Starting phenix.real_space_refine
on Thu Sep 18 05:14:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zj1_60135/09_2025/8zj1_60135.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zj1_60135/09_2025/8zj1_60135.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zj1_60135/09_2025/8zj1_60135.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zj1_60135/09_2025/8zj1_60135.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zj1_60135/09_2025/8zj1_60135.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zj1_60135/09_2025/8zj1_60135.map"
  }
  resolution = 4.25
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      10      5.49       5
     S     100      5.16       5
     C    9230      2.51       5
     N    2470      2.21       5
     O    2815      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14625
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "C"
      Number of atoms: 2898
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2898
          Classifications: {'peptide': 371}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 351}
    Chain: "D"
      Number of atoms: 2898
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2898
          Classifications: {'peptide': 371}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 351}
    Chain: "E"
      Number of atoms: 2898
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2898
          Classifications: {'peptide': 371}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 351}
    Chain: "F"
      Number of atoms: 2898
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2898
          Classifications: {'peptide': 371}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 351}
    Chain: "A"
      Number of atoms: 2898
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2898
          Classifications: {'peptide': 371}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 351}
    Chain: "C"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
    Chain: "E"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
    Chain: "F"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.93, per 1000 atoms: 0.27
  Number of scatterers: 14625
  At special positions: 0
  Unit cell: (98.77, 77.19, 193.39, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S     100     16.00
     P      10     15.00
     O    2815      8.00
     N    2470      7.00
     C    9230      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.27
  Conformation dependent library (CDL) restraints added in 725.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3690 Ramachandran restraints generated.
    1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3430

  Finding SS restraints...
    Secondary structure from input PDB file:
      102 helices and 30 sheets defined
      49.8% alpha, 15.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'C' and resid 56 through 60
    Processing helix  chain 'C' and resid 79 through 92
    Processing helix  chain 'C' and resid 112 through 126
      removed outlier: 4.199A  pdb=" N   ARG C 116 " --> pdb=" O   PRO C 112 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 137 through 146
    Processing helix  chain 'C' and resid 172 through 175
    Processing helix  chain 'C' and resid 181 through 194
      removed outlier: 3.725A  pdb=" N   THR C 194 " --> pdb=" O   MET C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 195 through 197
      No H-bonds generated for 'chain 'C' and resid 195 through 197'
    Processing helix  chain 'C' and resid 202 through 217
      removed outlier: 3.951A  pdb=" N   GLU C 207 " --> pdb=" O   THR C 203 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ILE C 208 " --> pdb=" O   ALA C 204 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 233
    Processing helix  chain 'C' and resid 252 through 257
      removed outlier: 3.548A  pdb=" N   CYS C 257 " --> pdb=" O   GLU C 253 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 258 through 262
    Processing helix  chain 'C' and resid 263 through 268
    Processing helix  chain 'C' and resid 273 through 284
    Processing helix  chain 'C' and resid 289 through 296
    Processing helix  chain 'C' and resid 301 through 305
    Processing helix  chain 'C' and resid 308 through 321
    Processing helix  chain 'C' and resid 334 through 336
      No H-bonds generated for 'chain 'C' and resid 334 through 336'
    Processing helix  chain 'C' and resid 337 through 348
    Processing helix  chain 'C' and resid 349 through 353
    Processing helix  chain 'C' and resid 359 through 366
    Processing helix  chain 'C' and resid 367 through 371
    Processing helix  chain 'D' and resid 56 through 61
      removed outlier: 3.681A  pdb=" N   SER D  60 " --> pdb=" O   ASP D  56 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LYS D  61 " --> pdb=" O   GLU D  57 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 56 through 61'
    Processing helix  chain 'D' and resid 78 through 92
    Processing helix  chain 'D' and resid 97 through 101
      removed outlier: 3.845A  pdb=" N   HIS D 101 " --> pdb=" O   PRO D  98 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 112 through 126
      removed outlier: 4.116A  pdb=" N   ARG D 116 " --> pdb=" O   PRO D 112 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 137 through 145
    Processing helix  chain 'D' and resid 172 through 175
    Processing helix  chain 'D' and resid 181 through 194
      removed outlier: 3.866A  pdb=" N   THR D 194 " --> pdb=" O   MET D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 202 through 217
      removed outlier: 3.963A  pdb=" N   GLU D 207 " --> pdb=" O   THR D 203 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ILE D 208 " --> pdb=" O   ALA D 204 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 222 through 233
    Processing helix  chain 'D' and resid 252 through 257
      removed outlier: 3.758A  pdb=" N   CYS D 257 " --> pdb=" O   GLU D 253 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 258 through 262
    Processing helix  chain 'D' and resid 263 through 268
      removed outlier: 3.511A  pdb=" N   ILE D 267 " --> pdb=" O   PRO D 264 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 273 through 285
    Processing helix  chain 'D' and resid 290 through 296
    Processing helix  chain 'D' and resid 301 through 305
    Processing helix  chain 'D' and resid 308 through 321
    Processing helix  chain 'D' and resid 337 through 349
    Processing helix  chain 'D' and resid 350 through 355
      removed outlier: 3.719A  pdb=" N   GLN D 354 " --> pdb=" O   THR D 351 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 359 through 366
    Processing helix  chain 'D' and resid 367 through 371
    Processing helix  chain 'E' and resid 55 through 61
      removed outlier: 3.813A  pdb=" N   GLN E  59 " --> pdb=" O   GLY E  55 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   SER E  60 " --> pdb=" O   ASP E  56 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 78 through 92
    Processing helix  chain 'E' and resid 97 through 101
      removed outlier: 3.775A  pdb=" N   HIS E 101 " --> pdb=" O   PRO E  98 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 112 through 126
      removed outlier: 4.100A  pdb=" N   ARG E 116 " --> pdb=" O   PRO E 112 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 137 through 146
    Processing helix  chain 'E' and resid 172 through 175
    Processing helix  chain 'E' and resid 181 through 193
    Processing helix  chain 'E' and resid 194 through 197
    Processing helix  chain 'E' and resid 204 through 217
      removed outlier: 4.008A  pdb=" N   ILE E 208 " --> pdb=" O   ALA E 204 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 222 through 233
    Processing helix  chain 'E' and resid 252 through 257
      removed outlier: 3.830A  pdb=" N   CYS E 257 " --> pdb=" O   GLU E 253 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 258 through 262
    Processing helix  chain 'E' and resid 263 through 268
    Processing helix  chain 'E' and resid 273 through 285
      removed outlier: 3.541A  pdb=" N   TYR E 279 " --> pdb=" O   HIS E 275 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 289 through 296
    Processing helix  chain 'E' and resid 301 through 305
    Processing helix  chain 'E' and resid 308 through 321
    Processing helix  chain 'E' and resid 337 through 349
    Processing helix  chain 'E' and resid 350 through 355
      removed outlier: 3.836A  pdb=" N   GLN E 354 " --> pdb=" O   THR E 351 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 359 through 366
    Processing helix  chain 'E' and resid 367 through 371
    Processing helix  chain 'F' and resid 56 through 61
      removed outlier: 3.597A  pdb=" N   SER F  60 " --> pdb=" O   ASP F  56 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 78 through 93
      removed outlier: 3.757A  pdb=" N   GLU F  93 " --> pdb=" O   THR F  89 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 97 through 101
      removed outlier: 3.814A  pdb=" N   HIS F 101 " --> pdb=" O   PRO F  98 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 112 through 126
      removed outlier: 4.256A  pdb=" N   ARG F 116 " --> pdb=" O   PRO F 112 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 137 through 145
    Processing helix  chain 'F' and resid 172 through 175
    Processing helix  chain 'F' and resid 181 through 194
    Processing helix  chain 'F' and resid 202 through 217
      removed outlier: 3.884A  pdb=" N   GLU F 207 " --> pdb=" O   THR F 203 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ILE F 208 " --> pdb=" O   ALA F 204 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 222 through 233
    Processing helix  chain 'F' and resid 252 through 257
    Processing helix  chain 'F' and resid 258 through 262
    Processing helix  chain 'F' and resid 273 through 285
      removed outlier: 3.537A  pdb=" N   TYR F 279 " --> pdb=" O   HIS F 275 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 289 through 296
    Processing helix  chain 'F' and resid 301 through 306
      removed outlier: 4.274A  pdb=" N   TYR F 306 " --> pdb=" O   THR F 303 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 308 through 321
    Processing helix  chain 'F' and resid 337 through 349
    Processing helix  chain 'F' and resid 350 through 355
      removed outlier: 3.866A  pdb=" N   GLN F 354 " --> pdb=" O   THR F 351 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 359 through 366
    Processing helix  chain 'F' and resid 367 through 372
      removed outlier: 3.536A  pdb=" N   ARG F 372 " --> pdb=" O   ILE F 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 61
      removed outlier: 3.813A  pdb=" N   GLN A  59 " --> pdb=" O   GLY A  55 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   SER A  60 " --> pdb=" O   ASP A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 92
    Processing helix  chain 'A' and resid 97 through 101
      removed outlier: 3.774A  pdb=" N   HIS A 101 " --> pdb=" O   PRO A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 126
      removed outlier: 4.100A  pdb=" N   ARG A 116 " --> pdb=" O   PRO A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 146
    Processing helix  chain 'A' and resid 172 through 175
    Processing helix  chain 'A' and resid 181 through 193
    Processing helix  chain 'A' and resid 194 through 197
    Processing helix  chain 'A' and resid 204 through 217
      removed outlier: 4.008A  pdb=" N   ILE A 208 " --> pdb=" O   ALA A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 233
    Processing helix  chain 'A' and resid 252 through 257
      removed outlier: 3.830A  pdb=" N   CYS A 257 " --> pdb=" O   GLU A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 262
    Processing helix  chain 'A' and resid 263 through 268
    Processing helix  chain 'A' and resid 273 through 285
      removed outlier: 3.541A  pdb=" N   TYR A 279 " --> pdb=" O   HIS A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 296
    Processing helix  chain 'A' and resid 301 through 305
    Processing helix  chain 'A' and resid 308 through 321
    Processing helix  chain 'A' and resid 337 through 349
    Processing helix  chain 'A' and resid 350 through 355
      removed outlier: 3.836A  pdb=" N   GLN A 354 " --> pdb=" O   THR A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 366
    Processing helix  chain 'A' and resid 367 through 371
    Processing sheet with id=AA1, first strand: chain 'C' and resid 8 through 10
      removed outlier: 6.484A  pdb=" N   LEU C   8 " --> pdb=" O   LEU C 104 " (cutoff:3.500A)
      removed outlier: 8.318A  pdb=" N   THR C 106 " --> pdb=" O   LEU C   8 " (cutoff:3.500A)
      removed outlier: 8.397A  pdb=" N   CYS C  10 " --> pdb=" O   THR C 106 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   THR C 103 " --> pdb=" O   TYR C 133 " (cutoff:3.500A)
      removed outlier: 7.866A  pdb=" N   ALA C 135 " --> pdb=" O   THR C 103 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   LEU C 105 " --> pdb=" O   ALA C 135 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 17 through 19
    Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54
    Processing sheet with id=AA4, first strand: chain 'C' and resid 169 through 170
    Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 170
      removed outlier: 3.567A  pdb=" N   HIS C 161 " --> pdb=" O   ASP C 154 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 238 through 242
      removed outlier: 3.728A  pdb=" N   LEU C 242 " --> pdb=" O   GLN C 246 " (cutoff:3.500A)
      removed outlier: 5.367A  pdb=" N   GLN C 246 " --> pdb=" O   LEU C 242 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 8 through 10
      removed outlier: 6.557A  pdb=" N   LEU D   8 " --> pdb=" O   LEU D 104 " (cutoff:3.500A)
      removed outlier: 8.420A  pdb=" N   THR D 106 " --> pdb=" O   LEU D   8 " (cutoff:3.500A)
      removed outlier: 8.386A  pdb=" N   CYS D  10 " --> pdb=" O   THR D 106 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 17 through 19
    Processing sheet with id=AA9, first strand: chain 'D' and resid 53 through 54
    Processing sheet with id=AB1, first strand: chain 'D' and resid 169 through 170
    Processing sheet with id=AB2, first strand: chain 'D' and resid 169 through 170
      removed outlier: 3.542A  pdb=" N   HIS D 161 " --> pdb=" O   ASP D 154 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 238 through 240
    Processing sheet with id=AB4, first strand: chain 'E' and resid 8 through 10
      removed outlier: 6.652A  pdb=" N   LEU E   8 " --> pdb=" O   LEU E 104 " (cutoff:3.500A)
      removed outlier: 8.422A  pdb=" N   THR E 106 " --> pdb=" O   LEU E   8 " (cutoff:3.500A)
      removed outlier: 8.321A  pdb=" N   CYS E  10 " --> pdb=" O   THR E 106 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 17 through 19
    Processing sheet with id=AB6, first strand: chain 'E' and resid 53 through 54
    Processing sheet with id=AB7, first strand: chain 'E' and resid 169 through 170
    Processing sheet with id=AB8, first strand: chain 'E' and resid 169 through 170
    Processing sheet with id=AB9, first strand: chain 'E' and resid 238 through 242
      removed outlier: 4.573A  pdb=" N   LEU E 242 " --> pdb=" O   GLN E 246 " (cutoff:3.500A)
      removed outlier: 5.744A  pdb=" N   GLN E 246 " --> pdb=" O   LEU E 242 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 8 through 10
      removed outlier: 6.445A  pdb=" N   LEU F   8 " --> pdb=" O   LEU F 104 " (cutoff:3.500A)
      removed outlier: 8.166A  pdb=" N   THR F 106 " --> pdb=" O   LEU F   8 " (cutoff:3.500A)
      removed outlier: 8.334A  pdb=" N   CYS F  10 " --> pdb=" O   THR F 106 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'F' and resid 17 through 19
    Processing sheet with id=AC3, first strand: chain 'F' and resid 53 through 54
    Processing sheet with id=AC4, first strand: chain 'F' and resid 169 through 170
    Processing sheet with id=AC5, first strand: chain 'F' and resid 169 through 170
      removed outlier: 6.521A  pdb=" N   ASN F 297 " --> pdb=" O   ILE F 330 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'F' and resid 238 through 242
      removed outlier: 4.408A  pdb=" N   LEU F 242 " --> pdb=" O   GLN F 246 " (cutoff:3.500A)
      removed outlier: 5.693A  pdb=" N   GLN F 246 " --> pdb=" O   LEU F 242 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'A' and resid 8 through 10
      removed outlier: 6.652A  pdb=" N   LEU A   8 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 8.422A  pdb=" N   THR A 106 " --> pdb=" O   LEU A   8 " (cutoff:3.500A)
      removed outlier: 8.320A  pdb=" N   CYS A  10 " --> pdb=" O   THR A 106 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'A' and resid 17 through 19
    Processing sheet with id=AC9, first strand: chain 'A' and resid 53 through 54
    Processing sheet with id=AD1, first strand: chain 'A' and resid 169 through 170
    Processing sheet with id=AD2, first strand: chain 'A' and resid 169 through 170
    Processing sheet with id=AD3, first strand: chain 'A' and resid 238 through 242
      removed outlier: 4.572A  pdb=" N   LEU A 242 " --> pdb=" O   GLN A 246 " (cutoff:3.500A)
      removed outlier: 5.744A  pdb=" N   GLN A 246 " --> pdb=" O   LEU A 242 " (cutoff:3.500A)

