Starting phenix.real_space_refine
on Tue Mar  3 23:00:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6lbh_0869/03_2026/6lbh_0869.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6lbh_0869/03_2026/6lbh_0869.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6lbh_0869/03_2026/6lbh_0869.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6lbh_0869/03_2026/6lbh_0869.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6lbh_0869/03_2026/6lbh_0869.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6lbh_0869/03_2026/6lbh_0869.cif"
  }
  resolution = 3.7
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     C    5907      2.51       5
     N    1507      2.21       5
     O    1771      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 77 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9219
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1352
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 178, 1352
          Classifications: {'peptide': 178}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 170}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 1356
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 178, 1356
          Classifications: {'peptide': 178}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 170}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 1618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1618
          Classifications: {'peptide': 216}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 204}
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 49
          Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 40
    Chain: "C"
      Number of atoms: 1637
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1637
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212}
          Unresolved non-hydrogen bonds: 58
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 28
    Chain: "F"
      Number of atoms: 1612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1612
          Classifications: {'peptide': 216}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 204}
          Unresolved non-hydrogen bonds: 65
          Unresolved non-hydrogen angles: 76
          Unresolved non-hydrogen dihedrals: 54
          Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 4, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 45
    Chain: "E"
      Number of atoms: 1644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1644
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212}
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 45
          Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 28
  Time building chain proxies: 2.22, per 1000 atoms: 0.24
  Number of scatterers: 9219
  At special positions: 0
  Unit cell: (113.98, 122.18, 125.46, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      34     16.00
     O    1771      8.00
     N    1507      7.00
     C    5907      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  93 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 139 " - pdb=" SG  CYS D 199 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 151 " - pdb=" SG  CYS C 206 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  23 " - pdb=" SG  CYS F  93 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 139 " - pdb=" SG  CYS F 199 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 151 " - pdb=" SG  CYS E 206 " distance=2.03

  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: 0.71
  Conformation dependent library (CDL) restraints added in 308.7 milliseconds
  

