restraints excluded: chain B residue  194 ASP
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  314 GLN
Chi-restraints excluded: chain B residue  334 THR
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  194 ASP
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain C residue  314 GLN
Chi-restraints excluded: chain C residue  334 THR
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 53 optimal weight:    2.9990
   chunk 119 optimal weight:    6.9990
   chunk 16 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0170
   chunk 43 optimal weight:    3.9990
   chunk 86 optimal weight:    0.6980
   chunk 64 optimal weight:    6.9990
   chunk 67 optimal weight:    4.9990
   chunk 75 optimal weight:    0.0050
   chunk 97 optimal weight:    4.9990
   chunk 10 optimal weight:    0.1980
   overall best weight:    0.7834

-------------------------------------------------------------------------------
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 = 0.3797 r_free = 0.3797 target = 0.145119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.127601 restraints weight = 14977.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 1.91
r_work: 0.3488 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3350 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.3876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11124  Z= 0.130
  Angle     :  0.500   7.658  15068  Z= 0.271
  Chirality :  0.043   0.158   1668
  Planarity :  0.003   0.029   1884
  Dihedral  :  4.400  28.978   1460
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 16.02 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.48 (0.24), residues: 1312
  helix: -0.55 (0.28), residues: 344
  sheet: -0.11 (0.28), residues: 356
  loop : -0.11 (0.27), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 371 
 TYR   0.007   0.001   TYR B 287 
 PHE   0.015   0.001   PHE B 292 
 TRP   0.012   0.001   TRP C 312 
 HIS   0.002   0.000   HIS D 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (11124)
  covalent geometry    : angle       0.50049 (15068)
  hydrogen bonds       : bond        0.03077 (  456)
  hydrogen bonds       : angle       4.63794 ( 1260)

********************** 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
  146 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 122
  time to evaluate  : 0.456 
Fit side-chains
REVERT: A  104 MET cc_start: 0.7766 (mtm) cc_final: 0.7426 (mtp)
REVERT: A  205 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7757 (m-30)
REVERT: A  345 ARG cc_start: 0.8113 (mmt-90) cc_final: 0.7803 (mmm160)
REVERT: B  162 GLU cc_start: 0.7435 (tm-30) cc_final: 0.6896 (tm-30)
REVERT: B  233 LYS cc_start: 0.7320 (mmtt) cc_final: 0.6811 (mtmt)
REVERT: B  241 ASP cc_start: 0.7745 (t0) cc_final: 0.7445 (t0)
REVERT: B  256 ASP cc_start: 0.8371 (t0) cc_final: 0.8056 (m-30)
REVERT: B  314 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.6766 (mp10)
REVERT: B  338 ARG cc_start: 0.7424 (ptp90) cc_final: 0.7150 (ptm-80)
REVERT: C  162 GLU cc_start: 0.7438 (tm-30) cc_final: 0.6942 (tm-30)
REVERT: C  241 ASP cc_start: 0.7723 (t0) cc_final: 0.7381 (t0)
REVERT: C  256 ASP cc_start: 0.8321 (t0) cc_final: 0.7992 (m-30)
REVERT: C  314 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.6922 (mp10)
REVERT: C  338 ARG cc_start: 0.7369 (ptp90) cc_final: 0.7097 (ptm-80)
REVERT: C  346 ASP cc_start: 0.8100 (m-30) cc_final: 0.7719 (m-30)
REVERT: C  358 GLN cc_start: 0.7653 (mt0) cc_final: 0.7403 (pt0)
  outliers start: 24
  outliers final: 20
  residues processed: 134
  average time/residue: 0.1194
  time to fit residues: 22.9154
Evaluate side-chains
  142 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue   62 ILE
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  205 ASP
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  164 MET
Chi-restraints excluded: chain B residue  194 ASP
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  262 VAL
Chi-restraints excluded: chain B residue  314 GLN
Chi-restraints excluded: chain B residue  334 THR
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  194 ASP
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain C residue  314 GLN
Chi-restraints excluded: chain C residue  334 THR
Chi-restraints excluded: chain D residue  164 MET
Chi-restraints excluded: chain D residue  335 ILE
Chi-restraints excluded: chain D residue  353 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 54 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 77 optimal weight:    0.0980
   chunk 112 optimal weight:    0.6980
   chunk 117 optimal weight:    3.9990
   chunk 55 optimal weight:    0.0040
   chunk 43 optimal weight:    0.9990
   chunk 129 optimal weight:    0.8980
   chunk 123 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.4592

-------------------------------------------------------------------------------
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 = 0.3825 r_free = 0.3825 target = 0.147476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.130101 restraints weight = 15047.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 1.91
r_work: 0.3520 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3382 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.3983

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= 0.102
  Angle     :  0.486   7.604  15068  Z= 0.264
  Chirality :  0.042   0.149   1668
  Planarity :  0.003   0.031   1884
  Dihedral  :  4.304  27.407   1460
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 16.11 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.24), residues: 1312
  helix: -0.49 (0.28), residues: 344
  sheet: -0.02 (0.29), residues: 356
  loop : -0.07 (0.27), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 371 
 TYR   0.007   0.001   TYR D 309 
 PHE   0.014   0.001   PHE B 292 
 TRP   0.014   0.001   TRP C 312 
 HIS   0.002   0.000   HIS D 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (11124)
  covalent geometry    : angle       0.48648 (15068)
  hydrogen bonds       : bond        0.02871 (  456)
  hydrogen bonds       : angle       4.52124 ( 1260)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2838.47 seconds
wall clock time: 49 minutes 38.24 seconds (2978.24 seconds total)