    708 hydrogen bonds defined for protein.
    1752 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: 2.89

  Time building geometry restraints manager: 1.71 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.33: 4722
        1.33 -     1.45: 2115
        1.45 -     1.57: 7923
        1.57 -     1.69: 15
        1.69 -     1.80: 175
  Bond restraints: 14950
  Sorted by residual:
  bond pdb=" N   ILE D 287 "
       pdb=" CA  ILE D 287 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.90e+00
  bond pdb=" N   ILE D 289 "
       pdb=" CA  ILE D 289 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.78e+00
  bond pdb=" N   ASP D 286 "
       pdb=" CA  ASP D 286 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.033 1.27e-02 6.20e+03 6.73e+00
  bond pdb=" N   ASP D 288 "
       pdb=" CA  ASP D 288 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.42e-02 4.96e+03 5.78e+00
  bond pdb=" CB  ARG D 335 "
       pdb=" CG  ARG D 335 "
    ideal  model  delta    sigma   weight residual
    1.520  1.452  0.068 3.00e-02 1.11e+03 5.07e+00
  ... (remaining 14945 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 19319
        1.69 -     3.37: 819
        3.37 -     5.06: 117
        5.06 -     6.74: 34
        6.74 -     8.43: 1
  Bond angle restraints: 20290
  Sorted by residual:
  angle pdb=" C   ASN D  12 "
        pdb=" N   GLY D  13 "
        pdb=" CA  GLY D  13 "
      ideal   model   delta    sigma   weight residual
     121.44  115.69    5.75 1.45e+00 4.76e-01 1.57e+01
  angle pdb=" N   ASP D 288 "
        pdb=" CA  ASP D 288 "
        pdb=" C   ASP D 288 "
      ideal   model   delta    sigma   weight residual
     114.12  109.72    4.40 1.39e+00 5.18e-01 1.00e+01
  angle pdb=" CA  ASP D 286 "
        pdb=" C   ASP D 286 "
        pdb=" O   ASP D 286 "
      ideal   model   delta    sigma   weight residual
     121.56  118.32    3.24 1.09e+00 8.42e-01 8.82e+00
  angle pdb=" N   CYS D 374 "
        pdb=" CA  CYS D 374 "
        pdb=" C   CYS D 374 "
      ideal   model   delta    sigma   weight residual
     110.80  105.38    5.42 2.13e+00 2.20e-01 6.49e+00
  angle pdb=" CA  LEU F 171 "
        pdb=" CB  LEU F 171 "
        pdb=" CG  LEU F 171 "
      ideal   model   delta    sigma   weight residual
     116.30  124.73   -8.43 3.50e+00 8.16e-02 5.80e+00
  ... (remaining 20285 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 8225
       17.87 -    35.75: 600
       35.75 -    53.62: 144
       53.62 -    71.49: 12
       71.49 -    89.37: 14
  Dihedral angle restraints: 8995
    sinusoidal: 3635
      harmonic: 5360
  Sorted by residual:
  dihedral pdb=" C5' ADP C 401 "
           pdb=" O5' ADP C 401 "
           pdb=" PA  ADP C 401 "
           pdb=" O2A ADP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   17.94  -77.93     1      2.00e+01 2.50e-03 1.90e+01
  dihedral pdb=" C5' ADP A 401 "
           pdb=" O5' ADP A 401 "
           pdb=" PA  ADP A 401 "
           pdb=" O2A ADP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   14.31  -74.31     1      2.00e+01 2.50e-03 1.75e+01
  dihedral pdb=" C5' ADP E 401 "
           pdb=" O5' ADP E 401 "
           pdb=" PA  ADP E 401 "
           pdb=" O2A ADP E 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   14.25  -74.25     1      2.00e+01 2.50e-03 1.75e+01
  ... (remaining 8992 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1185
       0.043 -    0.086: 758
       0.086 -    0.129: 286
       0.129 -    0.172: 25
       0.172 -    0.215: 1
  Chirality restraints: 2255
  Sorted by residual:
  chirality pdb=" CB  ILE F  71 "
            pdb=" CA  ILE F  71 "
            pdb=" CG1 ILE F  71 "
            pdb=" CG2 ILE F  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CB  ILE F 151 "
            pdb=" CA  ILE F 151 "
            pdb=" CG1 ILE F 151 "
            pdb=" CG2 ILE F 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.70e-01
  chirality pdb=" CA  ILE D 289 "
            pdb=" N   ILE D 289 "
            pdb=" C   ILE D 289 "
            pdb=" CB  ILE D 289 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.42e-01
  ... (remaining 2252 not shown)