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2276

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 22 sheets defined
      30.7% alpha, 27.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 277 through 306
      removed outlier: 4.020A  pdb=" N   ALA A 284 " --> pdb=" O   ALA A 280 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LEU A 294 " --> pdb=" O   VAL A 290 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   THR A 295 " --> pdb=" O   ILE A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 311
      removed outlier: 3.855A  pdb=" N   LEU A 310 " --> pdb=" O   PHE A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 318
    Processing helix  chain 'A' and resid 319 through 343
      removed outlier: 4.230A  pdb=" N   ASN A 329 " --> pdb=" O   GLY A 325 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ASN A 332 " --> pdb=" O   GLY A 328 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   THR A 336 " --> pdb=" O   ASN A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 350
      No H-bonds generated for 'chain 'A' and resid 348 through 350'
    Processing helix  chain 'A' and resid 351 through 382
      removed outlier: 3.879A  pdb=" N   LEU A 357 " --> pdb=" O   ARG A 353 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   LYS A 358 " --> pdb=" O   ARG A 354 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   GLY A 361 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   THR A 369 " --> pdb=" O   LEU A 365 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   PHE A 372 " --> pdb=" O   LEU A 368 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   GLY A 376 " --> pdb=" O   PHE A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 385
      No H-bonds generated for 'chain 'A' and resid 383 through 385'
    Processing helix  chain 'A' and resid 386 through 416
      removed outlier: 3.755A  pdb=" N   VAL A 395 " --> pdb=" O   GLY A 391 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   PHE A 400 " --> pdb=" O   LEU A 396 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   VAL A 404 " --> pdb=" O   PHE A 400 " (cutoff:3.500A)
      Proline residue:  A 409  - end of helix
    Processing helix  chain 'A' and resid 418 through 423
      removed outlier: 3.920A  pdb=" N   VAL A 422 " --> pdb=" O   ASP A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 447
      removed outlier: 3.717A  pdb=" N   ALA A 428 " --> pdb=" O   ASN A 424 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   THR A 434 " --> pdb=" O   LEU A 430 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ILE A 438 " --> pdb=" O   THR A 434 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   SER A 441 " --> pdb=" O   LEU A 437 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 277 through 306
      removed outlier: 4.376A  pdb=" N   ILE B 291 " --> pdb=" O   ARG B 287 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   PHE B 306 " --> pdb=" O   ILE B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 311
      removed outlier: 3.587A  pdb=" N   LEU B 310 " --> pdb=" O   PHE B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 315 through 318
    Processing helix  chain 'B' and resid 319 through 344
      removed outlier: 3.572A  pdb=" N   ASN B 332 " --> pdb=" O   GLY B 328 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   THR B 336 " --> pdb=" O   ASN B 332 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   ARG B 340 " --> pdb=" O   THR B 336 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ALA B 341 " --> pdb=" O   LEU B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 382
      removed outlier: 3.744A  pdb=" N   VAL B 355 " --> pdb=" O   ASP B 351 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LEU B 357 " --> pdb=" O   ARG B 353 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   LYS B 358 " --> pdb=" O   ARG B 354 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   GLY B 361 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   THR B 369 " --> pdb=" O   LEU B 365 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   LEU B 373 " --> pdb=" O   THR B 369 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLY B 376 " --> pdb=" O   PHE B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 385
      No H-bonds generated for 'chain 'B' and resid 383 through 385'
    Processing helix  chain 'B' and resid 386 through 401
      removed outlier: 3.699A  pdb=" N   VAL B 395 " --> pdb=" O   GLY B 391 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   PHE B 400 " --> pdb=" O   LEU B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 401 through 416
      Proline residue:  B 409  - end of helix
    Processing helix  chain 'B' and resid 423 through 433
      removed outlier: 3.748A  pdb=" N   ALA B 428 " --> pdb=" O   ASN B 424 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 438
    Processing helix  chain 'B' and resid 438 through 447
    Processing helix  chain 'D' and resid 126 through 131
      removed outlier: 3.691A  pdb=" N   THR D 131 " --> pdb=" O   SER D 127 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 187 through 194
      removed outlier: 3.661A  pdb=" N   HIS D 194 " --> pdb=" O   GLU D 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 30
      No H-bonds generated for 'chain 'C' and resid 28 through 30'
    Processing helix  chain 'C' and resid 61 through 65
      removed outlier: 3.625A  pdb=" N   LYS C  65 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 87 through 91
    Processing helix  chain 'F' and resid 126 through 131
      removed outlier: 3.639A  pdb=" N   THR F 131 " --> pdb=" O   SER F 127 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 187 through 194
      removed outlier: 3.625A  pdb=" N   HIS F 194 " --> pdb=" O   GLU F 190 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 30
      No H-bonds generated for 'chain 'E' and resid 28 through 30'
    Processing helix  chain 'E' and resid 61 through 65
      removed outlier: 3.670A  pdb=" N   LYS E  65 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.531A  pdb=" N   SER E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 5 through 7
      removed outlier: 3.585A  pdb=" N   THR D   5 " --> pdb=" O   ARG D  24 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   THR D   7 " --> pdb=" O   SER D  22 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   ASP D  75 " --> pdb=" O   SER D  72 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   SER D  72 " --> pdb=" O   ASP D  75 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 12 through 13
      removed outlier: 6.029A  pdb=" N   GLU D 110 " --> pdb=" O   VAL D  13 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'D' and resid 50 through 53
      removed outlier: 5.455A  pdb=" N   LEU D  51 " --> pdb=" O   LEU D  42 " (cutoff:3.500A)
      removed outlier: 5.724A  pdb=" N   LEU D  42 " --> pdb=" O   LEU D  51 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 119 through 123
      removed outlier: 3.665A  pdb=" N   ASN D 142 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
      removed outlier: 6.066A  pdb=" N   TYR D 178 " --> pdb=" O   ASN D 143 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU D 165 " --> pdb=" O   THR D 183 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 158 through 159
    Processing sheet with id=AA6, first strand: chain 'C' and resid 5 through 6
      removed outlier: 3.729A  pdb=" N   THR C  78 " --> pdb=" O   ASP C  73 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 11
      removed outlier: 3.698A  pdb=" N   ILE C 121 " --> pdb=" O   GLU C  10 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   ASN C  33 " --> pdb=" O   GLY C  99 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   LYS C  38 " --> pdb=" O   TRP C  47 " (cutoff:3.500A)
      removed outlier: 5.479A  pdb=" N   TRP C  47 " --> pdb=" O   LYS C  38 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 11
      removed outlier: 3.698A  pdb=" N   ILE C 121 " --> pdb=" O   GLU C  10 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 131 through 133
      removed outlier: 3.550A  pdb=" N   SER C 131 " --> pdb=" O   LYS C 154 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   TYR C 186 " --> pdb=" O   GLY C 155 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 131 through 133
      removed outlier: 3.550A  pdb=" N   SER C 131 " --> pdb=" O   LYS C 154 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   TYR C 186 " --> pdb=" O   GLY C 155 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   VAL C 180 " --> pdb=" O   THR C 187 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 162 through 165
      removed outlier: 3.607A  pdb=" N   THR C 162 " --> pdb=" O   ALA C 209 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ASN C 207 " --> pdb=" O   THR C 164 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 5 through 7
      removed outlier: 3.569A  pdb=" N   THR F   5 " --> pdb=" O   ARG F  24 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   THR F   7 " --> pdb=" O   SER F  22 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ASP F  75 " --> pdb=" O   SER F  72 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   SER F  72 " --> pdb=" O   ASP F  75 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 12 through 13
      removed outlier: 5.959A  pdb=" N   GLU F 110 " --> pdb=" O   VAL F  13 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'F' and resid 50 through 53
      removed outlier: 5.429A  pdb=" N   LEU F  51 " --> pdb=" O   LEU F  42 " (cutoff:3.500A)
      removed outlier: 5.727A  pdb=" N   LEU F  42 " --> pdb=" O   LEU F  51 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'F' and resid 119 through 123
      removed outlier: 3.764A  pdb=" N   ASN F 142 " --> pdb=" O   THR F 119 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   TYR F 178 " --> pdb=" O   ASN F 143 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LEU F 165 " --> pdb=" O   THR F 183 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 158 through 159
    Processing sheet with id=AB8, first strand: chain 'E' and resid 5 through 6
      removed outlier: 3.727A  pdb=" N   THR E  78 " --> pdb=" O   ASP E  73 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 12
      removed outlier: 3.570A  pdb=" N   ILE E 121 " --> pdb=" O   GLU E  10 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ASN E  33 " --> pdb=" O   GLY E  99 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   LYS E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 5.469A  pdb=" N   TRP E  47 " --> pdb=" O   LYS E  38 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 3.570A  pdb=" N   ILE E 121 " --> pdb=" O   GLU E  10 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 131 through 133
    Processing sheet with id=AC3, first strand: chain 'E' and resid 131 through 133
      removed outlier: 3.690A  pdb=" N   VAL E 180 " --> pdb=" O   THR E 187 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'E' and resid 162 through 165
      removed outlier: 3.522A  pdb=" N   THR E 162 " --> pdb=" O   ALA E 209 " (cutoff:3.500A)

    432 hydrogen bonds defined for protein.
    1185 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.49

