Starting phenix.real_space_refine
on Wed Jul 30 14:15:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6v0b_20986/07_2025/6v0b_20986.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6v0b_20986/07_2025/6v0b_20986.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6v0b_20986/07_2025/6v0b_20986.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6v0b_20986/07_2025/6v0b_20986.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6v0b_20986/07_2025/6v0b_20986.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6v0b_20986/07_2025/6v0b_20986.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.009
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      30      5.16       5
     C    8135      2.51       5
     N    2075      2.21       5
     O    2245      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12485
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2497
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2497
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 14, 'TRANS': 291}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 5.11, per 1000 atoms: 0.41
  Number of scatterers: 12485
  At special positions: 0
  Unit cell: (92.0724, 92.0724, 117.283, 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      30     16.00
     O    2245      8.00
     N    2075      7.00
     C    8135      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.41
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2900

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 20 sheets defined
      25.2% alpha, 32.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 62 through 67
      removed outlier: 3.594A  pdb=" N   TRP A  66 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 207
      removed outlier: 3.935A  pdb=" N   SER A 207 " --> pdb=" O   TYR A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 220
      removed outlier: 4.135A  pdb=" N   ILE A 216 " --> pdb=" O   LEU A 212 " (cutoff:3.500A)
      removed outlier: 4.706A  pdb=" N   ALA A 217 " --> pdb=" O   GLY A 213 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   TRP A 220 " --> pdb=" O   ILE A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 253
      removed outlier: 3.558A  pdb=" N   THR A 234 " --> pdb=" O   GLU A 230 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   VAL A 243 " --> pdb=" O   MET A 239 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   SER A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
      removed outlier: 4.975A  pdb=" N   ASN A 251 " --> pdb=" O   PHE A 247 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   ILE A 252 " --> pdb=" O   TYR A 248 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   LEU A 253 " --> pdb=" O   THR A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 264
      removed outlier: 3.674A  pdb=" N   GLN A 264 " --> pdb=" O   VAL A 261 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 261 through 264'
    Processing helix  chain 'A' and resid 265 through 285
      removed outlier: 4.374A  pdb=" N   ILE A 273 " --> pdb=" O   GLY A 269 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   LEU A 278 " --> pdb=" O   PHE A 274 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU A 279 " --> pdb=" O   ALA A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 307
    Processing helix  chain 'B' and resid 62 through 67
      removed outlier: 3.592A  pdb=" N   TRP B  66 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 207
      removed outlier: 3.935A  pdb=" N   SER B 207 " --> pdb=" O   TYR B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 220
      removed outlier: 4.136A  pdb=" N   ILE B 216 " --> pdb=" O   LEU B 212 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   ALA B 217 " --> pdb=" O   GLY B 213 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   TRP B 220 " --> pdb=" O   ILE B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 253
      removed outlier: 3.558A  pdb=" N   THR B 234 " --> pdb=" O   GLU B 230 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   VAL B 243 " --> pdb=" O   MET B 239 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   SER B 250 " --> pdb=" O   ALA B 246 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   ASN B 251 " --> pdb=" O   PHE B 247 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   ILE B 252 " --> pdb=" O   TYR B 248 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   LEU B 253 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 261 through 264
      removed outlier: 3.674A  pdb=" N   GLN B 264 " --> pdb=" O   VAL B 261 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 261 through 264'
    Processing helix  chain 'B' and resid 265 through 285
      removed outlier: 4.374A  pdb=" N   ILE B 273 " --> pdb=" O   GLY B 269 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LEU B 278 " --> pdb=" O   PHE B 274 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU B 279 " --> pdb=" O   ALA B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 307
    Processing helix  chain 'C' and resid 62 through 67
      removed outlier: 3.593A  pdb=" N   TRP C  66 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 207
      removed outlier: 3.934A  pdb=" N   SER C 207 " --> pdb=" O   TYR C 203 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 211 through 220
      removed outlier: 4.136A  pdb=" N   ILE C 216 " --> pdb=" O   LEU C 212 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   ALA C 217 " --> pdb=" O   GLY C 213 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   TRP C 220 " --> pdb=" O   ILE C 216 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 230 through 253
      removed outlier: 3.558A  pdb=" N   THR C 234 " --> pdb=" O   GLU C 230 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   VAL C 243 " --> pdb=" O   MET C 239 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   SER C 250 " --> pdb=" O   ALA C 246 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   ASN C 251 " --> pdb=" O   PHE C 247 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   ILE C 252 " --> pdb=" O   TYR C 248 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   LEU C 253 " --> pdb=" O   THR C 249 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 261 through 264
      removed outlier: 3.674A  pdb=" N   GLN C 264 " --> pdb=" O   VAL C 261 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 261 through 264'
    Processing helix  chain 'C' and resid 265 through 285
      removed outlier: 4.373A  pdb=" N   ILE C 273 " --> pdb=" O   GLY C 269 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LEU C 278 " --> pdb=" O   PHE C 274 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU C 279 " --> pdb=" O   ALA C 275 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 302 through 307
    Processing helix  chain 'D' and resid 62 through 67
      removed outlier: 3.593A  pdb=" N   TRP D  66 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 202 through 207
      removed outlier: 3.934A  pdb=" N   SER D 207 " --> pdb=" O   TYR D 203 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 211 through 220
      removed outlier: 4.135A  pdb=" N   ILE D 216 " --> pdb=" O   LEU D 212 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   ALA D 217 " --> pdb=" O   GLY D 213 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   TRP D 220 " --> pdb=" O   ILE D 216 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 230 through 253
      removed outlier: 3.558A  pdb=" N   THR D 234 " --> pdb=" O   GLU D 230 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   VAL D 243 " --> pdb=" O   MET D 239 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   SER D 250 " --> pdb=" O   ALA D 246 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   ASN D 251 " --> pdb=" O   PHE D 247 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   ILE D 252 " --> pdb=" O   TYR D 248 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   LEU D 253 " --> pdb=" O   THR D 249 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 261 through 264
      removed outlier: 3.674A  pdb=" N   GLN D 264 " --> pdb=" O   VAL D 261 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 261 through 264'
    Processing helix  chain 'D' and resid 265 through 285
      removed outlier: 4.374A  pdb=" N   ILE D 273 " --> pdb=" O   GLY D 269 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LEU D 278 " --> pdb=" O   PHE D 274 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU D 279 " --> pdb=" O   ALA D 275 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 302 through 307
    Processing helix  chain 'E' and resid 62 through 67
      removed outlier: 3.594A  pdb=" N   TRP E  66 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 202 through 207
      removed outlier: 3.935A  pdb=" N   SER E 207 " --> pdb=" O   TYR E 203 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 211 through 220
      removed outlier: 4.136A  pdb=" N   ILE E 216 " --> pdb=" O   LEU E 212 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   ALA E 217 " --> pdb=" O   GLY E 213 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   TRP E 220 " --> pdb=" O   ILE E 216 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 230 through 253