  Planarity restraints: 2595
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 332 "   -0.037 5.00e-02 4.00e+02   5.59e-02 5.01e+00
        pdb=" N   PRO C 333 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO C 333 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO C 333 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO D 332 "    0.036 5.00e-02 4.00e+02   5.41e-02 4.69e+00
        pdb=" N   PRO D 333 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO D 333 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO D 333 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO E 332 "    0.032 5.00e-02 4.00e+02   4.84e-02 3.75e+00
        pdb=" N   PRO E 333 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO E 333 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO E 333 "    0.027 5.00e-02 4.00e+02
  ... (remaining 2592 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 2050
        2.74 -     3.28: 13760
        3.28 -     3.82: 23648
        3.82 -     4.36: 29908
        4.36 -     4.90: 52425
  Nonbonded interactions: 121791
  Sorted by model distance:
  nonbonded pdb=" CB  SER D 155 "
            pdb=" CG2 THR D 303 "
     model   vdw
     2.196 3.860
  nonbonded pdb=" O   ASP D 288 "
            pdb=" OD1 ASP D 288 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" CB  SER C 155 "
            pdb=" CG2 THR C 303 "
     model   vdw
     2.243 3.860
  nonbonded pdb=" NZ  LYS C 213 "
            pdb=" O2' ADP C 401 "
     model   vdw
     2.265 3.120
  nonbonded pdb=" NZ  LYS F 213 "
            pdb=" O2' ADP F 401 "
     model   vdw
     2.268 3.120
  ... (remaining 121786 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             0.740
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.820
  Find NCS groups from input model:        0.290
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
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      :  0.012   0.087  14950  Z= 0.497
  Angle     :  0.815   8.430  20290  Z= 0.438
  Chirality :  0.057   0.215   2255
  Planarity :  0.005   0.056   2595
  Dihedral  : 13.665  89.369   5565
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.24 (0.18), residues: 1845
  helix: -1.36 (0.17), residues: 695
  sheet: -1.50 (0.25), residues: 345
  loop : -1.42 (0.21), residues: 805

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 256 
 TYR   0.013   0.002   TYR D 143 
 PHE   0.021   0.002   PHE C 375 
 TRP   0.020   0.004   TRP D 340 
 HIS   0.008   0.002   HIS D 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.01187 (14950)
  covalent geometry    : angle       0.81508 (20290)
  hydrogen bonds       : bond        0.17540 (  698)
  hydrogen bonds       : angle       6.18499 ( 1752)

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

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

  3690 Ramachandran restraints generated.
    1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3690 Ramachandran restraints generated.
    1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  436 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 436
  time to evaluate  : 0.600 
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: C   11 ASP cc_start: 0.7216 (t0) cc_final: 0.6651 (p0)
REVERT: C   81 ASP cc_start: 0.7778 (p0) cc_final: 0.7502 (p0)
REVERT: C  190 MET cc_start: 0.8177 (mtp) cc_final: 0.7846 (mtm)
REVERT: C  303 THR cc_start: 0.8495 (t) cc_final: 0.7970 (t)
REVERT: D  236 LEU cc_start: 0.8386 (mt) cc_final: 0.7965 (mm)
REVERT: E   82 MET cc_start: 0.7386 (tpp) cc_final: 0.7101 (tpp)
REVERT: E  157 ASP cc_start: 0.7415 (t0) cc_final: 0.6873 (t70)
REVERT: E  305 MET cc_start: 0.8342 (mmm) cc_final: 0.8122 (mmt)
REVERT: F   34 ILE cc_start: 0.9257 (mt) cc_final: 0.9047 (tp)
REVERT: F   67 LEU cc_start: 0.8874 (mt) cc_final: 0.8650 (mt)
REVERT: F  330 ILE cc_start: 0.8999 (mp) cc_final: 0.8798 (mm)
REVERT: F  346 LEU cc_start: 0.9306 (tp) cc_final: 0.9086 (tt)
REVERT: A  190 MET cc_start: 0.7694 (mtp) cc_final: 0.7339 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 436
  average time/residue: 0.1240
  time to fit residues: 81.2506
Evaluate side-chains
  231 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 231
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    5.9990
   chunk 149 optimal weight:    7.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
C  59 GLN
C 121 GLN
C 275 HIS
C 280 ASN
C 297 ASN
** D  12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  87 HIS
** D  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 173 HIS
D 353 GLN
E  40 HIS
E  92 ASN
E 353 GLN
F  49 GLN
F 101 HIS
F 353 GLN
A  73 HIS
** A  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 161 HIS
A 162 ASN
A 173 HIS
A 275 HIS
A 297 ASN
A 353 GLN
A 371 HIS

Total number of N/Q/H flips: 22

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.058354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2614 r_free = 0.2614 target = 0.045079 restraints weight = 61649.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.046754 restraints weight = 34047.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.047934 restraints weight = 22422.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.048723 restraints weight = 16286.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2738 r_free = 0.2738 target = 0.049295 restraints weight = 12926.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8639
moved from start:          0.3790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  14950  Z= 0.231
  Angle     :  0.699   8.313  20290  Z= 0.354
  Chirality :  0.047   0.165   2255
  Planarity :  0.005   0.037   2595
  Dihedral  :  6.121  51.238   2080
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.18 %
    Favored  : 96.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.67 (0.20), residues: 1845
  helix: -0.09 (0.19), residues: 755
  sheet: -0.89 (0.28), residues: 340
  loop : -0.37 (0.23), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 290 
 TYR   0.018   0.002   TYR A 143 
 PHE   0.032   0.002   PHE D 262 
 TRP   0.033   0.003   TRP A  79 
 HIS   0.016   0.002   HIS D  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 (14950)
  covalent geometry    : angle       0.69852 (20290)
  hydrogen bonds       : bond        0.03858 (  698)
  hydrogen bonds       : angle       4.82610 ( 1752)

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

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

  3690 Ramachandran restraints generated.
    1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3690 Ramachandran restraints generated.
    1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 271
  time to evaluate  : 0.616 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   10 CYS cc_start: 0.8296 (p) cc_final: 0.7923 (p)
REVERT: C   47 MET cc_start: 0.3284 (ttm) cc_final: 0.2657 (ttm)
REVERT: C   81 ASP cc_start: 0.9080 (p0) cc_final: 0.8825 (p0)
REVERT: C  154 ASP cc_start: 0.8133 (t0) cc_final: 0.7918 (t0)
REVERT: C  205 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8639 (pm20)
REVERT: C  246 GLN cc_start: 0.8803 (tp-100) cc_final: 0.8332 (tp-100)
REVERT: D   56 ASP cc_start: 0.9019 (t0) cc_final: 0.8793 (p0)
REVERT: D   82 MET cc_start: 0.9239 (tpt) cc_final: 0.8890 (tpt)
REVERT: D  107 GLU cc_start: 0.8981 (pt0) cc_final: 0.8541 (pt0)
REVERT: D  179 ASP cc_start: 0.8644 (p0) cc_final: 0.8334 (t0)
REVERT: D  184 ASP cc_start: 0.9047 (m-30) cc_final: 0.8807 (m-30)
REVERT: D  205 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8541 (mt-10)
REVERT: D  217 CYS cc_start: 0.9017 (m) cc_final: 0.8581 (m)
REVERT: D  226 GLU cc_start: 0.9193 (tp30) cc_final: 0.8919 (tp30)
REVERT: D  257 CYS cc_start: 0.9262 (t) cc_final: 0.9032 (t)
REVERT: D  283 MET cc_start: 0.8818 (mmm) cc_final: 0.8571 (mmm)
REVERT: D  305 MET cc_start: 0.9013 (tpp) cc_final: 0.8551 (mmt)
REVERT: D  355 MET cc_start: 0.8627 (mtp) cc_final: 0.8416 (mtp)
REVERT: D  372 ARG cc_start: 0.9145 (mmm-85) cc_final: 0.8938 (mmm-85)
REVERT: E  121 GLN cc_start: 0.9444 (tt0) cc_final: 0.9066 (tp40)
REVERT: E  124 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.7920 (m-10)
REVERT: E  128 ASN cc_start: 0.9164 (t0) cc_final: 0.8919 (t0)
REVERT: E  179 ASP cc_start: 0.7907 (p0) cc_final: 0.7524 (t0)
REVERT: E  180 LEU cc_start: 0.9100 (tp) cc_final: 0.8884 (tp)
REVERT: E  205 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8424 (mt-10)
REVERT: E  217 CYS cc_start: 0.8790 (m) cc_final: 0.8393 (m)
REVERT: E  285 CYS cc_start: 0.8637 (m) cc_final: 0.8434 (m)
REVERT: E  286 ASP cc_start: 0.8674 (t0) cc_final: 0.8407 (t70)
REVERT: E  362 TYR cc_start: 0.8915 (t80) cc_final: 0.7709 (t80)
REVERT: F   82 MET cc_start: 0.9355 (tpt) cc_final: 0.9082 (tpt)
REVERT: F  205 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8420 (mt-10)
REVERT: F  225 ASN cc_start: 0.9259 (m110) cc_final: 0.9035 (m110)
REVERT: F  285 CYS cc_start: 0.8944 (m) cc_final: 0.8674 (m)
REVERT: F  286 ASP cc_start: 0.8705 (t0) cc_final: 0.8453 (t70)
REVERT: A   11 ASP cc_start: 0.8988 (t0) cc_final: 0.6683 (p0)
REVERT: A   44 MET cc_start: 0.4838 (pmm) cc_final: 0.4592 (pmm)
REVERT: A  103 THR cc_start: 0.9293 (m) cc_final: 0.8996 (m)
REVERT: A  119 MET cc_start: 0.8881 (ptm) cc_final: 0.8432 (ptp)
REVERT: A  179 ASP cc_start: 0.7817 (p0) cc_final: 0.7337 (t70)
REVERT: A  227 MET cc_start: 0.8868 (mmm) cc_final: 0.8618 (mmm)
REVERT: A  246 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8173 (tm-30)
  outliers start: 2
  outliers final: 0
  residues processed: 272
  average time/residue: 0.1157
  time to fit residues: 48.6011
Evaluate side-chains
  182 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 181
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 70 optimal weight:   10.0000
   chunk 121 optimal weight:    0.6980
   chunk 104 optimal weight:    7.9990
   chunk 164 optimal weight:    9.9990
   chunk 73 optimal weight:   20.0000
   chunk 61 optimal weight:    0.0870
   chunk 40 optimal weight:    8.9990
   chunk 36 optimal weight:   20.0000
   chunk 165 optimal weight:    9.9990
   chunk 168 optimal weight:    5.9990
   overall best weight:    4.5564