  Time building geometry restraints manager: 0.97 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2896
        1.34 -     1.46: 2284
        1.46 -     1.58: 4205
        1.58 -     1.70: 0
        1.70 -     1.81: 50
  Bond restraints: 9435
  Sorted by residual:
  bond pdb=" CB  VAL B 398 "
       pdb=" CG2 VAL B 398 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.49e+00
  bond pdb=" N   TYR E 109E"
       pdb=" CA  TYR E 109E"
    ideal  model  delta    sigma   weight residual
    1.459  1.446  0.013 9.10e-03 1.21e+04 2.06e+00
  bond pdb=" CG1 ILE B 339 "
       pdb=" CD1 ILE B 339 "
    ideal  model  delta    sigma   weight residual
    1.513  1.457  0.056 3.90e-02 6.57e+02 2.03e+00
  bond pdb=" N   TYR C 109E"
       pdb=" CA  TYR C 109E"
    ideal  model  delta    sigma   weight residual
    1.459  1.447  0.012 9.10e-03 1.21e+04 1.85e+00
  bond pdb=" CB  VAL E  37 "
       pdb=" CG1 VAL E  37 "
    ideal  model  delta    sigma   weight residual
    1.521  1.478  0.043 3.30e-02 9.18e+02 1.68e+00
  ... (remaining 9430 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 12285
        1.64 -     3.29: 489
        3.29 -     4.93: 98
        4.93 -     6.57: 22
        6.57 -     8.22: 14
  Bond angle restraints: 12908
  Sorted by residual:
  angle pdb=" N   MET E 111G"
        pdb=" CA  MET E 111G"
        pdb=" C   MET E 111G"
      ideal   model   delta    sigma   weight residual
     110.06  117.32   -7.26 1.43e+00 4.89e-01 2.58e+01
  angle pdb=" N   ALA C 110F"
        pdb=" CA  ALA C 110F"
        pdb=" C   ALA C 110F"
      ideal   model   delta    sigma   weight residual
     111.34  118.66   -7.32 1.49e+00 4.50e-01 2.42e+01
  angle pdb=" N   ALA E 110F"
        pdb=" CA  ALA E 110F"
        pdb=" C   ALA E 110F"
      ideal   model   delta    sigma   weight residual
     112.12  118.67   -6.55 1.34e+00 5.57e-01 2.39e+01
  angle pdb=" C   TYR C 109E"
        pdb=" N   ALA C 110F"
        pdb=" CA  ALA C 110F"
      ideal   model   delta    sigma   weight residual
     121.90  116.05    5.85 1.26e+00 6.30e-01 2.15e+01
  angle pdb=" N   MET C 111G"
        pdb=" CA  MET C 111G"
        pdb=" C   MET C 111G"
      ideal   model   delta    sigma   weight residual
     109.83  116.94   -7.11 1.55e+00 4.16e-01 2.10e+01
  ... (remaining 12903 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.34: 5008
       17.34 -    34.69: 418
       34.69 -    52.03: 88
       52.03 -    69.37: 7
       69.37 -    86.72: 7
  Dihedral angle restraints: 5528
    sinusoidal: 1968
      harmonic: 3560
  Sorted by residual:
  dihedral pdb=" CA  LYS F  55 "
           pdb=" C   LYS F  55 "
           pdb=" N   VAL F  56 "
           pdb=" CA  VAL F  56 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -139.17  -40.83     0      5.00e+00 4.00e-02 6.67e+01
  dihedral pdb=" CA  LYS D  55 "
           pdb=" C   LYS D  55 "
           pdb=" N   VAL D  56 "
           pdb=" CA  VAL D  56 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -139.69  -40.31     0      5.00e+00 4.00e-02 6.50e+01
  dihedral pdb=" CA  ASN D  35E"
           pdb=" C   ASN D  35E"
           pdb=" N   THR D  36 "
           pdb=" CA  THR D  36 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  141.92   38.08     0      5.00e+00 4.00e-02 5.80e+01
  ... (remaining 5525 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 956
       0.037 -    0.073: 414
       0.073 -    0.110: 131
       0.110 -    0.147: 32
       0.147 -    0.183: 6
  Chirality restraints: 1539
  Sorted by residual:
  chirality pdb=" CA  THR F  36 "
            pdb=" N   THR F  36 "
            pdb=" C   THR F  36 "
            pdb=" CB  THR F  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.18 2.00e-01 2.50e+01 8.41e-01
  chirality pdb=" CA  THR D  36 "
            pdb=" N   THR D  36 "
            pdb=" C   THR D  36 "
            pdb=" CB  THR D  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.18 2.00e-01 2.50e+01 8.34e-01
  chirality pdb=" CA  ALA E 110F"
            pdb=" N   ALA E 110F"
            pdb=" C   ALA E 110F"
            pdb=" CB  ALA E 110F"
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.31    0.17 2.00e-01 2.50e+01 7.32e-01
  ... (remaining 1536 not shown)

  Planarity restraints: 1612
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 331 "   -0.012 2.00e-02 2.50e+03   2.48e-02 6.14e+00
        pdb=" C   GLY B 331 "    0.043 2.00e-02 2.50e+03
        pdb=" O   GLY B 331 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ASN B 332 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 331 "    0.012 2.00e-02 2.50e+03   2.30e-02 5.28e+00
        pdb=" C   GLY A 331 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   GLY A 331 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ASN A 332 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR D 145 "    0.027 5.00e-02 4.00e+02   4.02e-02 2.58e+00
        pdb=" N   PRO D 146 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO D 146 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO D 146 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1609 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 179
        2.64 -     3.21: 9089
        3.21 -     3.77: 14396
        3.77 -     4.34: 20067
        4.34 -     4.90: 33017
  Nonbonded interactions: 76748
  Sorted by model distance:
  nonbonded pdb=" O   GLN F 129 "
            pdb=" NZ  LYS F 188 "
     model   vdw
     2.079 3.120
  nonbonded pdb=" OH  TYR A 273 "
            pdb=" OE2 GLU B 359 "
     model   vdw
     2.143 3.040
  nonbonded pdb=" OD1 ASN F 150 "
            pdb=" OG1 THR F 202 "
     model   vdw
     2.161 3.040
  nonbonded pdb=" OE2 GLU A 359 "
            pdb=" OH  TYR B 273 "
     model   vdw
     2.161 3.040
  nonbonded pdb=" OD1 ASN D 150 "
            pdb=" OG1 THR D 202 "
     model   vdw
     2.171 3.040
  ... (remaining 76743 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 271 through 339 or (resid 340 and (name N or name CA or na \ 
me C or name O or name CB or name CG or name CD )) or resid 341 through 448))
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'E' and (resid 1 through 12 or (resid 13 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 14 through 121 or (resid 122 through 126 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 127 through 224))
}
ncs_group {
  reference = (chain 'D' and (resid 1 through 112 or (resid 113 through 114 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 115 through 216))
  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:             1.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.810
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   9443  Z= 0.257
  Angle     :  0.825   8.217  12924  Z= 0.450
  Chirality :  0.046   0.183   1539
  Planarity :  0.005   0.040   1612
  Dihedral  : 13.616  86.716   3228
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 18.56
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.68 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.10 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.24 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.34 %