      removed outlier: 3.558A  pdb=" N   THR E 234 " --> pdb=" O   GLU E 230 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   VAL E 243 " --> pdb=" O   MET E 239 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   SER E 250 " --> pdb=" O   ALA E 246 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   ASN E 251 " --> pdb=" O   PHE E 247 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   ILE E 252 " --> pdb=" O   TYR E 248 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   LEU E 253 " --> pdb=" O   THR E 249 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 261 through 264
      removed outlier: 3.675A  pdb=" N   GLN E 264 " --> pdb=" O   VAL E 261 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 261 through 264'
    Processing helix  chain 'E' and resid 265 through 285
      removed outlier: 4.374A  pdb=" N   ILE E 273 " --> pdb=" O   GLY E 269 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LEU E 278 " --> pdb=" O   PHE E 274 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU E 279 " --> pdb=" O   ALA E 275 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 302 through 307
    Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 27
      removed outlier: 5.530A  pdb=" N   ILE A  23 " --> pdb=" O   ASP A  36 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   ASP A  36 " --> pdb=" O   ILE A  23 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   GLY A  25 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   LYS A  34 " --> pdb=" O   GLY A  25 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   VAL A  35 " --> pdb=" O   GLY A 108 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   GLY A 108 " --> pdb=" O   VAL A  35 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLY A  37 " --> pdb=" O   PHE A 106 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 27
      removed outlier: 5.530A  pdb=" N   ILE A  23 " --> pdb=" O   ASP A  36 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   ASP A  36 " --> pdb=" O   ILE A  23 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   GLY A  25 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   LYS A  34 " --> pdb=" O   GLY A  25 " (cutoff:3.500A)
      removed outlier: 5.934A  pdb=" N   VAL A  14 " --> pdb=" O   LEU A 140 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 77
      removed outlier: 3.780A  pdb=" N   GLU A 131 " --> pdb=" O   GLU A  77 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ARG A 194 " --> pdb=" O   SER A 167 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   SER A 167 " --> pdb=" O   ARG A 194 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 77
      removed outlier: 3.780A  pdb=" N   GLU A 131 " --> pdb=" O   GLU A  77 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 22 through 27
      removed outlier: 5.531A  pdb=" N   ILE B  23 " --> pdb=" O   ASP B  36 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   ASP B  36 " --> pdb=" O   ILE B  23 " (cutoff:3.500A)
      removed outlier: 5.116A  pdb=" N   GLY B  25 " --> pdb=" O   LYS B  34 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   LYS B  34 " --> pdb=" O   GLY B  25 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   VAL B  35 " --> pdb=" O   GLY B 108 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   GLY B 108 " --> pdb=" O   VAL B  35 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLY B  37 " --> pdb=" O   PHE B 106 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 22 through 27
      removed outlier: 5.531A  pdb=" N   ILE B  23 " --> pdb=" O   ASP B  36 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   ASP B  36 " --> pdb=" O   ILE B  23 " (cutoff:3.500A)
      removed outlier: 5.116A  pdb=" N   GLY B  25 " --> pdb=" O   LYS B  34 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   LYS B  34 " --> pdb=" O   GLY B  25 " (cutoff:3.500A)
      removed outlier: 5.934A  pdb=" N   VAL B  14 " --> pdb=" O   LEU B 140 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 77
      removed outlier: 3.780A  pdb=" N   GLU B 131 " --> pdb=" O   GLU B  77 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ARG B 194 " --> pdb=" O   SER B 167 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   SER B 167 " --> pdb=" O   ARG B 194 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 77
      removed outlier: 3.780A  pdb=" N   GLU B 131 " --> pdb=" O   GLU B  77 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 22 through 27
      removed outlier: 5.531A  pdb=" N   ILE C  23 " --> pdb=" O   ASP C  36 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   ASP C  36 " --> pdb=" O   ILE C  23 " (cutoff:3.500A)
      removed outlier: 5.116A  pdb=" N   GLY C  25 " --> pdb=" O   LYS C  34 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   LYS C  34 " --> pdb=" O   GLY C  25 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   VAL C  35 " --> pdb=" O   GLY C 108 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   GLY C 108 " --> pdb=" O   VAL C  35 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLY C  37 " --> pdb=" O   PHE C 106 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 22 through 27
      removed outlier: 5.531A  pdb=" N   ILE C  23 " --> pdb=" O   ASP C  36 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   ASP C  36 " --> pdb=" O   ILE C  23 " (cutoff:3.500A)
      removed outlier: 5.116A  pdb=" N   GLY C  25 " --> pdb=" O   LYS C  34 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   LYS C  34 " --> pdb=" O   GLY C  25 " (cutoff:3.500A)
      removed outlier: 5.934A  pdb=" N   VAL C  14 " --> pdb=" O   LEU C 140 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 77
      removed outlier: 3.779A  pdb=" N   GLU C 131 " --> pdb=" O   GLU C  77 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ARG C 194 " --> pdb=" O   SER C 167 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   SER C 167 " --> pdb=" O   ARG C 194 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 77
      removed outlier: 3.779A  pdb=" N   GLU C 131 " --> pdb=" O   GLU C  77 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 22 through 27
      removed outlier: 5.531A  pdb=" N   ILE D  23 " --> pdb=" O   ASP D  36 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   ASP D  36 " --> pdb=" O   ILE D  23 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   GLY D  25 " --> pdb=" O   LYS D  34 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   LYS D  34 " --> pdb=" O   GLY D  25 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   VAL D  35 " --> pdb=" O   GLY D 108 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   GLY D 108 " --> pdb=" O   VAL D  35 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLY D  37 " --> pdb=" O   PHE D 106 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 22 through 27
      removed outlier: 5.531A  pdb=" N   ILE D  23 " --> pdb=" O   ASP D  36 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   ASP D  36 " --> pdb=" O   ILE D  23 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   GLY D  25 " --> pdb=" O   LYS D  34 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   LYS D  34 " --> pdb=" O   GLY D  25 " (cutoff:3.500A)
      removed outlier: 5.934A  pdb=" N   VAL D  14 " --> pdb=" O   LEU D 140 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 77
      removed outlier: 3.779A  pdb=" N   GLU D 131 " --> pdb=" O   GLU D  77 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ARG D 194 " --> pdb=" O   SER D 167 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   SER D 167 " --> pdb=" O   ARG D 194 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 76 through 77
      removed outlier: 3.779A  pdb=" N   GLU D 131 " --> pdb=" O   GLU D  77 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 22 through 27
      removed outlier: 5.531A  pdb=" N   ILE E  23 " --> pdb=" O   ASP E  36 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   ASP E  36 " --> pdb=" O   ILE E  23 " (cutoff:3.500A)
      removed outlier: 5.116A  pdb=" N   GLY E  25 " --> pdb=" O   LYS E  34 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   LYS E  34 " --> pdb=" O   GLY E  25 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   VAL E  35 " --> pdb=" O   GLY E 108 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   GLY E 108 " --> pdb=" O   VAL E  35 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLY E  37 " --> pdb=" O   PHE E 106 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 22 through 27
      removed outlier: 5.531A  pdb=" N   ILE E  23 " --> pdb=" O   ASP E  36 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   ASP E  36 " --> pdb=" O   ILE E  23 " (cutoff:3.500A)
      removed outlier: 5.116A  pdb=" N   GLY E  25 " --> pdb=" O   LYS E  34 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   LYS E  34 " --> pdb=" O   GLY E  25 " (cutoff:3.500A)
      removed outlier: 5.933A  pdb=" N   VAL E  14 " --> pdb=" O   LEU E 140 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 77
      removed outlier: 3.780A  pdb=" N   GLU E 131 " --> pdb=" O   GLU E  77 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ARG E 194 " --> pdb=" O   SER E 167 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   SER E 167 " --> pdb=" O   ARG E 194 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 77
      removed outlier: 3.780A  pdb=" N   GLU E 131 " --> pdb=" O   GLU E  77 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)