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

Flipped N/Q/H residues before XYZ refinement:
** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 353 GLN
D  40 HIS
D  88 HIS
D  92 ASN
F 275 HIS
F 371 HIS
** A  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 161 HIS
A 275 HIS
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.057793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2597 r_free = 0.2597 target = 0.044297 restraints weight = 64058.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2645 r_free = 0.2645 target = 0.045956 restraints weight = 35790.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.2677 r_free = 0.2677 target = 0.047090 restraints weight = 23693.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.047912 restraints weight = 17590.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.048442 restraints weight = 14004.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.2710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8700
moved from start:          0.4579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  14950  Z= 0.194
  Angle     :  0.651  10.734  20290  Z= 0.322
  Chirality :  0.045   0.157   2255
  Planarity :  0.004   0.038   2595
  Dihedral  :  5.722  54.531   2080
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.04 (0.20), residues: 1845
  helix:  0.40 (0.19), residues: 755
  sheet: -0.29 (0.30), residues: 320
  loop :  0.00 (0.24), residues: 770

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 372 
 TYR   0.022   0.001   TYR A 143 
 PHE   0.019   0.002   PHE D 262 
 TRP   0.031   0.002   TRP A  79 
 HIS   0.012   0.001   HIS D  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 (14950)
  covalent geometry    : angle       0.65073 (20290)
  hydrogen bonds       : bond        0.03594 (  698)
  hydrogen bonds       : angle       4.67512 ( 1752)

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

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

  3690 Ramachandran restraints generated.
    1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3690 Ramachandran restraints generated.
    1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
REVERT: C   47 MET cc_start: 0.5700 (ttt) cc_final: 0.5291 (ttm)
REVERT: C  119 MET cc_start: 0.9227 (ttt) cc_final: 0.8953 (ttm)
REVERT: C  154 ASP cc_start: 0.7978 (t0) cc_final: 0.7683 (t0)
REVERT: C  179 ASP cc_start: 0.7460 (t0) cc_final: 0.7243 (t0)
REVERT: C  285 CYS cc_start: 0.9071 (m) cc_final: 0.8860 (m)
REVERT: D   44 MET cc_start: 0.8725 (mmm) cc_final: 0.8449 (mmm)
REVERT: D   82 MET cc_start: 0.9177 (tpt) cc_final: 0.8520 (tpp)
REVERT: D  107 GLU cc_start: 0.8914 (pt0) cc_final: 0.8572 (pt0)
REVERT: D  117 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8829 (mm-30)
REVERT: D  179 ASP cc_start: 0.8614 (p0) cc_final: 0.8251 (t0)
REVERT: D  205 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8381 (mt-10)
REVERT: D  226 GLU cc_start: 0.9204 (tp30) cc_final: 0.8860 (tp30)
REVERT: D  257 CYS cc_start: 0.9233 (t) cc_final: 0.8994 (t)
REVERT: D  313 MET cc_start: 0.9065 (tpp) cc_final: 0.8644 (tpp)
REVERT: D  372 ARG cc_start: 0.9189 (mmm-85) cc_final: 0.8980 (mmm-85)
REVERT: E   81 ASP cc_start: 0.8773 (t70) cc_final: 0.8119 (t70)
REVERT: E   82 MET cc_start: 0.8837 (tpt) cc_final: 0.8422 (tpp)
REVERT: E  128 ASN cc_start: 0.9118 (t0) cc_final: 0.8821 (t0)
REVERT: E  179 ASP cc_start: 0.8033 (p0) cc_final: 0.7505 (t0)
REVERT: E  205 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8455 (mt-10)
REVERT: E  244 ASP cc_start: 0.7624 (t70) cc_final: 0.7255 (t0)
REVERT: E  362 TYR cc_start: 0.8876 (t80) cc_final: 0.8513 (t80)
REVERT: F   44 MET cc_start: 0.8838 (mmm) cc_final: 0.8615 (mmm)
REVERT: F  285 CYS cc_start: 0.8862 (m) cc_final: 0.8558 (m)
REVERT: F  286 ASP cc_start: 0.8719 (t0) cc_final: 0.8479 (t70)
REVERT: F  313 MET cc_start: 0.9170 (ttm) cc_final: 0.8941 (tpp)
REVERT: F  318 THR cc_start: 0.9257 (m) cc_final: 0.9051 (p)
REVERT: F  375 PHE cc_start: 0.7215 (t80) cc_final: 0.6563 (t80)
REVERT: A   11 ASP cc_start: 0.8968 (t0) cc_final: 0.6772 (p0)
REVERT: A   47 MET cc_start: 0.6875 (tpt) cc_final: 0.6244 (ttm)
REVERT: A   59 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8071 (mm-40)
REVERT: A  105 LEU cc_start: 0.9347 (mt) cc_final: 0.8977 (mp)
REVERT: A  132 MET cc_start: 0.9377 (ppp) cc_final: 0.8941 (ppp)
REVERT: A  176 MET cc_start: 0.9524 (mmm) cc_final: 0.8945 (mpp)
REVERT: A  227 MET cc_start: 0.8853 (mmm) cc_final: 0.8584 (mmm)
REVERT: A  246 GLN cc_start: 0.8362 (tm-30) cc_final: 0.8118 (tm-30)
REVERT: A  297 ASN cc_start: 0.9011 (m-40) cc_final: 0.8714 (m-40)
REVERT: A  305 MET cc_start: 0.8895 (mmt) cc_final: 0.8672 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.1096
  time to fit residues: 34.4031
Evaluate side-chains
  156 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.650 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 166 optimal weight:   10.0000
   chunk 82 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 86 optimal weight:    9.9990
   chunk 83 optimal weight:    7.9990
   chunk 78 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 116 optimal weight:    9.9990
   chunk 64 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 95 optimal weight:    5.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 162 ASN
F 225 ASN
** A  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 121 GLN
A 161 HIS
A 275 HIS
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.059170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2631 r_free = 0.2631 target = 0.045570 restraints weight = 62769.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.047247 restraints weight = 35409.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.048409 restraints weight = 23649.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2735 r_free = 0.2735 target = 0.049203 restraints weight = 17380.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2751 r_free = 0.2751 target = 0.049794 restraints weight = 13914.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8672
moved from start:          0.4960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  14950  Z= 0.116
  Angle     :  0.585   7.043  20290  Z= 0.285
  Chirality :  0.045   0.167   2255
  Planarity :  0.004   0.039   2595
  Dihedral  :  5.480  47.373   2080
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.20), residues: 1845
  helix:  1.04 (0.20), residues: 720
  sheet: -0.17 (0.31), residues: 310
  loop :  0.20 (0.23), residues: 815

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 256 
 TYR   0.014   0.001   TYR C 143 
 PHE   0.012   0.001   PHE D 262 
 TRP   0.020   0.001   TRP A  79 
 HIS   0.008   0.001   HIS D  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (14950)
  covalent geometry    : angle       0.58514 (20290)
  hydrogen bonds       : bond        0.03066 (  698)
  hydrogen bonds       : angle       4.43775 ( 1752)