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 are not related in a simple way.
  whole: -2.87 (0.23), residues: 1224
  helix: -1.18 (0.29), residues: 310
  sheet: -2.12 (0.23), residues: 418
  loop : -1.95 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 350 
 TYR   0.026   0.002   TYR E 133 
 PHE   0.024   0.002   PHE E 177 
 TRP   0.015   0.002   TRP E  47 
 HIS   0.011   0.001   HIS F  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00580 ( 9435)
  covalent geometry    : angle       0.82493 (12908)
  SS BOND              : bond        0.00284 (    8)
  SS BOND              : angle       0.96994 (   16)
  hydrogen bonds       : bond        0.21679 (  401)
  hydrogen bonds       : angle       9.17509 ( 1185)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 253
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 LYS cc_start: 0.8128 (tppt) cc_final: 0.7892 (mmmt)
REVERT: F  188 LYS cc_start: 0.6457 (mmtt) cc_final: 0.6156 (mmtt)
REVERT: E  109 TYR cc_start: 0.7789 (t80) cc_final: 0.7515 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 253
  average time/residue: 0.0821
  time to fit residues: 29.5412
Evaluate side-chains
  215 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    8.9990
   chunk 113 optimal weight:    0.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0970
   chunk 117 optimal weight:    9.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
D   6 GLN
D  58 ASN
** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 194 HIS
F   6 GLN
** F  39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  43 GLN
F  58 ASN
** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 194 HIS
E  39 GLN
E 104 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.149758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.113538 restraints weight = 13722.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.111576 restraints weight = 14854.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.113586 restraints weight = 13668.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.114140 restraints weight = 9393.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.114183 restraints weight = 9017.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.1470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9443  Z= 0.184
  Angle     :  0.708   8.910  12924  Z= 0.366
  Chirality :  0.045   0.171   1539
  Planarity :  0.005   0.036   1612
  Dihedral  :  5.643  43.162   1322
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 11.92 %
    Favored  : 85.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.24 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.34 %

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 are not related in a simple way.
  whole: -2.57 (0.24), residues: 1224
  helix: -1.09 (0.28), residues: 328
  sheet: -1.88 (0.25), residues: 390
  loop : -1.77 (0.29), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 354 
 TYR   0.015   0.002   TYR E 109E
 PHE   0.014   0.001   PHE E 177 
 TRP   0.010   0.001   TRP C 165 
 HIS   0.003   0.001   HIS F  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 9435)
  covalent geometry    : angle       0.70794 (12908)
  SS BOND              : bond        0.00098 (    8)
  SS BOND              : angle       1.00664 (   16)
  hydrogen bonds       : bond        0.05366 (  401)
  hydrogen bonds       : angle       6.59316 ( 1185)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 245
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  307 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7603 (tm-30)
REVERT: D  128 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7503 (tm-30)
REVERT: F  172 ASP cc_start: 0.7035 (t70) cc_final: 0.6666 (t0)
REVERT: F  175 ASP cc_start: 0.8078 (p0) cc_final: 0.7714 (p0)
  outliers start: 27
  outliers final: 19
  residues processed: 254
  average time/residue: 0.0819
  time to fit residues: 29.4077
Evaluate side-chains
  249 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 230
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  301 SER
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   50 LYS
Chi-restraints excluded: chain D residue  179 SER
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain C residue  192 VAL
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain F residue    2 VAL
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   50 LYS
Chi-restraints excluded: chain F residue  179 SER
Chi-restraints excluded: chain E residue   18 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue  164 THR
Chi-restraints excluded: chain E residue  170 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 78 optimal weight:    8.9990
   chunk 54 optimal weight:    0.5980
   chunk 84 optimal weight:    3.9990
   chunk 53 optimal weight:    7.9990
   chunk 37 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 52 optimal weight:    9.9990
   chunk 74 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 90 optimal weight:    6.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 383 HIS
** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   6 GLN
D  58 ASN
** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F   6 GLN
** F  39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  58 ASN
** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 171 GLN ** 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 = 0.3815 r_free = 0.3815 target = 0.153726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.118347 restraints weight = 13711.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.116599 restraints weight = 13165.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.118148 restraints weight = 12706.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.119375 restraints weight = 8879.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.119774 restraints weight = 7446.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.1912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9443  Z= 0.152
  Angle     :  0.676  10.016  12924  Z= 0.342
  Chirality :  0.044   0.171   1539
  Planarity :  0.004   0.035   1612
  Dihedral  :  5.408  41.540   1322
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 13.80 %
    Favored  : 82.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.24 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.34 %