    390 hydrogen bonds defined for protein.
    1125 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.44

  Time building geometry restraints manager: 3.69 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: 3952
        1.34 -     1.46: 2919
        1.46 -     1.58: 5904
        1.58 -     1.69: 0
        1.69 -     1.81: 50
  Bond restraints: 12825
  Sorted by residual:
  bond pdb=" N   CYS B 300 "
       pdb=" CA  CYS B 300 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.034 1.32e-02 5.74e+03 6.55e+00
  bond pdb=" N   CYS E 300 "
       pdb=" CA  CYS E 300 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.32e-02 5.74e+03 6.36e+00
  bond pdb=" N   CYS D 300 "
       pdb=" CA  CYS D 300 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.32e-02 5.74e+03 6.34e+00
  bond pdb=" N   CYS A 300 "
       pdb=" CA  CYS A 300 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.32e-02 5.74e+03 6.25e+00
  bond pdb=" N   CYS C 300 "
       pdb=" CA  CYS C 300 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.32e-02 5.74e+03 6.24e+00
  ... (remaining 12820 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 16337
        1.82 -     3.65: 969
        3.65 -     5.47: 124
        5.47 -     7.29: 40
        7.29 -     9.12: 10
  Bond angle restraints: 17480
  Sorted by residual:
  angle pdb=" C   PRO C 183 "
        pdb=" N   ASN C 184 "
        pdb=" CA  ASN C 184 "
      ideal   model   delta    sigma   weight residual
     121.54  130.66   -9.12 1.91e+00 2.74e-01 2.28e+01
  angle pdb=" C   PRO D 183 "
        pdb=" N   ASN D 184 "
        pdb=" CA  ASN D 184 "
      ideal   model   delta    sigma   weight residual
     121.54  130.64   -9.10 1.91e+00 2.74e-01 2.27e+01
  angle pdb=" C   PRO B 183 "
        pdb=" N   ASN B 184 "
        pdb=" CA  ASN B 184 "
      ideal   model   delta    sigma   weight residual
     121.54  130.61   -9.07 1.91e+00 2.74e-01 2.26e+01
  angle pdb=" C   PRO E 183 "
        pdb=" N   ASN E 184 "
        pdb=" CA  ASN E 184 "
      ideal   model   delta    sigma   weight residual
     121.54  130.58   -9.04 1.91e+00 2.74e-01 2.24e+01
  angle pdb=" C   PRO A 183 "
        pdb=" N   ASN A 184 "
        pdb=" CA  ASN A 184 "
      ideal   model   delta    sigma   weight residual
     121.54  130.55   -9.01 1.91e+00 2.74e-01 2.22e+01
  ... (remaining 17475 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.11: 6291
       14.11 -    28.22: 851
       28.22 -    42.33: 272
       42.33 -    56.44: 61
       56.44 -    70.55: 25
  Dihedral angle restraints: 7500
    sinusoidal: 3010
      harmonic: 4490
  Sorted by residual:
  dihedral pdb=" CA  ASN B 289 "
           pdb=" C   ASN B 289 "
           pdb=" N   GLY B 290 "
           pdb=" CA  GLY B 290 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.07   28.93     0      5.00e+00 4.00e-02 3.35e+01
  dihedral pdb=" CA  ASN E 289 "
           pdb=" C   ASN E 289 "
           pdb=" N   GLY E 290 "
           pdb=" CA  GLY E 290 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.11   28.89     0      5.00e+00 4.00e-02 3.34e+01
  dihedral pdb=" CA  ASN A 289 "
           pdb=" C   ASN A 289 "
           pdb=" N   GLY A 290 "
           pdb=" CA  GLY A 290 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.11   28.89     0      5.00e+00 4.00e-02 3.34e+01
  ... (remaining 7497 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1498
       0.066 -    0.132: 374
       0.132 -    0.198: 61
       0.198 -    0.263: 2
       0.263 -    0.329: 5
  Chirality restraints: 1940
  Sorted by residual:
  chirality pdb=" CG  LEU E 214 "
            pdb=" CB  LEU E 214 "
            pdb=" CD1 LEU E 214 "
            pdb=" CD2 LEU E 214 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.26   -0.33 2.00e-01 2.50e+01 2.71e+00
  chirality pdb=" CG  LEU A 214 "
            pdb=" CB  LEU A 214 "
            pdb=" CD1 LEU A 214 "
            pdb=" CD2 LEU A 214 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.26   -0.33 2.00e-01 2.50e+01 2.70e+00
  chirality pdb=" CG  LEU D 214 "
            pdb=" CB  LEU D 214 "
            pdb=" CD1 LEU D 214 "
            pdb=" CD2 LEU D 214 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.26   -0.33 2.00e-01 2.50e+01 2.69e+00
  ... (remaining 1937 not shown)