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

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

  3690 Ramachandran restraints generated.
    1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3690 Ramachandran restraints generated.
    1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   47 MET cc_start: 0.5990 (ttt) cc_final: 0.5559 (ttm)
REVERT: C  154 ASP cc_start: 0.7756 (t0) cc_final: 0.7427 (t0)
REVERT: C  176 MET cc_start: 0.9151 (tpp) cc_final: 0.8869 (mmm)
REVERT: D   82 MET cc_start: 0.9237 (tpt) cc_final: 0.8865 (tpt)
REVERT: D  107 GLU cc_start: 0.8787 (pt0) cc_final: 0.8499 (pt0)
REVERT: D  117 GLU cc_start: 0.9281 (mt-10) cc_final: 0.8813 (mm-30)
REVERT: D  179 ASP cc_start: 0.8488 (p0) cc_final: 0.8274 (t0)
REVERT: D  205 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8448 (mt-10)
REVERT: D  217 CYS cc_start: 0.9138 (m) cc_final: 0.8679 (m)
REVERT: D  226 GLU cc_start: 0.9190 (tp30) cc_final: 0.8765 (tp30)
REVERT: D  248 ILE cc_start: 0.9454 (pt) cc_final: 0.9213 (mt)
REVERT: D  313 MET cc_start: 0.8962 (tpp) cc_final: 0.8584 (tpp)
REVERT: D  355 MET cc_start: 0.8709 (mtp) cc_final: 0.8475 (mtp)
REVERT: E   12 ASN cc_start: 0.9274 (p0) cc_final: 0.9035 (p0)
REVERT: E   82 MET cc_start: 0.8784 (tpt) cc_final: 0.8424 (tpp)
REVERT: E  128 ASN cc_start: 0.9099 (t0) cc_final: 0.8802 (t0)
REVERT: E  176 MET cc_start: 0.8982 (tpp) cc_final: 0.8744 (mmm)
REVERT: E  179 ASP cc_start: 0.7948 (p0) cc_final: 0.7587 (t0)
REVERT: E  205 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8293 (mt-10)
REVERT: E  244 ASP cc_start: 0.7483 (t70) cc_final: 0.7191 (t0)
REVERT: E  318 THR cc_start: 0.9359 (m) cc_final: 0.9153 (p)
REVERT: E  362 TYR cc_start: 0.8860 (t80) cc_final: 0.8577 (t80)
REVERT: F   82 MET cc_start: 0.9099 (tpt) cc_final: 0.8859 (tpp)
REVERT: F  107 GLU cc_start: 0.7341 (tt0) cc_final: 0.6913 (tt0)
REVERT: F  132 MET cc_start: 0.9400 (tmm) cc_final: 0.9157 (tmm)
REVERT: F  205 GLU cc_start: 0.8873 (mp0) cc_final: 0.8527 (pm20)
REVERT: F  285 CYS cc_start: 0.8836 (m) cc_final: 0.8537 (m)
REVERT: F  355 MET cc_start: 0.8274 (mtm) cc_final: 0.8029 (ttm)
REVERT: F  375 PHE cc_start: 0.7118 (t80) cc_final: 0.6726 (t80)
REVERT: A   11 ASP cc_start: 0.8933 (t0) cc_final: 0.6721 (p0)
REVERT: A   25 ASP cc_start: 0.9233 (m-30) cc_final: 0.8924 (p0)
REVERT: A   47 MET cc_start: 0.7141 (tpt) cc_final: 0.6526 (ttm)
REVERT: A  176 MET cc_start: 0.9563 (mmm) cc_final: 0.9057 (mpp)
REVERT: A  227 MET cc_start: 0.8754 (mmm) cc_final: 0.8491 (mmm)
REVERT: A  314 GLN cc_start: 0.9437 (tt0) cc_final: 0.9177 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 215
  average time/residue: 0.1079
  time to fit residues: 36.8610
Evaluate side-chains
  159 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 180 optimal weight:    2.9990
   chunk 181 optimal weight:    4.9990
   chunk 20 optimal weight:    7.9990
   chunk 136 optimal weight:    5.9990
   chunk 89 optimal weight:   10.0000
   chunk 112 optimal weight:   20.0000
   chunk 129 optimal weight:    1.9990
   chunk 124 optimal weight:    4.9990
   chunk 179 optimal weight:   10.0000
   chunk 22 optimal weight:   20.0000
   chunk 123 optimal weight:   10.0000
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 128 ASN
** A  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 161 HIS
A 275 HIS
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.057258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2584 r_free = 0.2584 target = 0.043701 restraints weight = 62630.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2634 r_free = 0.2634 target = 0.045343 restraints weight = 35643.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.046500 restraints weight = 23871.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.047295 restraints weight = 17514.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.047863 restraints weight = 13959.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.2703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8722
moved from start:          0.5380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027  14950  Z= 0.172
  Angle     :  0.611   7.224  20290  Z= 0.299
  Chirality :  0.045   0.158   2255
  Planarity :  0.004   0.036   2595
  Dihedral  :  5.462  49.394   2080
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.21), residues: 1845
  helix:  1.22 (0.20), residues: 720
  sheet: -0.08 (0.31), residues: 320
  loop :  0.44 (0.24), residues: 805

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 372 
 TYR   0.013   0.001   TYR A  91 
 PHE   0.011   0.001   PHE E 124 
 TRP   0.019   0.001   TRP A  79 
 HIS   0.009   0.001   HIS D  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (14950)
  covalent geometry    : angle       0.61130 (20290)
  hydrogen bonds       : bond        0.03268 (  698)
  hydrogen bonds       : angle       4.44949 ( 1752)

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

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

  3690 Ramachandran restraints generated.
    1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3690 Ramachandran restraints generated.
    1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.618 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   47 MET cc_start: 0.5942 (ttt) cc_final: 0.5474 (ttm)
REVERT: C  154 ASP cc_start: 0.7915 (t0) cc_final: 0.7544 (t0)
REVERT: C  176 MET cc_start: 0.9149 (tpp) cc_final: 0.8831 (mmm)
REVERT: C  285 CYS cc_start: 0.9126 (m) cc_final: 0.8908 (m)
REVERT: D   82 MET cc_start: 0.9245 (tpt) cc_final: 0.8803 (tpt)
REVERT: D  107 GLU cc_start: 0.8845 (pt0) cc_final: 0.8521 (pt0)
REVERT: D  179 ASP cc_start: 0.8626 (p0) cc_final: 0.8316 (t0)
REVERT: D  205 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8540 (mt-10)
REVERT: D  217 CYS cc_start: 0.9247 (m) cc_final: 0.8886 (m)
REVERT: D  226 GLU cc_start: 0.9251 (tp30) cc_final: 0.8753 (tp30)
REVERT: D  248 ILE cc_start: 0.9447 (pt) cc_final: 0.9163 (mt)
REVERT: D  313 MET cc_start: 0.9022 (tpp) cc_final: 0.8728 (tpp)
REVERT: D  326 LYS cc_start: 0.8765 (tptp) cc_final: 0.8356 (tptp)
REVERT: D  330 ILE cc_start: 0.9031 (tt) cc_final: 0.8726 (pt)
REVERT: D  355 MET cc_start: 0.8721 (mtp) cc_final: 0.8487 (mtp)
REVERT: E   81 ASP cc_start: 0.8774 (t70) cc_final: 0.8238 (t70)
REVERT: E  128 ASN cc_start: 0.9117 (t0) cc_final: 0.8808 (t0)
REVERT: E  179 ASP cc_start: 0.8101 (p0) cc_final: 0.7583 (t0)
REVERT: E  205 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8290 (mt-10)
REVERT: E  244 ASP cc_start: 0.7437 (t70) cc_final: 0.7178 (t0)
REVERT: E  305 MET cc_start: 0.8751 (mmp) cc_final: 0.8512 (mmp)
REVERT: E  318 THR cc_start: 0.9398 (m) cc_final: 0.9157 (p)
REVERT: E  362 TYR cc_start: 0.8886 (t80) cc_final: 0.8555 (t80)
REVERT: F  107 GLU cc_start: 0.7599 (tt0) cc_final: 0.7250 (tt0)
REVERT: F  132 MET cc_start: 0.9405 (tmm) cc_final: 0.9194 (tmm)
REVERT: F  285 CYS cc_start: 0.8909 (m) cc_final: 0.8649 (m)
REVERT: F  313 MET cc_start: 0.9097 (tpp) cc_final: 0.8847 (tpp)
REVERT: A   11 ASP cc_start: 0.8998 (t0) cc_final: 0.6790 (p0)
REVERT: A   25 ASP cc_start: 0.9248 (m-30) cc_final: 0.8904 (p0)
REVERT: A  104 LEU cc_start: 0.9168 (tt) cc_final: 0.8964 (tp)
REVERT: A  105 LEU cc_start: 0.9238 (mt) cc_final: 0.9029 (mt)
REVERT: A  132 MET cc_start: 0.9355 (ppp) cc_final: 0.9137 (ppp)
REVERT: A  176 MET cc_start: 0.9565 (mmm) cc_final: 0.8998 (mpp)
REVERT: A  227 MET cc_start: 0.8731 (mmm) cc_final: 0.8449 (mmm)
REVERT: A  297 ASN cc_start: 0.8992 (m-40) cc_final: 0.8658 (m-40)
REVERT: A  314 GLN cc_start: 0.9450 (tt0) cc_final: 0.9168 (tm-30)
REVERT: A  355 MET cc_start: 0.8663 (mmp) cc_final: 0.8041 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.1132
  time to fit residues: 35.5688
Evaluate side-chains
  153 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 132 optimal weight:    5.9990
   chunk 184 optimal weight:    0.8980
   chunk 29 optimal weight:    7.9990
   chunk 182 optimal weight:   20.0000
   chunk 143 optimal weight:    0.0770
   chunk 148 optimal weight:   40.0000
   chunk 81 optimal weight:    2.9990
   chunk 55 optimal weight:    6.9990
   chunk 57 optimal weight:    0.9990
   chunk 66 optimal weight:   20.0000
   overall best weight:    1.7944