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 are not related in a simple way.
  whole: -2.28 (0.24), residues: 1224
  helix: -0.90 (0.28), residues: 326
  sheet: -1.66 (0.25), residues: 414
  loop : -1.57 (0.30), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 113 
 TYR   0.018   0.001   TYR D 145 
 PHE   0.011   0.001   PHE E 177 
 TRP   0.011   0.001   TRP F 168 
 HIS   0.006   0.001   HIS C 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 9435)
  covalent geometry    : angle       0.67589 (12908)
  SS BOND              : bond        0.00081 (    8)
  SS BOND              : angle       1.05494 (   16)
  hydrogen bonds       : bond        0.04790 (  401)
  hydrogen bonds       : angle       6.08987 ( 1185)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 244
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: A  288 TRP cc_start: 0.6985 (t-100) cc_final: 0.6600 (t60)
REVERT: A  307 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7492 (tm-30)
REVERT: A  381 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.7102 (m-30)
REVERT: B  303 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8909 (tt)
REVERT: D  128 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7579 (tm-30)
REVERT: D  194 HIS cc_start: 0.7028 (m170) cc_final: 0.6808 (m170)
REVERT: F  175 ASP cc_start: 0.8051 (p0) cc_final: 0.7781 (p0)
  outliers start: 35
  outliers final: 26
  residues processed: 255
  average time/residue: 0.0833
  time to fit residues: 30.0739
Evaluate side-chains
  256 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 228
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  301 SER
Chi-restraints excluded: chain A residue  381 ASP
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   50 LYS
Chi-restraints excluded: chain D residue  160 ARG
Chi-restraints excluded: chain D residue  179 SER
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  192 VAL
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain F residue    2 VAL
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   50 LYS
Chi-restraints excluded: chain F residue  179 SER
Chi-restraints excluded: chain E residue   18 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   72 VAL
Chi-restraints excluded: chain E residue  164 THR
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain E residue  208 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 84 optimal weight:    7.9990
   chunk 99 optimal weight:    0.0980
   chunk 26 optimal weight:    0.7980
   chunk 115 optimal weight:    7.9990
   chunk 108 optimal weight:    3.9990
   chunk 72 optimal weight:    4.9990
   chunk 88 optimal weight:    8.9990
   chunk 103 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 67 optimal weight:    7.9990
   chunk 104 optimal weight:    0.8980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 424 ASN
B 329 ASN
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  58 ASN
** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F   6 GLN
** F  39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  58 ASN
** F 171 GLN ** 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 = 0.3822 r_free = 0.3822 target = 0.154383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.119518 restraints weight = 13720.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.115886 restraints weight = 15518.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.117843 restraints weight = 13812.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.118519 restraints weight = 10075.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.118659 restraints weight = 10397.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.2278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9443  Z= 0.151
  Angle     :  0.663   9.592  12924  Z= 0.335
  Chirality :  0.044   0.169   1539
  Planarity :  0.004   0.034   1612
  Dihedral  :  5.239  40.409   1322
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 15.99 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.24 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.34 %

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 are not related in a simple way.
  whole: -2.11 (0.24), residues: 1224
  helix: -0.77 (0.29), residues: 316
  sheet: -1.53 (0.25), residues: 410
  loop : -1.49 (0.30), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 113 
 TYR   0.020   0.001   TYR D 145 
 PHE   0.010   0.001   PHE E 177 
 TRP   0.017   0.001   TRP C  36 
 HIS   0.003   0.001   HIS F 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 9435)
  covalent geometry    : angle       0.66259 (12908)
  SS BOND              : bond        0.00205 (    8)
  SS BOND              : angle       1.08781 (   16)
  hydrogen bonds       : bond        0.04564 (  401)
  hydrogen bonds       : angle       5.82343 ( 1185)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 230
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  307 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7400 (tm-30)
REVERT: A  381 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.7139 (m-30)
REVERT: B  303 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8943 (tt)
REVERT: D  128 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7577 (tm-30)
  outliers start: 39
  outliers final: 28
  residues processed: 251
  average time/residue: 0.0858
  time to fit residues: 30.4991
Evaluate side-chains
  245 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 215
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  301 SER
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  356 PHE
Chi-restraints excluded: chain A residue  381 ASP
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   21 ILE
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   50 LYS
Chi-restraints excluded: chain D residue  107 THR
Chi-restraints excluded: chain D residue  160 ARG
Chi-restraints excluded: chain D residue  179 SER
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  192 VAL
Chi-restraints excluded: chain F residue    2 VAL
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   50 LYS
Chi-restraints excluded: chain F residue  179 SER
Chi-restraints excluded: chain E residue   18 VAL
Chi-restraints excluded: chain E residue   72 VAL
Chi-restraints excluded: chain E residue  112 ASP
Chi-restraints excluded: chain E residue  164 THR
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain E residue  208 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 100 optimal weight:    4.9990
   chunk 97 optimal weight:   20.0000
   chunk 99 optimal weight:    0.7980
   chunk 49 optimal weight:    8.9990
   chunk 39 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 83 optimal weight:    0.9990
   chunk 96 optimal weight:    8.9990
   chunk 113 optimal weight:    4.9990
   chunk 69 optimal weight:    6.9990
   chunk 53 optimal weight:    9.9990
   overall best weight:    3.3588

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

Flipped N/Q/H residues before XYZ refinement:
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  58 ASN
** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  58 ASN
** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 104 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.145068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.109733 restraints weight = 13951.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.106701 restraints weight = 16232.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.109353 restraints weight = 17940.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.109383 restraints weight = 10805.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.110001 restraints weight = 9668.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.2167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.074   9443  Z= 0.343
  Angle     :  0.793  11.453  12924  Z= 0.401
  Chirality :  0.049   0.233   1539
  Planarity :  0.005   0.041   1612
  Dihedral  :  5.572  40.760   1322
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 14.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 17.18 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.24 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.34 %

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 are not related in a simple way.
  whole: -2.30 (0.24), residues: 1224
  helix: -1.06 (0.28), residues: 328
  sheet: -1.57 (0.24), residues: 414
  loop : -1.58 (0.30), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 113 
 TYR   0.023   0.002   TYR F 145 
 PHE   0.018   0.002   PHE F 103 
 TRP   0.033   0.002   TRP C  36 
 HIS   0.006   0.001   HIS D  31A