  Planarity restraints: 2230
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 274 "    0.035 2.00e-02 2.50e+03   3.46e-02 2.09e+01
        pdb=" CG  PHE A 274 "   -0.078 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 274 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 274 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 274 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 274 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 274 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 274 "    0.035 2.00e-02 2.50e+03   3.46e-02 2.09e+01
        pdb=" CG  PHE C 274 "   -0.078 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 274 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 274 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 274 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 274 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 274 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D 274 "    0.035 2.00e-02 2.50e+03   3.45e-02 2.09e+01
        pdb=" CG  PHE D 274 "   -0.078 2.00e-02 2.50e+03
        pdb=" CD1 PHE D 274 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 PHE D 274 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE D 274 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE D 274 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ  PHE D 274 "    0.000 2.00e-02 2.50e+03
  ... (remaining 2227 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 3323
        2.80 -     3.32: 11440
        3.32 -     3.85: 21011
        3.85 -     4.37: 23553
        4.37 -     4.90: 39449
  Nonbonded interactions: 98776
  Sorted by model distance:
  nonbonded pdb=" OG  SER D 143 "
            pdb=" OG1 THR D 168 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OG  SER E 143 "
            pdb=" OG1 THR E 168 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OG  SER C 143 "
            pdb=" OG1 THR C 168 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OG  SER B 143 "
            pdb=" OG1 THR B 168 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OG  SER A 143 "
            pdb=" OG1 THR A 168 "
     model   vdw
     2.273 3.040
  ... (remaining 98771 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: 0.10
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.660
  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:             0.020
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     27.150
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
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      :  0.006   0.060  12825  Z= 0.279
  Angle     :  0.981   9.117  17480  Z= 0.552
  Chirality :  0.059   0.329   1940
  Planarity :  0.007   0.051   2230
  Dihedral  : 15.045  70.555   4600
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 10.22 %
    Favored  : 89.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.96 (0.18), residues: 1520
  helix: -4.23 (0.15), residues: 345
  sheet: -3.11 (0.22), residues: 395
  loop : -2.89 (0.20), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 160 
 HIS   0.006   0.003   HIS D 169 
 PHE   0.078   0.003   PHE D 274 
 TYR   0.024   0.003   TYR C 102 
 ARG   0.008   0.001   ARG A 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18482 (  335)
  hydrogen bonds       : angle      10.14840 ( 1125)
  covalent geometry    : bond        0.00572 (12825)
  covalent geometry    : angle       0.98149 (17480)

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

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

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 215
  time to evaluate  : 1.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 LEU cc_start: 0.9030 (tp) cc_final: 0.8802 (tp)
REVERT: A  131 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7906 (mm-30)
REVERT: A  154 ASN cc_start: 0.7762 (m-40) cc_final: 0.7513 (t0)
REVERT: A  239 MET cc_start: 0.9116 (mmm) cc_final: 0.8802 (mmm)
REVERT: B  130 LEU cc_start: 0.9119 (tp) cc_final: 0.8845 (tp)
REVERT: B  154 ASN cc_start: 0.7727 (m-40) cc_final: 0.7466 (m-40)
REVERT: B  239 MET cc_start: 0.9159 (mmm) cc_final: 0.8528 (mpp)
REVERT: C  154 ASN cc_start: 0.7940 (m-40) cc_final: 0.7577 (t0)
REVERT: C  308 PHE cc_start: 0.5863 (m-80) cc_final: 0.5636 (m-10)
REVERT: D  131 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8114 (mt-10)
REVERT: D  239 MET cc_start: 0.9106 (mmm) cc_final: 0.8435 (mpp)
REVERT: E  239 MET cc_start: 0.9082 (mmm) cc_final: 0.8704 (mmm)
  outliers start: 7
  outliers final: 2
  residues processed: 222
  average time/residue: 0.2078
  time to fit residues: 69.7358
Evaluate side-chains
  150 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 148
  time to evaluate  : 1.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    0.4980
   chunk 113 optimal weight:    1.9990
   chunk 63 optimal weight:    6.9990
   chunk 38 optimal weight:    0.6980
   chunk 76 optimal weight:    9.9990
   chunk 60 optimal weight:    9.9990
   chunk 117 optimal weight:   20.0000
   chunk 45 optimal weight:    5.9990
   chunk 71 optimal weight:    8.9990
   chunk 87 optimal weight:   10.0000
   chunk 136 optimal weight:    7.9990
   overall best weight:    3.2386