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

Flipped N/Q/H residues before XYZ refinement:
** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 225 ASN
** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 225 ASN
** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 128 ASN
** A  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 275 HIS
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.057728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2600 r_free = 0.2600 target = 0.044284 restraints weight = 61375.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.046002 restraints weight = 33815.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2687 r_free = 0.2687 target = 0.047218 restraints weight = 21995.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.048063 restraints weight = 15914.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.048662 restraints weight = 12463.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8682
moved from start:          0.5564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  14950  Z= 0.107
  Angle     :  0.578   6.613  20290  Z= 0.277
  Chirality :  0.044   0.150   2255
  Planarity :  0.004   0.034   2595
  Dihedral  :  5.320  47.737   2080
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.21), residues: 1845
  helix:  1.40 (0.20), residues: 720
  sheet: -0.12 (0.30), residues: 335
  loop :  0.61 (0.24), residues: 790

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 206 
 TYR   0.012   0.001   TYR A  91 
 PHE   0.009   0.001   PHE D 266 
 TRP   0.019   0.001   TRP A  79 
 HIS   0.006   0.001   HIS D  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 (14950)
  covalent geometry    : angle       0.57794 (20290)
  hydrogen bonds       : bond        0.02935 (  698)
  hydrogen bonds       : angle       4.33558 ( 1752)

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

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

  3690 Ramachandran restraints generated.
    1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3690 Ramachandran restraints generated.
    1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   47 MET cc_start: 0.6055 (ttt) cc_final: 0.5566 (ttm)
REVERT: C  154 ASP cc_start: 0.7841 (t0) cc_final: 0.7485 (t0)
REVERT: C  176 MET cc_start: 0.9197 (tpp) cc_final: 0.8884 (mmm)
REVERT: C  285 CYS cc_start: 0.9157 (m) cc_final: 0.8923 (m)
REVERT: D   82 MET cc_start: 0.9231 (tpt) cc_final: 0.8764 (tpt)
REVERT: D  107 GLU cc_start: 0.8818 (pt0) cc_final: 0.8468 (pt0)
REVERT: D  179 ASP cc_start: 0.8648 (p0) cc_final: 0.8282 (t0)
REVERT: D  184 ASP cc_start: 0.9167 (m-30) cc_final: 0.8937 (m-30)
REVERT: D  205 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8494 (mt-10)
REVERT: D  217 CYS cc_start: 0.9228 (m) cc_final: 0.8845 (m)
REVERT: D  226 GLU cc_start: 0.9251 (tp30) cc_final: 0.8758 (tp30)
REVERT: D  313 MET cc_start: 0.9011 (tpp) cc_final: 0.8723 (tpp)
REVERT: D  325 MET cc_start: 0.8120 (tpp) cc_final: 0.7537 (tmm)
REVERT: D  330 ILE cc_start: 0.8974 (tt) cc_final: 0.8672 (pt)
REVERT: D  355 MET cc_start: 0.8749 (mtp) cc_final: 0.8493 (mtp)
REVERT: E   81 ASP cc_start: 0.8824 (t70) cc_final: 0.8239 (t70)
REVERT: E  128 ASN cc_start: 0.9127 (t0) cc_final: 0.8794 (t0)
REVERT: E  176 MET cc_start: 0.9050 (tpp) cc_final: 0.8774 (mmm)
REVERT: E  179 ASP cc_start: 0.8111 (p0) cc_final: 0.7626 (t0)
REVERT: E  180 LEU cc_start: 0.9182 (tp) cc_final: 0.8980 (tp)
REVERT: E  205 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8315 (mt-10)
REVERT: E  225 ASN cc_start: 0.9097 (m-40) cc_final: 0.8815 (m110)
REVERT: E  244 ASP cc_start: 0.7436 (t70) cc_final: 0.7171 (t0)
REVERT: E  318 THR cc_start: 0.9367 (m) cc_final: 0.9118 (p)
REVERT: E  362 TYR cc_start: 0.8912 (t80) cc_final: 0.8660 (t80)
REVERT: F   82 MET cc_start: 0.9181 (tpt) cc_final: 0.8925 (tpp)
REVERT: F  132 MET cc_start: 0.9384 (tmm) cc_final: 0.9142 (tmm)
REVERT: F  285 CYS cc_start: 0.8862 (m) cc_final: 0.8571 (m)
REVERT: F  305 MET cc_start: 0.9025 (mmt) cc_final: 0.8441 (mmt)
REVERT: A   11 ASP cc_start: 0.8936 (t0) cc_final: 0.6697 (p0)
REVERT: A   25 ASP cc_start: 0.9261 (m-30) cc_final: 0.8925 (p0)
REVERT: A   59 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8247 (mm-40)
REVERT: A  107 GLU cc_start: 0.9022 (tt0) cc_final: 0.8808 (tt0)
REVERT: A  176 MET cc_start: 0.9526 (mmm) cc_final: 0.8945 (mpp)
REVERT: A  227 MET cc_start: 0.8729 (mmm) cc_final: 0.8430 (mmm)
REVERT: A  297 ASN cc_start: 0.8819 (m-40) cc_final: 0.8525 (m-40)
REVERT: A  314 GLN cc_start: 0.9431 (tt0) cc_final: 0.9143 (tm-30)
REVERT: A  355 MET cc_start: 0.8658 (mmp) cc_final: 0.7954 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 209
  average time/residue: 0.1096
  time to fit residues: 36.1094
Evaluate side-chains
  159 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 130 optimal weight:    8.9990
   chunk 126 optimal weight:   20.0000
   chunk 183 optimal weight:    3.9990
   chunk 48 optimal weight:    9.9990
   chunk 128 optimal weight:    0.9990
   chunk 65 optimal weight:    6.9990
   chunk 86 optimal weight:    0.0670
   chunk 37 optimal weight:   30.0000
   chunk 178 optimal weight:    9.9990
   chunk 133 optimal weight:    3.9990
   chunk 21 optimal weight:    7.9990
   overall best weight:    3.2126

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

Flipped N/Q/H residues before XYZ refinement:
** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 162 ASN
** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 128 ASN
** A  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 161 HIS
A 275 HIS
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.057312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2587 r_free = 0.2587 target = 0.044114 restraints weight = 61546.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.045783 restraints weight = 34413.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2670 r_free = 0.2670 target = 0.046936 restraints weight = 22630.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.047744 restraints weight = 16604.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.048320 restraints weight = 13200.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8702
moved from start:          0.5760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  14950  Z= 0.141
  Angle     :  0.591   6.793  20290  Z= 0.286
  Chirality :  0.045   0.177   2255
  Planarity :  0.004   0.035   2595
  Dihedral  :  5.322  47.654   2080
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.21), residues: 1845
  helix:  1.38 (0.20), residues: 725
  sheet:  0.10 (0.31), residues: 310
  loop :  0.71 (0.24), residues: 810

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 372 
 TYR   0.014   0.001   TYR E 143 
 PHE   0.015   0.001   PHE C 124 
 TRP   0.030   0.001   TRP A  86 
 HIS   0.007   0.001   HIS D  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (14950)
  covalent geometry    : angle       0.59118 (20290)
  hydrogen bonds       : bond        0.03028 (  698)
  hydrogen bonds       : angle       4.33600 ( 1752)