Details of bonding type rmsd
  covalent geometry    : bond        0.00795 ( 9435)
  covalent geometry    : angle       0.79205 (12908)
  SS BOND              : bond        0.00428 (    8)
  SS BOND              : angle       1.48724 (   16)
  hydrogen bonds       : bond        0.05239 (  401)
  hydrogen bonds       : angle       6.14487 ( 1185)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 218
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A  288 TRP cc_start: 0.7392 (t-100) cc_final: 0.6898 (t60)
REVERT: A  292 LEU cc_start: 0.8645 (tt) cc_final: 0.8307 (mt)
REVERT: A  307 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7554 (tm-30)
REVERT: A  354 ARG cc_start: 0.8243 (tmm-80) cc_final: 0.7992 (tmm-80)
REVERT: A  381 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.7123 (m-30)
REVERT: B  359 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7546 (mm-30)
REVERT: D   38 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8155 (tm)
REVERT: C  108 TYR cc_start: 0.8116 (p90) cc_final: 0.7903 (p90)
REVERT: F   38 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8239 (tm)
  outliers start: 56
  outliers final: 42
  residues processed: 250
  average time/residue: 0.0802
  time to fit residues: 28.5025
Evaluate side-chains
  252 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 207
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  301 SER
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  356 PHE
Chi-restraints excluded: chain A residue  381 ASP
Chi-restraints excluded: chain B residue  297 MET
Chi-restraints excluded: chain B residue  299 THR
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  390 VAL
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   21 ILE
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   50 LYS
Chi-restraints excluded: chain D residue  102 THR
Chi-restraints excluded: chain D residue  107 THR
Chi-restraints excluded: chain D residue  155 ILE
Chi-restraints excluded: chain D residue  160 ARG
Chi-restraints excluded: chain D residue  179 SER
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  192 VAL
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain F residue    2 VAL
Chi-restraints excluded: chain F residue   21 ILE
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   50 LYS
Chi-restraints excluded: chain F residue   63 VAL
Chi-restraints excluded: chain F residue  102 THR
Chi-restraints excluded: chain F residue  107 THR
Chi-restraints excluded: chain F residue  179 SER
Chi-restraints excluded: chain E residue   18 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue   72 VAL
Chi-restraints excluded: chain E residue  104 ASN
Chi-restraints excluded: chain E residue  164 THR
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain E residue  208 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 44 optimal weight:    0.2980
   chunk 116 optimal weight:    4.9990
   chunk 57 optimal weight:    0.0770
   chunk 40 optimal weight:    0.0070
   chunk 86 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 76 optimal weight:   30.0000
   chunk 64 optimal weight:    1.9990
   chunk 78 optimal weight:    9.9990
   chunk 24 optimal weight:    0.8980
   chunk 28 optimal weight:    0.2980
   overall best weight:    0.3156

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

Flipped N/Q/H residues before XYZ refinement:
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  58 ASN
** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84AASN
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  58 ASN
E 104 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.155677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.119887 restraints weight = 13757.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.118530 restraints weight = 14498.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.120365 restraints weight = 12897.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.120765 restraints weight = 9218.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.121746 restraints weight = 8181.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.2642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9443  Z= 0.138
  Angle     :  0.666   8.050  12924  Z= 0.341
  Chirality :  0.045   0.203   1539
  Planarity :  0.004   0.033   1612
  Dihedral  :  5.283  41.100   1322
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 19.86 %
    Favored  : 76.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.24 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.34 %

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 are not related in a simple way.
  whole: -1.92 (0.24), residues: 1224
  helix: -0.75 (0.29), residues: 314
  sheet: -1.30 (0.25), residues: 396
  loop : -1.42 (0.30), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 113 
 TYR   0.021   0.001   TYR F 145 
 PHE   0.008   0.001   PHE D 140 
 TRP   0.018   0.001   TRP E  36 
 HIS   0.003   0.001   HIS D  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 9435)
  covalent geometry    : angle       0.66535 (12908)
  SS BOND              : bond        0.00144 (    8)
  SS BOND              : angle       1.17660 (   16)
  hydrogen bonds       : bond        0.04460 (  401)
  hydrogen bonds       : angle       5.64902 ( 1185)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 223
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A  307 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7363 (tm-30)
REVERT: A  381 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.6915 (m-30)
REVERT: D  128 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7725 (tm-30)
REVERT: D  178 TYR cc_start: 0.8901 (m-80) cc_final: 0.8336 (m-80)
REVERT: D  180 MET cc_start: 0.8387 (tpt) cc_final: 0.8099 (tpt)
REVERT: F  180 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7539 (ttt)
REVERT: E  219 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7703 (mtmm)
  outliers start: 38
  outliers final: 24
  residues processed: 241
  average time/residue: 0.0824
  time to fit residues: 28.2602
Evaluate side-chains
  243 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 216
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  301 SER
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  381 ASP
Chi-restraints excluded: chain B residue  297 MET
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   21 ILE
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue  160 ARG
Chi-restraints excluded: chain D residue  179 SER
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain F residue    2 VAL
Chi-restraints excluded: chain F residue   21 ILE
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   63 VAL
Chi-restraints excluded: chain F residue  179 SER
Chi-restraints excluded: chain F residue  180 MET
Chi-restraints excluded: chain E residue   72 VAL
Chi-restraints excluded: chain E residue  164 THR
Chi-restraints excluded: chain E residue  192 VAL
Chi-restraints excluded: chain E residue  219 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 45 optimal weight:    8.9990
   chunk 98 optimal weight:   10.0000
   chunk 109 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 97 optimal weight:   20.0000
   chunk 11 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 107 optimal weight:    1.9990
   chunk 85 optimal weight:    8.9990
   chunk 111 optimal weight:   20.0000
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  58 ASN
D 171 GLN
C  84AASN
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  58 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.154064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.117783 restraints weight = 13855.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.116414 restraints weight = 13904.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.118252 restraints weight = 11539.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.118053 restraints weight = 10864.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.119365 restraints weight = 8612.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9443  Z= 0.165
  Angle     :  0.676   9.357  12924  Z= 0.341
  Chirality :  0.045   0.184   1539
  Planarity :  0.004   0.033   1612
  Dihedral  :  5.145  40.048   1322
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 19.86 %
    Favored  : 75.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.24 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.34 %