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN
A  80 ASN
A 125 GLN
** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 177 HIS
A 264 GLN
** B  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  80 ASN
B 125 GLN
** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 177 HIS
B 264 GLN
C  21 ASN
C  80 ASN
C 125 GLN
C 177 HIS
C 264 GLN
D  62 GLN
D  80 ASN
D 125 GLN
** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 177 HIS
D 264 GLN
E  80 ASN
E 125 GLN
E 177 HIS

Total number of N/Q/H flips: 22

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.108392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.086372 restraints weight = 42821.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.089135 restraints weight = 26106.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.090923 restraints weight = 18853.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12825  Z= 0.202
  Angle     :  0.710   8.716  17480  Z= 0.380
  Chirality :  0.047   0.151   1940
  Planarity :  0.005   0.049   2230
  Dihedral  :  6.957  24.600   1680
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.30 (0.19), residues: 1520
  helix: -3.25 (0.19), residues: 375
  sheet: -2.87 (0.21), residues: 410
  loop : -2.51 (0.22), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  72 
 HIS   0.007   0.002   HIS C 177 
 PHE   0.026   0.002   PHE E 247 
 TYR   0.019   0.002   TYR C 270 
 ARG   0.004   0.001   ARG C 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04659 (  335)
  hydrogen bonds       : angle       7.82762 ( 1125)
  covalent geometry    : bond        0.00429 (12825)
  covalent geometry    : angle       0.70951 (17480)

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

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

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 1.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 GLU cc_start: 0.8463 (mt-10) cc_final: 0.7903 (mt-10)
REVERT: A  199 ARG cc_start: 0.8150 (mtm180) cc_final: 0.7558 (mtm180)
REVERT: B  127 VAL cc_start: 0.9170 (t) cc_final: 0.8935 (p)
REVERT: B  131 GLU cc_start: 0.8465 (mt-10) cc_final: 0.7841 (mm-30)
REVERT: B  185 GLN cc_start: 0.2300 (mm-40) cc_final: 0.2061 (mm-40)
REVERT: B  199 ARG cc_start: 0.8087 (mtm180) cc_final: 0.7288 (mtm180)
REVERT: C  131 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7836 (mm-30)
REVERT: D  131 GLU cc_start: 0.8488 (mt-10) cc_final: 0.7941 (mt-10)
REVERT: E  131 GLU cc_start: 0.8465 (mt-10) cc_final: 0.7684 (mt-10)
REVERT: E  239 MET cc_start: 0.8955 (mmm) cc_final: 0.8711 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.2351
  time to fit residues: 60.6189
Evaluate side-chains
  110 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 1.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 119 optimal weight:    9.9990
   chunk 115 optimal weight:    4.9990
   chunk 22 optimal weight:    5.9990
   chunk 40 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 80 optimal weight:    0.5980
   chunk 7 optimal weight:    0.0060
   chunk 27 optimal weight:   10.0000
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.0798

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
** B  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 138 GLN
C  21 ASN
C 138 GLN
D 138 GLN
E 138 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.112133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.089566 restraints weight = 42652.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.092416 restraints weight = 26019.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.094353 restraints weight = 18811.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.2556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  12825  Z= 0.127
  Angle     :  0.635   8.609  17480  Z= 0.331
  Chirality :  0.046   0.159   1940
  Planarity :  0.004   0.042   2230
  Dihedral  :  6.365  21.521   1680
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.78 (0.19), residues: 1520
  helix: -2.53 (0.22), residues: 375
  sheet: -2.51 (0.22), residues: 395
  loop : -2.40 (0.21), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 220 
 HIS   0.003   0.001   HIS E 177 
 PHE   0.029   0.002   PHE C 247 
 TYR   0.017   0.001   TYR E 270 
 ARG   0.002   0.000   ARG B  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03614 (  335)
  hydrogen bonds       : angle       7.07405 ( 1125)
  covalent geometry    : bond        0.00281 (12825)
  covalent geometry    : angle       0.63501 (17480)

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

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

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 1.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7771 (mt-10)
REVERT: A  265 MET cc_start: 0.5838 (mpp) cc_final: 0.5466 (mmm)
REVERT: B  131 GLU cc_start: 0.8377 (mt-10) cc_final: 0.7823 (mt-10)
REVERT: C  128 LEU cc_start: 0.8863 (tt) cc_final: 0.8640 (tt)
REVERT: C  130 LEU cc_start: 0.8739 (tp) cc_final: 0.8215 (tp)
REVERT: C  131 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7446 (mm-30)
REVERT: D  128 LEU cc_start: 0.8655 (tt) cc_final: 0.8114 (mp)
REVERT: D  131 GLU cc_start: 0.8431 (mt-10) cc_final: 0.7948 (mt-10)
REVERT: D  270 TYR cc_start: 0.8155 (m-80) cc_final: 0.7879 (m-80)
REVERT: E  131 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7767 (mt-10)
REVERT: E  239 MET cc_start: 0.8951 (mmm) cc_final: 0.8739 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.2341
  time to fit residues: 57.3457
Evaluate side-chains
  115 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 1.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 100 optimal weight:    0.2980
   chunk 139 optimal weight:   10.0000
   chunk 69 optimal weight:   10.0000
   chunk 6 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 34 optimal weight:    9.9990
   chunk 55 optimal weight:    0.9990
   chunk 25 optimal weight:    6.9990
   chunk 20 optimal weight:    0.4980
   chunk 89 optimal weight:    9.9990
   chunk 39 optimal weight:    9.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
** B  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.110932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.088848 restraints weight = 42147.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.091690 restraints weight = 25552.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.093538 restraints weight = 18323.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.2788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12825  Z= 0.147
  Angle     :  0.637   8.383  17480  Z= 0.329
  Chirality :  0.045   0.138   1940
  Planarity :  0.004   0.045   2230
  Dihedral  :  6.163  20.637   1680
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.45 (0.19), residues: 1520
  helix: -2.15 (0.23), residues: 380
  sheet: -2.28 (0.23), residues: 395
  loop : -2.29 (0.21), residues: 745