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

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

  3690 Ramachandran restraints generated.
    1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3690 Ramachandran restraints generated.
    1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  154 ASP cc_start: 0.7919 (t0) cc_final: 0.7578 (t0)
REVERT: C  176 MET cc_start: 0.9176 (tpp) cc_final: 0.8865 (mmm)
REVERT: C  285 CYS cc_start: 0.9162 (m) cc_final: 0.8928 (m)
REVERT: D   82 MET cc_start: 0.9187 (tpt) cc_final: 0.8799 (tpt)
REVERT: D  107 GLU cc_start: 0.8774 (pt0) cc_final: 0.8453 (pt0)
REVERT: D  166 TYR cc_start: 0.8590 (t80) cc_final: 0.8340 (t80)
REVERT: D  179 ASP cc_start: 0.8531 (p0) cc_final: 0.8300 (t0)
REVERT: D  217 CYS cc_start: 0.9244 (m) cc_final: 0.8886 (m)
REVERT: D  226 GLU cc_start: 0.9284 (tp30) cc_final: 0.8764 (tp30)
REVERT: D  313 MET cc_start: 0.9040 (tpp) cc_final: 0.8784 (tpp)
REVERT: D  330 ILE cc_start: 0.8994 (tt) cc_final: 0.8699 (pt)
REVERT: D  355 MET cc_start: 0.8732 (mtp) cc_final: 0.8484 (mtp)
REVERT: E   82 MET cc_start: 0.8861 (tpt) cc_final: 0.8532 (tpp)
REVERT: E  128 ASN cc_start: 0.9162 (t0) cc_final: 0.8808 (t0)
REVERT: E  176 MET cc_start: 0.9039 (tpp) cc_final: 0.8630 (mmm)
REVERT: E  179 ASP cc_start: 0.8154 (p0) cc_final: 0.7683 (t0)
REVERT: E  205 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8320 (mt-10)
REVERT: E  225 ASN cc_start: 0.9125 (m-40) cc_final: 0.8889 (m110)
REVERT: E  227 MET cc_start: 0.9262 (mmp) cc_final: 0.9044 (mmm)
REVERT: E  244 ASP cc_start: 0.7348 (t70) cc_final: 0.7101 (t0)
REVERT: E  318 THR cc_start: 0.9363 (m) cc_final: 0.9113 (p)
REVERT: E  362 TYR cc_start: 0.8973 (t80) cc_final: 0.8678 (t80)
REVERT: F   82 MET cc_start: 0.9130 (tpt) cc_final: 0.8839 (tpp)
REVERT: F  132 MET cc_start: 0.9402 (tmm) cc_final: 0.9173 (tmm)
REVERT: F  205 GLU cc_start: 0.8900 (pm20) cc_final: 0.8600 (pm20)
REVERT: F  285 CYS cc_start: 0.8911 (m) cc_final: 0.8598 (m)
REVERT: F  305 MET cc_start: 0.9118 (mmt) cc_final: 0.8473 (mmt)
REVERT: A   25 ASP cc_start: 0.9258 (m-30) cc_final: 0.8972 (p0)
REVERT: A  176 MET cc_start: 0.9519 (mmm) cc_final: 0.8885 (mpp)
REVERT: A  227 MET cc_start: 0.8749 (mmm) cc_final: 0.8437 (mmm)
REVERT: A  285 CYS cc_start: 0.8816 (m) cc_final: 0.8612 (m)
REVERT: A  297 ASN cc_start: 0.8774 (m-40) cc_final: 0.8551 (m-40)
REVERT: A  314 GLN cc_start: 0.9458 (tt0) cc_final: 0.9153 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.1050
  time to fit residues: 33.7560
Evaluate side-chains
  151 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 60 optimal weight:    0.0470
   chunk 106 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 177 optimal weight:   10.0000
   chunk 104 optimal weight:    6.9990
   chunk 70 optimal weight:    9.9990
   chunk 94 optimal weight:    9.9990
   chunk 182 optimal weight:   20.0000
   chunk 113 optimal weight:    4.9990
   chunk 40 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   overall best weight:    4.2086

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

Flipped N/Q/H residues before XYZ refinement:
** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 161 HIS
** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 128 ASN
** A  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 161 HIS
A 275 HIS
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.056997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2578 r_free = 0.2578 target = 0.043398 restraints weight = 62087.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2628 r_free = 0.2628 target = 0.045068 restraints weight = 35385.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.046230 restraints weight = 23677.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.047053 restraints weight = 17436.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.047615 restraints weight = 13864.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8736
moved from start:          0.6013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14950  Z= 0.173
  Angle     :  0.621   7.796  20290  Z= 0.300
  Chirality :  0.045   0.175   2255
  Planarity :  0.004   0.034   2595
  Dihedral  :  5.395  49.014   2080
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.21), residues: 1845
  helix:  1.31 (0.20), residues: 730
  sheet:  0.15 (0.31), residues: 315
  loop :  0.70 (0.24), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 196 
 TYR   0.019   0.001   TYR C 143 
 PHE   0.015   0.001   PHE D 127 
 TRP   0.025   0.001   TRP A  86 
 HIS   0.008   0.001   HIS D  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (14950)
  covalent geometry    : angle       0.62111 (20290)
  hydrogen bonds       : bond        0.03173 (  698)
  hydrogen bonds       : angle       4.39879 ( 1752)

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

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

  3690 Ramachandran restraints generated.
    1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3690 Ramachandran restraints generated.
    1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.674 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  154 ASP cc_start: 0.8022 (t0) cc_final: 0.7678 (t0)
REVERT: C  176 MET cc_start: 0.9184 (tpp) cc_final: 0.8815 (mmm)
REVERT: C  285 CYS cc_start: 0.9160 (m) cc_final: 0.8918 (m)
REVERT: D   82 MET cc_start: 0.9260 (tpt) cc_final: 0.8925 (tpt)
REVERT: D  107 GLU cc_start: 0.8748 (pt0) cc_final: 0.8437 (pt0)
REVERT: D  226 GLU cc_start: 0.9271 (tp30) cc_final: 0.8719 (tp30)
REVERT: D  313 MET cc_start: 0.9058 (tpp) cc_final: 0.8808 (tpp)
REVERT: D  330 ILE cc_start: 0.9022 (tt) cc_final: 0.8728 (pt)
REVERT: E   47 MET cc_start: 0.5590 (ptt) cc_final: 0.5272 (ptt)
REVERT: E   82 MET cc_start: 0.8843 (tpt) cc_final: 0.8485 (tpp)
REVERT: E  128 ASN cc_start: 0.9133 (t0) cc_final: 0.8793 (t0)
REVERT: E  176 MET cc_start: 0.8990 (tpp) cc_final: 0.8624 (mmm)
REVERT: E  179 ASP cc_start: 0.8244 (p0) cc_final: 0.7552 (t0)
REVERT: E  205 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8371 (mt-10)
REVERT: E  225 ASN cc_start: 0.9145 (m-40) cc_final: 0.8916 (m110)
REVERT: E  244 ASP cc_start: 0.7286 (t70) cc_final: 0.7041 (t0)
REVERT: E  318 THR cc_start: 0.9379 (m) cc_final: 0.9140 (p)
REVERT: F   44 MET cc_start: 0.9061 (tpp) cc_final: 0.8778 (mmm)
REVERT: F  205 GLU cc_start: 0.8879 (pm20) cc_final: 0.8531 (pm20)
REVERT: F  285 CYS cc_start: 0.8938 (m) cc_final: 0.8647 (m)
REVERT: F  305 MET cc_start: 0.9113 (mmt) cc_final: 0.8497 (mmt)
REVERT: F  313 MET cc_start: 0.9136 (tpp) cc_final: 0.8854 (tpp)
REVERT: A   25 ASP cc_start: 0.9274 (m-30) cc_final: 0.9016 (p0)
REVERT: A  176 MET cc_start: 0.9494 (mmm) cc_final: 0.8811 (mpp)
REVERT: A  227 MET cc_start: 0.8720 (mmm) cc_final: 0.8422 (mmm)
REVERT: A  314 GLN cc_start: 0.9481 (tt0) cc_final: 0.9168 (tm-30)
REVERT: A  355 MET cc_start: 0.8682 (mmp) cc_final: 0.8216 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 0.1101
  time to fit residues: 34.1319
Evaluate side-chains
  148 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 141 optimal weight:    0.9980
   chunk 102 optimal weight:    0.0170
   chunk 129 optimal weight:    9.9990
   chunk 145 optimal weight:    4.9990
   chunk 99 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   chunk 149 optimal weight:   20.0000
   chunk 55 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 182 optimal weight:   20.0000
   chunk 18 optimal weight:    3.9990
   overall best weight:    2.2024

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

Flipped N/Q/H residues before XYZ refinement:
C  49 GLN
** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 128 ASN
** A  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.057495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2598 r_free = 0.2598 target = 0.044183 restraints weight = 61480.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.045887 restraints weight = 34297.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2683 r_free = 0.2683 target = 0.047066 restraints weight = 22466.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.047907 restraints weight = 16344.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.048501 restraints weight = 12880.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.2710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8700
moved from start:          0.6149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  14950  Z= 0.115
  Angle     :  0.598   8.364  20290  Z= 0.285
  Chirality :  0.045   0.158   2255
  Planarity :  0.004   0.036   2595
  Dihedral  :  5.292  45.445   2080
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.22 (0.21), residues: 1845
  helix:  1.44 (0.20), residues: 725
  sheet: -0.03 (0.29), residues: 340
  loop :  0.82 (0.25), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  95 
 TYR   0.015   0.001   TYR C 143 
 PHE   0.014   0.001   PHE C 124 
 TRP   0.037   0.002   TRP A  86 
 HIS   0.006   0.001   HIS D 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (14950)
  covalent geometry    : angle       0.59804 (20290)
  hydrogen bonds       : bond        0.02898 (  698)
  hydrogen bonds       : angle       4.31967 ( 1752)