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 are not related in a simple way.
  whole: -1.77 (0.24), residues: 1224
  helix: -0.65 (0.29), residues: 312
  sheet: -1.11 (0.25), residues: 400
  loop : -1.39 (0.29), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 354 
 TYR   0.023   0.001   TYR D 145 
 PHE   0.008   0.001   PHE F 103 
 TRP   0.033   0.001   TRP E  36 
 HIS   0.002   0.001   HIS F  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 9435)
  covalent geometry    : angle       0.67527 (12908)
  SS BOND              : bond        0.00217 (    8)
  SS BOND              : angle       1.09390 (   16)
  hydrogen bonds       : bond        0.04446 (  401)
  hydrogen bonds       : angle       5.56808 ( 1185)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 219
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A  292 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.7902 (mp)
REVERT: A  381 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.6973 (m-30)
REVERT: D  128 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7803 (tm-30)
REVERT: F  180 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7392 (ttt)
REVERT: E  219 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7796 (mtmm)
  outliers start: 43
  outliers final: 31
  residues processed: 243
  average time/residue: 0.0825
  time to fit residues: 28.6520
Evaluate side-chains
  248 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 213
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  301 SER
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  356 PHE
Chi-restraints excluded: chain A residue  381 ASP
Chi-restraints excluded: chain B residue  297 MET
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue  160 ARG
Chi-restraints excluded: chain D residue  179 SER
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain F residue    2 VAL
Chi-restraints excluded: chain F residue   21 ILE
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   50 LYS
Chi-restraints excluded: chain F residue   63 VAL
Chi-restraints excluded: chain F residue  179 SER
Chi-restraints excluded: chain F residue  180 MET
Chi-restraints excluded: chain E residue   18 VAL
Chi-restraints excluded: chain E residue   72 VAL
Chi-restraints excluded: chain E residue  164 THR
Chi-restraints excluded: chain E residue  192 VAL
Chi-restraints excluded: chain E residue  208 VAL
Chi-restraints excluded: chain E residue  219 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 72 optimal weight:    7.9990
   chunk 32 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 83 optimal weight:    8.9990
   chunk 28 optimal weight:    5.9990
   chunk 97 optimal weight:    8.9990
   chunk 49 optimal weight:    8.9990
   chunk 102 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  58 ASN
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  58 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.151342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.117236 restraints weight = 13826.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.116283 restraints weight = 15203.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.118320 restraints weight = 13554.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.118074 restraints weight = 8552.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.118648 restraints weight = 8263.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9443  Z= 0.229
  Angle     :  0.718  10.379  12924  Z= 0.363
  Chirality :  0.046   0.193   1539
  Planarity :  0.004   0.036   1612
  Dihedral  :  5.270  40.301   1322
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 20.36 %
    Favored  : 74.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.24 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.34 %

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 are not related in a simple way.
  whole: -1.87 (0.24), residues: 1224
  helix: -0.74 (0.28), residues: 326
  sheet: -1.07 (0.26), residues: 396
  loop : -1.54 (0.29), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 354 
 TYR   0.023   0.002   TYR D 145 
 PHE   0.013   0.002   PHE A 306 
 TRP   0.026   0.001   TRP E  36 
 HIS   0.003   0.001   HIS F  31A

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 ( 9435)
  covalent geometry    : angle       0.71618 (12908)
  SS BOND              : bond        0.00173 (    8)
  SS BOND              : angle       1.49801 (   16)
  hydrogen bonds       : bond        0.04684 (  401)
  hydrogen bonds       : angle       5.69837 ( 1185)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 219
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A  292 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.7916 (mp)
REVERT: A  337 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8630 (mp)
REVERT: A  381 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.7094 (m-30)
REVERT: D  128 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7843 (tm-30)
REVERT: D  180 MET cc_start: 0.8398 (tpt) cc_final: 0.8138 (tpt)
REVERT: F  175 ASP cc_start: 0.8194 (p0) cc_final: 0.7868 (p0)
REVERT: E  104 ASN cc_start: 0.9160 (OUTLIER) cc_final: 0.8921 (t0)
REVERT: E  219 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7801 (mtmm)
  outliers start: 48
  outliers final: 35
  residues processed: 249
  average time/residue: 0.0805
  time to fit residues: 28.4462
Evaluate side-chains
  249 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 209
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  301 SER
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  356 PHE
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  381 ASP
Chi-restraints excluded: chain B residue  297 MET
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue  155 ILE
Chi-restraints excluded: chain D residue  160 ARG
Chi-restraints excluded: chain D residue  179 SER
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain F residue    2 VAL
Chi-restraints excluded: chain F residue   21 ILE
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   63 VAL
Chi-restraints excluded: chain F residue  155 ILE
Chi-restraints excluded: chain F residue  179 SER
Chi-restraints excluded: chain E residue   18 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   72 VAL
Chi-restraints excluded: chain E residue  104 ASN
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  164 THR
Chi-restraints excluded: chain E residue  192 VAL
Chi-restraints excluded: chain E residue  208 VAL
Chi-restraints excluded: chain E residue  219 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 99 optimal weight:    0.9980
   chunk 52 optimal weight:    6.9990
   chunk 85 optimal weight:    7.9990
   chunk 84 optimal weight:    3.9990
   chunk 101 optimal weight:    0.6980
   chunk 90 optimal weight:    6.9990
   chunk 91 optimal weight:    0.9980
   chunk 81 optimal weight:    0.7980
   chunk 82 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  58 ASN
** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  58 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.154861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.120923 restraints weight = 13711.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.117523 restraints weight = 15032.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.119805 restraints weight = 13690.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.120329 restraints weight = 9231.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.121510 restraints weight = 8253.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.2959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9443  Z= 0.155
  Angle     :  0.688  10.244  12924  Z= 0.346
  Chirality :  0.045   0.191   1539
  Planarity :  0.004   0.038   1612
  Dihedral  :  5.129  39.768   1322
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 21.55 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.24 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.34 %