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 220 
 HIS   0.005   0.001   HIS A 177 
 PHE   0.024   0.002   PHE D 274 
 TYR   0.022   0.002   TYR A 270 
 ARG   0.002   0.000   ARG C 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03547 (  335)
  hydrogen bonds       : angle       6.72311 ( 1125)
  covalent geometry    : bond        0.00325 (12825)
  covalent geometry    : angle       0.63748 (17480)

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

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

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 1.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 GLU cc_start: 0.8377 (mt-10) cc_final: 0.7709 (mt-10)
REVERT: A  265 MET cc_start: 0.5617 (mpp) cc_final: 0.5302 (mmm)
REVERT: B  199 ARG cc_start: 0.8122 (mtm180) cc_final: 0.7879 (mtm180)
REVERT: C  131 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7824 (mm-30)
REVERT: D  128 LEU cc_start: 0.8648 (tt) cc_final: 0.8095 (mp)
REVERT: D  131 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8024 (mt-10)
REVERT: D  270 TYR cc_start: 0.8318 (m-80) cc_final: 0.8049 (m-80)
REVERT: E  131 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7606 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.2947
  time to fit residues: 67.1248
Evaluate side-chains
  117 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 1.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 12 optimal weight:    4.9990
   chunk 56 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 124 optimal weight:    7.9990
   chunk 145 optimal weight:    4.9990
   chunk 130 optimal weight:    3.9990
   chunk 74 optimal weight:   20.0000
   chunk 31 optimal weight:    6.9990
   chunk 100 optimal weight:    0.5980
   chunk 91 optimal weight:    4.9990
   overall best weight:    3.1186

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN
E 264 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.109855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.087354 restraints weight = 42610.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.090175 restraints weight = 25919.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.092042 restraints weight = 18661.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.2938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  12825  Z= 0.186
  Angle     :  0.677   8.315  17480  Z= 0.351
  Chirality :  0.046   0.145   1940
  Planarity :  0.004   0.044   2230
  Dihedral  :  6.257  21.558   1680
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 14.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.49 %
    Favored  : 91.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.37 (0.19), residues: 1520
  helix: -1.87 (0.24), residues: 375
  sheet: -2.23 (0.22), residues: 430
  loop : -2.34 (0.21), residues: 715

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 220 
 HIS   0.012   0.002   HIS E 177 
 PHE   0.034   0.002   PHE C 274 
 TYR   0.022   0.002   TYR B 270 
 ARG   0.003   0.000   ARG D 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03739 (  335)
  hydrogen bonds       : angle       6.64827 ( 1125)
  covalent geometry    : bond        0.00408 (12825)
  covalent geometry    : angle       0.67652 (17480)

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

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

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 LEU cc_start: 0.8848 (tt) cc_final: 0.8071 (mp)
REVERT: A  131 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7820 (mt-10)
REVERT: B  199 ARG cc_start: 0.8151 (mtm180) cc_final: 0.7892 (mtm180)
REVERT: C  131 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7705 (mm-30)
REVERT: C  203 TYR cc_start: 0.8833 (t80) cc_final: 0.8620 (t80)
REVERT: D  131 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8002 (mt-10)
REVERT: D  270 TYR cc_start: 0.8307 (m-80) cc_final: 0.7960 (m-80)
REVERT: E  239 MET cc_start: 0.8950 (mmm) cc_final: 0.8740 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.2780
  time to fit residues: 60.8642
Evaluate side-chains
  119 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 1.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 55 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 109 optimal weight:    5.9990
   chunk 84 optimal weight:    0.0980
   chunk 53 optimal weight:    1.9990
   chunk 2 optimal weight:    9.9990
   chunk 4 optimal weight:    6.9990
   chunk 44 optimal weight:   20.0000
   chunk 25 optimal weight:    4.9990
   chunk 113 optimal weight:    2.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
A  21 ASN
** B  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 146 GLN
D 151 ASN
D 185 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.112336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.089569 restraints weight = 42451.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.092543 restraints weight = 25666.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.094523 restraints weight = 18332.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.3201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  12825  Z= 0.126
  Angle     :  0.623   8.104  17480  Z= 0.320
  Chirality :  0.045   0.139   1940
  Planarity :  0.004   0.037   2230
  Dihedral  :  5.940  20.018   1680
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.14 (0.20), residues: 1520
  helix: -1.54 (0.25), residues: 375
  sheet: -2.07 (0.22), residues: 430
  loop : -2.32 (0.22), residues: 715

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 220 
 HIS   0.011   0.001   HIS E 177 
 PHE   0.040   0.002   PHE D 274 
 TYR   0.020   0.002   TYR A 270 
 ARG   0.001   0.000   ARG E 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03242 (  335)
  hydrogen bonds       : angle       6.36109 ( 1125)
  covalent geometry    : bond        0.00284 (12825)
  covalent geometry    : angle       0.62282 (17480)