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

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

  3690 Ramachandran restraints generated.
    1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3690 Ramachandran restraints generated.
    1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   47 MET cc_start: 0.7159 (ptm) cc_final: 0.6545 (ptp)
REVERT: C  154 ASP cc_start: 0.7944 (t0) cc_final: 0.7642 (t0)
REVERT: C  176 MET cc_start: 0.9230 (tpp) cc_final: 0.8846 (mmm)
REVERT: C  285 CYS cc_start: 0.9175 (m) cc_final: 0.8919 (m)
REVERT: D   44 MET cc_start: 0.9203 (mmm) cc_final: 0.8919 (mmm)
REVERT: D   82 MET cc_start: 0.9268 (tpt) cc_final: 0.8910 (tpt)
REVERT: D  107 GLU cc_start: 0.8699 (pt0) cc_final: 0.8349 (pt0)
REVERT: D  205 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8546 (tt0)
REVERT: D  217 CYS cc_start: 0.9268 (m) cc_final: 0.8877 (m)
REVERT: D  226 GLU cc_start: 0.9273 (tp30) cc_final: 0.8673 (tp30)
REVERT: D  313 MET cc_start: 0.9161 (tpp) cc_final: 0.8874 (tpp)
REVERT: D  330 ILE cc_start: 0.8968 (tt) cc_final: 0.8680 (pt)
REVERT: E   47 MET cc_start: 0.5564 (ptt) cc_final: 0.5332 (ptt)
REVERT: E  128 ASN cc_start: 0.9196 (t0) cc_final: 0.8843 (t0)
REVERT: E  176 MET cc_start: 0.9066 (tpp) cc_final: 0.8642 (mmm)
REVERT: E  179 ASP cc_start: 0.8287 (p0) cc_final: 0.7522 (t0)
REVERT: E  205 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8273 (mt-10)
REVERT: E  225 ASN cc_start: 0.9168 (m-40) cc_final: 0.8932 (m110)
REVERT: E  244 ASP cc_start: 0.7287 (t70) cc_final: 0.7038 (t0)
REVERT: E  283 MET cc_start: 0.8979 (tpp) cc_final: 0.8504 (mmm)
REVERT: E  285 CYS cc_start: 0.8805 (m) cc_final: 0.8581 (m)
REVERT: E  318 THR cc_start: 0.9347 (m) cc_final: 0.9085 (p)
REVERT: E  362 TYR cc_start: 0.8906 (t80) cc_final: 0.8667 (t80)
REVERT: F  107 GLU cc_start: 0.7566 (tt0) cc_final: 0.7321 (tt0)
REVERT: F  205 GLU cc_start: 0.8855 (pm20) cc_final: 0.8471 (pm20)
REVERT: F  285 CYS cc_start: 0.8900 (m) cc_final: 0.8616 (m)
REVERT: F  305 MET cc_start: 0.9083 (mmt) cc_final: 0.8506 (mmt)
REVERT: A   25 ASP cc_start: 0.9251 (m-30) cc_final: 0.8990 (p0)
REVERT: A  176 MET cc_start: 0.9466 (mmm) cc_final: 0.8772 (mpp)
REVERT: A  227 MET cc_start: 0.8671 (mmm) cc_final: 0.8368 (mmm)
REVERT: A  275 HIS cc_start: 0.9208 (p-80) cc_final: 0.7795 (p-80)
REVERT: A  297 ASN cc_start: 0.8889 (m-40) cc_final: 0.8487 (m-40)
REVERT: A  305 MET cc_start: 0.9188 (mtp) cc_final: 0.8956 (mtp)
REVERT: A  314 GLN cc_start: 0.9459 (tt0) cc_final: 0.9166 (tm-30)
REVERT: A  354 GLN cc_start: 0.8792 (mp10) cc_final: 0.8586 (mp10)
REVERT: A  355 MET cc_start: 0.8686 (mmp) cc_final: 0.8141 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 207
  average time/residue: 0.1122
  time to fit residues: 36.7323
Evaluate side-chains
  162 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 132 optimal weight:    5.9990
   chunk 40 optimal weight:    9.9990
   chunk 61 optimal weight:    0.0060
   chunk 138 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 52 optimal weight:   20.0000
   chunk 51 optimal weight:    9.9990
   chunk 59 optimal weight:    6.9990
   chunk 76 optimal weight:    6.9990
   overall best weight:    2.5202

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

Flipped N/Q/H residues before XYZ refinement:
** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 275 HIS
** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.057748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2604 r_free = 0.2604 target = 0.044422 restraints weight = 61571.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.046188 restraints weight = 33909.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2689 r_free = 0.2689 target = 0.047378 restraints weight = 21877.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.048237 restraints weight = 15901.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2730 r_free = 0.2730 target = 0.048830 restraints weight = 12460.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8695
moved from start:          0.6281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  14950  Z= 0.125
  Angle     :  0.605   8.599  20290  Z= 0.290
  Chirality :  0.045   0.161   2255
  Planarity :  0.004   0.034   2595
  Dihedral  :  5.247  46.767   2080
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.23 (0.21), residues: 1845
  helix:  1.36 (0.20), residues: 730
  sheet:  0.18 (0.30), residues: 315
  loop :  0.79 (0.24), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A  95 
 TYR   0.025   0.001   TYR E 143 
 PHE   0.010   0.001   PHE E 124 
 TRP   0.039   0.002   TRP A  86 
 HIS   0.006   0.001   HIS D  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (14950)
  covalent geometry    : angle       0.60545 (20290)
  hydrogen bonds       : bond        0.03011 (  698)
  hydrogen bonds       : angle       4.33693 ( 1752)

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

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

  3690 Ramachandran restraints generated.
    1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3690 Ramachandran restraints generated.
    1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   47 MET cc_start: 0.7030 (ptm) cc_final: 0.6223 (ptm)
REVERT: C  154 ASP cc_start: 0.7975 (t0) cc_final: 0.7644 (t0)
REVERT: C  176 MET cc_start: 0.9210 (tpp) cc_final: 0.8826 (mmm)
REVERT: C  285 CYS cc_start: 0.9160 (m) cc_final: 0.8927 (m)
REVERT: D   82 MET cc_start: 0.9260 (tpt) cc_final: 0.8902 (tpt)
REVERT: D  107 GLU cc_start: 0.8695 (pt0) cc_final: 0.8379 (pt0)
REVERT: D  217 CYS cc_start: 0.9298 (m) cc_final: 0.8918 (m)
REVERT: D  226 GLU cc_start: 0.9275 (tp30) cc_final: 0.8687 (tp30)
REVERT: D  313 MET cc_start: 0.9137 (tpp) cc_final: 0.8859 (tpp)
REVERT: D  325 MET cc_start: 0.8367 (mmm) cc_final: 0.8024 (mmm)
REVERT: D  330 ILE cc_start: 0.8996 (tt) cc_final: 0.8726 (pt)
REVERT: E   82 MET cc_start: 0.8864 (tpt) cc_final: 0.8589 (tpp)
REVERT: E  128 ASN cc_start: 0.9213 (t0) cc_final: 0.8875 (t0)
REVERT: E  176 MET cc_start: 0.9066 (tpp) cc_final: 0.8628 (mmm)
REVERT: E  179 ASP cc_start: 0.8292 (p0) cc_final: 0.7469 (t0)
REVERT: E  205 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8276 (mt-10)
REVERT: E  225 ASN cc_start: 0.9177 (m-40) cc_final: 0.8937 (m110)
REVERT: E  244 ASP cc_start: 0.7250 (t70) cc_final: 0.6974 (t0)
REVERT: E  285 CYS cc_start: 0.8817 (m) cc_final: 0.8602 (m)
REVERT: E  318 THR cc_start: 0.9336 (m) cc_final: 0.9080 (p)
REVERT: F   82 MET cc_start: 0.9122 (tpt) cc_final: 0.8815 (tpt)
REVERT: F  107 GLU cc_start: 0.7600 (tt0) cc_final: 0.7370 (tt0)
REVERT: F  176 MET cc_start: 0.8949 (tpp) cc_final: 0.8674 (tpp)
REVERT: F  205 GLU cc_start: 0.8861 (pm20) cc_final: 0.8486 (pm20)
REVERT: F  285 CYS cc_start: 0.8875 (m) cc_final: 0.8605 (m)
REVERT: F  305 MET cc_start: 0.9091 (mmt) cc_final: 0.8518 (mmt)
REVERT: A  176 MET cc_start: 0.9454 (mmm) cc_final: 0.8746 (mpp)
REVERT: A  227 MET cc_start: 0.8695 (mmm) cc_final: 0.8385 (mmm)
REVERT: A  297 ASN cc_start: 0.8864 (m-40) cc_final: 0.8497 (m-40)
REVERT: A  314 GLN cc_start: 0.9471 (tt0) cc_final: 0.9166 (tm-30)
REVERT: A  354 GLN cc_start: 0.8790 (mp10) cc_final: 0.8577 (mp10)
REVERT: A  355 MET cc_start: 0.8651 (mmp) cc_final: 0.8111 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 208
  average time/residue: 0.1021
  time to fit residues: 34.4807
Evaluate side-chains
  151 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 132 optimal weight:    0.9990
   chunk 167 optimal weight:    7.9990
   chunk 60 optimal weight:   10.0000
   chunk 35 optimal weight:    4.9990
   chunk 135 optimal weight:    9.9990
   chunk 100 optimal weight:    0.7980
   chunk 43 optimal weight:    9.9990
   chunk 9 optimal weight:   20.0000
   chunk 131 optimal weight:    0.8980
   chunk 183 optimal weight:    6.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 161 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 = 0.2956 r_free = 0.2956 target = 0.058017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2609 r_free = 0.2609 target = 0.044520 restraints weight = 60969.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.046241 restraints weight = 34399.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.047418 restraints weight = 22688.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.048269 restraints weight = 16543.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.048834 restraints weight = 13064.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.2724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8690
moved from start:          0.6396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  14950  Z= 0.116
  Angle     :  0.610   8.604  20290  Z= 0.293
  Chirality :  0.045   0.155   2255
  Planarity :  0.004   0.035   2595
  Dihedral  :  5.185  48.954   2080
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.06 %
    Favored  : 99.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.21), residues: 1845
  helix:  1.51 (0.20), residues: 690
  sheet:  0.02 (0.29), residues: 340
  loop :  1.00 (0.24), residues: 815

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  95 
 TYR   0.011   0.001   TYR E 143 
 PHE   0.019   0.001   PHE A 124 
 TRP   0.045   0.002   TRP A  86 
 HIS   0.006   0.001   HIS D  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (14950)
  covalent geometry    : angle       0.61014 (20290)
  hydrogen bonds       : bond        0.02919 (  698)
  hydrogen bonds       : angle       4.28672 ( 1752)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2196.24 seconds
wall clock time: 39 minutes 10.76 seconds (2350.76 seconds total)