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 are not related in a simple way.
  whole: -1.62 (0.24), residues: 1224
  helix: -0.54 (0.29), residues: 312
  sheet: -0.93 (0.26), residues: 400
  loop : -1.38 (0.29), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 354 
 TYR   0.021   0.001   TYR F 145 
 PHE   0.023   0.001   PHE F 140 
 TRP   0.032   0.001   TRP D 168 
 HIS   0.002   0.001   HIS D  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 9435)
  covalent geometry    : angle       0.68716 (12908)
  SS BOND              : bond        0.00393 (    8)
  SS BOND              : angle       1.28084 (   16)
  hydrogen bonds       : bond        0.04407 (  401)
  hydrogen bonds       : angle       5.50131 ( 1185)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 214
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
REVERT: A  381 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.6988 (m-30)
REVERT: D  128 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7917 (tm-30)
REVERT: D  180 MET cc_start: 0.8414 (tpt) cc_final: 0.7799 (tpt)
  outliers start: 38
  outliers final: 30
  residues processed: 237
  average time/residue: 0.0826
  time to fit residues: 27.9895
Evaluate side-chains
  242 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 211
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  301 SER
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  356 PHE
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  381 ASP
Chi-restraints excluded: chain B residue  297 MET
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue  160 ARG
Chi-restraints excluded: chain D residue  179 SER
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain F residue    2 VAL
Chi-restraints excluded: chain F residue   21 ILE
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   63 VAL
Chi-restraints excluded: chain F residue  155 ILE
Chi-restraints excluded: chain F residue  179 SER
Chi-restraints excluded: chain E residue   72 VAL
Chi-restraints excluded: chain E residue  112 ASP
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  164 THR
Chi-restraints excluded: chain E residue  192 VAL
Chi-restraints excluded: chain E residue  208 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 117 optimal weight:    9.9990
   chunk 69 optimal weight:    7.9990
   chunk 118 optimal weight:    7.9990
   chunk 110 optimal weight:    5.9990
   chunk 6 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 86 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  58 ASN
D 171 GLN
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  58 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.152824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.116977 restraints weight = 13880.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.114146 restraints weight = 13994.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.116138 restraints weight = 12854.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.116571 restraints weight = 9003.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.116740 restraints weight = 8887.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.2892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9443  Z= 0.205
  Angle     :  0.714  10.315  12924  Z= 0.359
  Chirality :  0.047   0.192   1539
  Planarity :  0.004   0.035   1612
  Dihedral  :  5.185  39.754   1322
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 21.75 %
    Favored  : 74.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.24 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.34 %

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 are not related in a simple way.
  whole: -1.66 (0.24), residues: 1224
  helix: -0.62 (0.28), residues: 326
  sheet: -0.92 (0.26), residues: 400
  loop : -1.40 (0.30), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 354 
 TYR   0.026   0.002   TYR F  91 
 PHE   0.029   0.002   PHE F 140 
 TRP   0.028   0.001   TRP D 168 
 HIS   0.003   0.001   HIS D  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 9435)
  covalent geometry    : angle       0.71295 (12908)
  SS BOND              : bond        0.00134 (    8)
  SS BOND              : angle       1.29439 (   16)
  hydrogen bonds       : bond        0.04584 (  401)
  hydrogen bonds       : angle       5.53690 ( 1185)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 213
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: A  292 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7840 (mp)
REVERT: A  381 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.7100 (m-30)
REVERT: D  128 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7934 (tm-30)
REVERT: D  180 MET cc_start: 0.8542 (tpt) cc_final: 0.8050 (tpt)
REVERT: D  188 LYS cc_start: 0.6079 (mmtp) cc_final: 0.5832 (mmtp)
REVERT: E  219 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7892 (mtmm)
  outliers start: 40
  outliers final: 35
  residues processed: 237
  average time/residue: 0.0835
  time to fit residues: 28.0490
Evaluate side-chains
  248 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 210
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  301 SER
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  336 THR
Chi-restraints excluded: chain A residue  356 PHE
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  381 ASP
Chi-restraints excluded: chain B residue  297 MET
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue  160 ARG
Chi-restraints excluded: chain D residue  179 SER
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain F residue    2 VAL
Chi-restraints excluded: chain F residue   21 ILE
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   63 VAL
Chi-restraints excluded: chain F residue  155 ILE
Chi-restraints excluded: chain F residue  179 SER
Chi-restraints excluded: chain E residue   18 VAL
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue   72 VAL
Chi-restraints excluded: chain E residue  112 ASP
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  164 THR
Chi-restraints excluded: chain E residue  192 VAL
Chi-restraints excluded: chain E residue  208 VAL
Chi-restraints excluded: chain E residue  219 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 104 optimal weight:    0.9990
   chunk 55 optimal weight:   10.0000
   chunk 10 optimal weight:    0.8980
   chunk 50 optimal weight:    6.9990
   chunk 77 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 45 optimal weight:    8.9990
   chunk 26 optimal weight:    0.8980
   chunk 71 optimal weight:   10.0000
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  58 ASN
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  58 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.155827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.120694 restraints weight = 13595.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.118656 restraints weight = 13255.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.120615 restraints weight = 13099.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.121327 restraints weight = 9613.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.121509 restraints weight = 9010.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9443  Z= 0.148
  Angle     :  0.693  10.962  12924  Z= 0.346
  Chirality :  0.045   0.197   1539
  Planarity :  0.004   0.034   1612
  Dihedral  :  5.076  39.438   1322
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 12.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 23.14 %
    Favored  : 73.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.24 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.34 %

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 are not related in a simple way.
  whole: -1.46 (0.25), residues: 1224
  helix: -0.46 (0.29), residues: 312
  sheet: -0.81 (0.26), residues: 400
  loop : -1.28 (0.29), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 354 
 TYR   0.022   0.001   TYR F 145 
 PHE   0.027   0.001   PHE F 140 
 TRP   0.027   0.001   TRP D 168 
 HIS   0.002   0.001   HIS D  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 9435)
  covalent geometry    : angle       0.69137 (12908)
  SS BOND              : bond        0.00143 (    8)
  SS BOND              : angle       1.55871 (   16)
  hydrogen bonds       : bond        0.04339 (  401)
  hydrogen bonds       : angle       5.37848 ( 1185)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1677.80 seconds
wall clock time: 29 minutes 45.50 seconds (1785.50 seconds total)