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

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

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 1.839 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 LEU cc_start: 0.8611 (tt) cc_final: 0.7927 (mp)
REVERT: A  131 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7760 (mt-10)
REVERT: A  199 ARG cc_start: 0.8023 (mtm180) cc_final: 0.7774 (mtm180)
REVERT: B  131 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7243 (mt-10)
REVERT: B  199 ARG cc_start: 0.8144 (mtm180) cc_final: 0.7898 (mtm180)
REVERT: C  131 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7669 (mm-30)
REVERT: C  199 ARG cc_start: 0.7951 (mtm180) cc_final: 0.7526 (mtm180)
REVERT: D  131 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7968 (mt-10)
REVERT: D  199 ARG cc_start: 0.7849 (mtm180) cc_final: 0.7036 (mtm180)
REVERT: E   22 LYS cc_start: 0.9395 (mtpp) cc_final: 0.9169 (tttt)
REVERT: E  128 LEU cc_start: 0.8560 (tt) cc_final: 0.7914 (mp)
REVERT: E  131 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7611 (mm-30)
REVERT: E  199 ARG cc_start: 0.7965 (mtm180) cc_final: 0.7654 (mtm180)
REVERT: E  239 MET cc_start: 0.9005 (mmm) cc_final: 0.8784 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.2475
  time to fit residues: 59.5887
Evaluate side-chains
  122 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 1.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   chunk 59 optimal weight:    7.9990
   chunk 95 optimal weight:    8.9990
   chunk 131 optimal weight:    0.9980
   chunk 17 optimal weight:    7.9990
   chunk 100 optimal weight:    0.6980
   chunk 37 optimal weight:    6.9990
   chunk 133 optimal weight:    1.9990
   chunk 45 optimal weight:    8.9990
   chunk 127 optimal weight:    7.9990
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.110799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.088019 restraints weight = 42689.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.090876 restraints weight = 25885.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.092805 restraints weight = 18639.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.3329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12825  Z= 0.170
  Angle     :  0.661   8.043  17480  Z= 0.342
  Chirality :  0.046   0.141   1940
  Planarity :  0.004   0.041   2230
  Dihedral  :  6.046  20.523   1680
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 14.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.63 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.86 (0.20), residues: 1520
  helix: -1.12 (0.27), residues: 365
  sheet: -1.92 (0.23), residues: 425
  loop : -2.23 (0.22), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 220 
 HIS   0.017   0.002   HIS A 177 
 PHE   0.039   0.002   PHE E 274 
 TYR   0.024   0.002   TYR B 270 
 ARG   0.004   0.000   ARG D 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03448 (  335)
  hydrogen bonds       : angle       6.40502 ( 1125)
  covalent geometry    : bond        0.00379 (12825)
  covalent geometry    : angle       0.66097 (17480)

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

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

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 1.451 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7944 (mt-10)
REVERT: B   77 GLU cc_start: 0.8138 (pt0) cc_final: 0.7393 (pp20)
REVERT: B  131 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7439 (pt0)
REVERT: C  131 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7764 (mm-30)
REVERT: D  131 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7868 (mt-10)
REVERT: E  131 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7657 (mm-30)
REVERT: E  239 MET cc_start: 0.9005 (mmm) cc_final: 0.8775 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.2398
  time to fit residues: 51.6304
Evaluate side-chains
  117 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 1.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:    8.9990
   chunk 27 optimal weight:   20.0000
   chunk 72 optimal weight:    2.9990
   chunk 61 optimal weight:    6.9990
   chunk 113 optimal weight:    0.5980
   chunk 32 optimal weight:    3.9990
   chunk 148 optimal weight:   20.0000
   chunk 13 optimal weight:   10.0000
   chunk 138 optimal weight:   10.0000
   chunk 56 optimal weight:    2.9990
   overall best weight:    3.5188

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

Flipped N/Q/H residues before XYZ refinement:
A 137 ASN
A 185 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.109364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.086804 restraints weight = 43110.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.089580 restraints weight = 26400.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.091370 restraints weight = 19133.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.3446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12825  Z= 0.202
  Angle     :  0.692   7.954  17480  Z= 0.357
  Chirality :  0.046   0.147   1940
  Planarity :  0.004   0.042   2230
  Dihedral  :  6.211  21.357   1680
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 15.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  1.31 %
    Favored  : 98.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.81 (0.20), residues: 1520
  helix: -1.05 (0.28), residues: 330
  sheet: -1.99 (0.23), residues: 430
  loop : -2.11 (0.22), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 220 
 HIS   0.014   0.002   HIS A 177 
 PHE   0.024   0.002   PHE A 247 
 TYR   0.024   0.002   TYR B 270 
 ARG   0.004   0.000   ARG B 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03624 (  335)
  hydrogen bonds       : angle       6.54354 ( 1125)
  covalent geometry    : bond        0.00445 (12825)
  covalent geometry    : angle       0.69180 (17480)

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

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

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 143
  time to evaluate  : 1.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8060 (mt-10)
REVERT: A  199 ARG cc_start: 0.8029 (mtm180) cc_final: 0.7230 (mtm180)
REVERT: B  131 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7383 (mt-10)
REVERT: C  131 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7706 (mm-30)
REVERT: D  131 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7993 (mt-10)
REVERT: D  199 ARG cc_start: 0.7882 (mtm180) cc_final: 0.7153 (mtm180)
REVERT: D  270 TYR cc_start: 0.8810 (m-80) cc_final: 0.8593 (m-80)
REVERT: E  131 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7776 (mm-30)
REVERT: E  199 ARG cc_start: 0.7953 (mtm180) cc_final: 0.7745 (mtm180)
REVERT: E  239 MET cc_start: 0.9011 (mmm) cc_final: 0.8775 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 144
  average time/residue: 0.2284
  time to fit residues: 48.7795
Evaluate side-chains
  112 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 1.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 13 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 17 optimal weight:    7.9990
   chunk 68 optimal weight:    9.9990
   chunk 97 optimal weight:    0.9990
   chunk 44 optimal weight:    7.9990
   chunk 61 optimal weight:    6.9990
   chunk 112 optimal weight:    8.9990
   chunk 4 optimal weight:    8.9990
   chunk 115 optimal weight:    0.1980
   chunk 85 optimal weight:    4.9990
   overall best weight:    4.2388

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

Flipped N/Q/H residues before XYZ refinement:
** E 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 177 HIS ** 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 = 0.3975 r_free = 0.3975 target = 0.107827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.085564 restraints weight = 42920.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.088225 restraints weight = 26293.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.090052 restraints weight = 19147.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.3534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  12825  Z= 0.235
  Angle     :  0.737   8.094  17480  Z= 0.381
  Chirality :  0.047   0.150   1940
  Planarity :  0.004   0.044   2230
  Dihedral  :  6.394  22.200   1680
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 17.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.47 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.73 (0.21), residues: 1520
  helix: -0.99 (0.28), residues: 325
  sheet: -2.03 (0.23), residues: 425
  loop : -1.99 (0.22), residues: 770

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 220 
 HIS   0.016   0.003   HIS A 177 
 PHE   0.048   0.002   PHE C 274 
 TYR   0.022   0.002   TYR D 102 
 ARG   0.004   0.001   ARG B 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03913 (  335)
  hydrogen bonds       : angle       6.68041 ( 1125)
  covalent geometry    : bond        0.00512 (12825)
  covalent geometry    : angle       0.73655 (17480)

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

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

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 1.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8097 (mt-10)
REVERT: B  131 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7344 (mt-10)
REVERT: C  131 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8040 (mm-30)
REVERT: C  265 MET cc_start: 0.4234 (mmt) cc_final: 0.3920 (mmt)
REVERT: D  131 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8089 (mt-10)
REVERT: D  158 ASP cc_start: 0.6312 (m-30) cc_final: 0.6067 (m-30)
REVERT: E   49 LYS cc_start: 0.8104 (pptt) cc_final: 0.7740 (tptt)
REVERT: E  131 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7864 (mm-30)
REVERT: E  239 MET cc_start: 0.9040 (mmm) cc_final: 0.8749 (mmm)
REVERT: E  270 TYR cc_start: 0.8577 (m-80) cc_final: 0.8300 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.2392
  time to fit residues: 48.0997
Evaluate side-chains
  113 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 1.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 140 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 104 optimal weight:    9.9990
   chunk 125 optimal weight:    1.9990
   chunk 81 optimal weight:   20.0000
   chunk 65 optimal weight:    7.9990
   chunk 124 optimal weight:    0.0270
   chunk 83 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 89 optimal weight:    9.9990
   overall best weight:    2.8046

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

Flipped N/Q/H residues before XYZ refinement:
** E 177 HIS ** 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 = 0.4006 r_free = 0.4006 target = 0.109805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.087325 restraints weight = 42597.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.090065 restraints weight = 25848.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.091935 restraints weight = 18743.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.3637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12825  Z= 0.179
  Angle     :  0.706   8.616  17480  Z= 0.362
  Chirality :  0.047   0.145   1940
  Planarity :  0.004   0.041   2230
  Dihedral  :  6.258  21.271   1680
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 16.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.22 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.64 (0.21), residues: 1520
  helix: -0.78 (0.29), residues: 325
  sheet: -2.06 (0.22), residues: 430
  loop : -1.93 (0.22), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 220 
 HIS   0.016   0.002   HIS E 177 
 PHE   0.047   0.002   PHE B 274 
 TYR   0.025   0.002   TYR B 270 
 ARG   0.003   0.000   ARG A 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03678 (  335)
  hydrogen bonds       : angle       6.58045 ( 1125)
  covalent geometry    : bond        0.00398 (12825)
  covalent geometry    : angle       0.70644 (17480)

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

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

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 1.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8050 (mt-10)
REVERT: B  131 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7423 (mt-10)
REVERT: C  131 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8013 (mm-30)
REVERT: C  265 MET cc_start: 0.4073 (mmt) cc_final: 0.3793 (mmt)
REVERT: D  131 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8065 (mt-10)
REVERT: E  128 LEU cc_start: 0.8653 (tt) cc_final: 0.8056 (mp)
REVERT: E  131 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7697 (mm-30)
REVERT: E  239 MET cc_start: 0.8999 (mmm) cc_final: 0.8684 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.2432
  time to fit residues: 50.7814
Evaluate side-chains
  116 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 1.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 70 optimal weight:    0.9990
   chunk 135 optimal weight:    0.6980
   chunk 105 optimal weight:    9.9990
   chunk 124 optimal weight:    0.0030
   chunk 147 optimal weight:    8.9990
   chunk 7 optimal weight:    4.9990
   chunk 35 optimal weight:    0.6980
   chunk 13 optimal weight:    7.9990
   chunk 103 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9990
   overall best weight:    0.6794

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

Flipped N/Q/H residues before XYZ refinement:
** E 177 HIS ** 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 = 0.4076 r_free = 0.4076 target = 0.114175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.091459 restraints weight = 41941.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.094516 restraints weight = 24999.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.096511 restraints weight = 17767.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.3870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12825  Z= 0.119
  Angle     :  0.657   8.325  17480  Z= 0.331
  Chirality :  0.046   0.167   1940
  Planarity :  0.004   0.036   2230
  Dihedral  :  5.823  21.412   1680
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.74 (0.20), residues: 1520
  helix: -0.65 (0.29), residues: 315
  sheet: -2.09 (0.21), residues: 455
  loop : -2.10 (0.22), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 161 
 HIS   0.011   0.001   HIS E 177 
 PHE   0.019   0.001   PHE A 247 
 TYR   0.027   0.002   TYR D 270 
 ARG   0.001   0.000   ARG B 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03090 (  335)
  hydrogen bonds       : angle       6.21350 ( 1125)
  covalent geometry    : bond        0.00274 (12825)
  covalent geometry    : angle       0.65678 (17480)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3912.96 seconds
wall clock time: 70 minutes 6.58 seconds (4206.58 seconds total)